@article{buscher_key_2025,
	title = {Key questions for future research in {Physiological} {Entomology}},
	journal = {Physiological Entomology},
	author = {Buscher, Thies and Appel, Arther and Luddekcke, Tim and Kostal, Valdimir and Block, William and Vale, Pedro F and Clissold, Fiona and Maestro, Jose L. and Numata, Hideharu and Tomioka, Kenji and Bruce, Toby},
	year = {2025},
}

@article{monteith_genetic_2024,
	title = {Genetic {Variation} in {Trophic} {Avoidance} {Behaviour} {Shows} {Fruit} {Flies} are {Generally} {Attracted} to {Bacterial} {Substrates}},
	volume = {14},
	copyright = {© 2024 The Author(s). Ecology and Evolution published by John Wiley \& Sons Ltd.},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.70541},
	doi = {10.1002/ece3.70541},
	abstract = {Pathogen avoidance behaviours are often assumed to be an adaptive host defence. However, there is limited experimental data on heritable, intrapopulation phenotypic variation for avoidance, a strong prerequisite for adaptive responses to selection. We investigated trophic pathogen avoidance in 122 inbred Drosophila melanogaster lines, and in a derived outbred population. Using the FlyPAD system, we tracked the feeding choice that flies made between substrates that were either clean or contained a bacterial pathogen. We uncovered significant, but weakly heritable variation in the preference index amongst fly lines. However, instead of avoidance, most lines demonstrated a preference for substrates containing several bacterial pathogens, showing avoidance only for extremely high bacterial concentrations. Bacterial preference was not associated with susceptibility to infection and was retained in flies with disrupted immune signalling. Phenotype–genotype association analysis indicated several novel genes (CG2321, CG2006, and ptp99A) associated with increased preference for the bacterial substrate, while the amino-acid transporter sobremesa was associated with greater aversion. Given the known fitness benefits of consuming high-protein diets, our results suggest that bacterial attraction may instead reflect a dietary preference for protein over carbohydrate. More work quantifying intrapopulation variation in avoidance behaviours is needed to fully assess its importance in host–pathogen evolutionary ecology.},
	language = {en},
	number = {11},
	urldate = {2024-11-13},
	journal = {Ecology and Evolution},
	author = {Monteith, Katy M. and Thornhill, Phoebe and Vale, Pedro F.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.70541},
	pages = {e70541},
	url_paper={https://api.zotero.org/users/837863/publications/items/I7HXEKSR/file/view}
}

Pathogen avoidance behaviours are often assumed to be an adaptive host defence. However, there is limited experimental data on heritable, intrapopulation phenotypic variation for avoidance, a strong prerequisite for adaptive responses to selection. We investigated trophic pathogen avoidance in 122 inbred Drosophila melanogaster lines, and in a derived outbred population. Using the FlyPAD system, we tracked the feeding choice that flies made between substrates that were either clean or contained a bacterial pathogen. We uncovered significant, but weakly heritable variation in the preference index amongst fly lines. However, instead of avoidance, most lines demonstrated a preference for substrates containing several bacterial pathogens, showing avoidance only for extremely high bacterial concentrations. Bacterial preference was not associated with susceptibility to infection and was retained in flies with disrupted immune signalling. Phenotype–genotype association analysis indicated several novel genes (CG2321, CG2006, and ptp99A) associated with increased preference for the bacterial substrate, while the amino-acid transporter sobremesa was associated with greater aversion. Given the known fitness benefits of consuming high-protein diets, our results suggest that bacterial attraction may instead reflect a dietary preference for protein over carbohydrate. More work quantifying intrapopulation variation in avoidance behaviours is needed to fully assess its importance in host–pathogen evolutionary ecology.

@article{salminen_naturally_2024,
	title = {A naturally occurring mitochondrial genome variant confers broad protection from infection in {Drosophila}},
	volume = {20},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011476},
	doi = {10.1371/journal.pgen.1011476},
	abstract = {The role of mitochondria in immunity is increasingly recognized, but it is unclear how variation in mitochondrial DNA (mtDNA) contributes to variable infection outcomes. To quantify the effect of mtDNA variation on humoral and cell-mediated innate immune responses, we utilized a panel of fruit fly Drosophila melanogaster cytoplasmic hybrids (cybrids), where unique mtDNAs (mitotypes) were introgressed into a controlled isogenic nuclear background. We observed substantial heterogeneity in infection outcomes within the cybrid panel upon bacterial, viral and parasitoid infections, driven by the mitotype. One of the mitotypes, mtKSA2 protected against bacterial, parasitoid, and to a lesser extent, viral infections. Enhanced survival was not a result of improved bacterial clearance, suggesting mtKSA2 confers increased disease tolerance. Transcriptome sequencing showed that the mtKSA2 mitotype had an upregulation of genes related to mitochondrial respiration and phagocytosis in uninfected flies. Upon infection, mtKSA2 flies exhibited infection type and duration specific transcriptomic changes. Furthermore, uninfected mtKSA2 larvae showed immune activation of hemocytes (immune cells), increased hemocyte numbers and ROS production, and enhanced encapsulation response against parasitoid wasp eggs and larvae. Our results show that mtDNA variation acts as an immunomodulatory factor in both humoral and cell-mediated innate immunity and that specific mitotypes can provide broad protection against infections.},
	language = {en},
	number = {11},
	urldate = {2024-11-13},
	journal = {PLOS Genetics},
	author = {Salminen, Tiina S. and Vesala, Laura and Basikhina, Yuliya and Kutzer, Megan and Tuomela, Tea and Lucas, Ryan and Monteith, Katy and Prakash, Arun and Tietz, Tilman and Vale, Pedro F.},
	month = nov,
	year = {2024},
	note = {Publisher: Public Library of Science},
	pages = {e1011476},
	url_paper={https://api.zotero.org/users/837863/publications/items/BKT9W8FW/file/view}
}

The role of mitochondria in immunity is increasingly recognized, but it is unclear how variation in mitochondrial DNA (mtDNA) contributes to variable infection outcomes. To quantify the effect of mtDNA variation on humoral and cell-mediated innate immune responses, we utilized a panel of fruit fly Drosophila melanogaster cytoplasmic hybrids (cybrids), where unique mtDNAs (mitotypes) were introgressed into a controlled isogenic nuclear background. We observed substantial heterogeneity in infection outcomes within the cybrid panel upon bacterial, viral and parasitoid infections, driven by the mitotype. One of the mitotypes, mtKSA2 protected against bacterial, parasitoid, and to a lesser extent, viral infections. Enhanced survival was not a result of improved bacterial clearance, suggesting mtKSA2 confers increased disease tolerance. Transcriptome sequencing showed that the mtKSA2 mitotype had an upregulation of genes related to mitochondrial respiration and phagocytosis in uninfected flies. Upon infection, mtKSA2 flies exhibited infection type and duration specific transcriptomic changes. Furthermore, uninfected mtKSA2 larvae showed immune activation of hemocytes (immune cells), increased hemocyte numbers and ROS production, and enhanced encapsulation response against parasitoid wasp eggs and larvae. Our results show that mtDNA variation acts as an immunomodulatory factor in both humoral and cell-mediated innate immunity and that specific mitotypes can provide broad protection against infections.

@article{kutzer_mitochondrial_2024,
	title = {Mitochondrial background can explain variable costs of immune deployment},
	volume = {37},
	copyright = {All rights reserved},
	issn = {1010-061X},
	url = {https://doi.org/10.1093/jeb/voae082},
	doi = {10.1093/jeb/voae082},
	abstract = {Organismal health and survival depend on the ability to mount an effective immune response against infection. Yet immune defence may be energy-demanding, resulting in fitness costs if investment in immune function deprives other physiological processes of resources. While evidence of costly immunity resulting in reduced longevity and reproduction is common, the role of energy-producing mitochondria on the magnitude of these costs is unknown. Here, we employed Drosophila melanogaster cybrid lines, where several mitochondrial genotypes (mitotypes) were introgressed onto a single nuclear genetic background, to explicitly test the role of mitochondrial variation on the costs of immune stimulation. We exposed female flies carrying one of nine distinct mitotypes to either a benign, heat-killed bacterial pathogen (stimulating immune deployment while avoiding pathology) or to a sterile control and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation in immune-stimulated flies between lifespan and the proportion of time cybrids spent moving while alive. Our results suggests that costs of immunity are highly variable depending on the mitochondrial genome, adding to a growing body of work highlighting the important role of mitochondrial variation in host–pathogen interactions.},
	number = {9},
	urldate = {2024-09-11},
	journal = {Journal of Evolutionary Biology},
	author = {Kutzer, Megan A M and Cornish, Beth and Jamieson, Michael and Zawistowska, Olga and Monteith, Katy M and Vale, Pedro F},
	month = sep,
	year = {2024},
	pages = {1125--1133},
}

Organismal health and survival depend on the ability to mount an effective immune response against infection. Yet immune defence may be energy-demanding, resulting in fitness costs if investment in immune function deprives other physiological processes of resources. While evidence of costly immunity resulting in reduced longevity and reproduction is common, the role of energy-producing mitochondria on the magnitude of these costs is unknown. Here, we employed Drosophila melanogaster cybrid lines, where several mitochondrial genotypes (mitotypes) were introgressed onto a single nuclear genetic background, to explicitly test the role of mitochondrial variation on the costs of immune stimulation. We exposed female flies carrying one of nine distinct mitotypes to either a benign, heat-killed bacterial pathogen (stimulating immune deployment while avoiding pathology) or to a sterile control and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation in immune-stimulated flies between lifespan and the proportion of time cybrids spent moving while alive. Our results suggests that costs of immunity are highly variable depending on the mitochondrial genome, adding to a growing body of work highlighting the important role of mitochondrial variation in host–pathogen interactions.

@article{prakash_negative_2024,
	title = {Negative immune regulation contributes to disease tolerance in {Drosophila} melanogaster},
	volume = {n/a},
	copyright = {© 2024 The Author(s). Physiological Entomology published by John Wiley \& Sons Ltd on behalf of Royal Entomological Society.},
	issn = {1365-3032},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/phen.12464},
	doi = {10.1111/phen.12464},
	abstract = {Disease tolerance is an infection phenotype where hosts show relatively high health despite harbouring elevated pathogen loads. Variation in the ability to reduce immunopathology may explain why some hosts can tolerate higher pathogen burdens with reduced pathology. Negative immune regulation would therefore appear to be a clear candidate for a mechanism underlying disease tolerance. Here, we examined how the negative regulation of the immune deficiency (IMD) pathway affects disease tolerance in Drosophila melanogaster when infected with four doses of the gram-negative bacterial pathogen Pseudomonas entomophila. We find that while flies unable to regulate the IMD response exhibited higher expression of antimicrobial peptides and lower bacterial loads as expected, this was not accompanied by a proportional reduction in mortality. Instead, ubiquitous UAS-RNAi knockdown of negative regulators of IMD (pirk and caudal) substantially increased the per-pathogen-mortality in both males and females across all tested infectious doses. Our results therefore highlight that in addition to regulating an efficient pathogen clearance response, negative regulators of IMD also contribute to disease tolerance.},
	language = {en},
	number = {n/a},
	urldate = {2024-08-21},
	journal = {Physiological Entomology},
	author = {Prakash, Arun and Monteith, Katy M. and Vale, Pedro F.},
	month = aug,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/phen.12464},
}

Disease tolerance is an infection phenotype where hosts show relatively high health despite harbouring elevated pathogen loads. Variation in the ability to reduce immunopathology may explain why some hosts can tolerate higher pathogen burdens with reduced pathology. Negative immune regulation would therefore appear to be a clear candidate for a mechanism underlying disease tolerance. Here, we examined how the negative regulation of the immune deficiency (IMD) pathway affects disease tolerance in Drosophila melanogaster when infected with four doses of the gram-negative bacterial pathogen Pseudomonas entomophila. We find that while flies unable to regulate the IMD response exhibited higher expression of antimicrobial peptides and lower bacterial loads as expected, this was not accompanied by a proportional reduction in mortality. Instead, ubiquitous UAS-RNAi knockdown of negative regulators of IMD (pirk and caudal) substantially increased the per-pathogen-mortality in both males and females across all tested infectious doses. Our results therefore highlight that in addition to regulating an efficient pathogen clearance response, negative regulators of IMD also contribute to disease tolerance.

@article{prakash_imd-mediated_2024,
	title = {{IMD}-mediated innate immune priming increases {Drosophila} survival and reduces pathogen transmission},
	volume = {20},
	copyright = {All rights reserved},
	issn = {1553-7374},
	url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012308},
	doi = {10.1371/journal.ppat.1012308},
	abstract = {Invertebrates lack the immune machinery underlying vertebrate-like acquired immunity. However, in many insects past infection by the same pathogen can ‘prime’ the immune response, resulting in improved survival upon reinfection. Here, we investigated the mechanistic basis and epidemiological consequences of innate immune priming in the fruit fly Drosophila melanogaster when infected with the gram-negative bacterial pathogen Providencia rettgeri. We find that priming in response to P. rettgeri infection is long-lasting and sexually dimorphic response. We further explore the epidemiological consequences of immune priming and find it has the potential to curtail pathogen transmission by reducing pathogen shedding and spread. The enhanced survival of individuals previously exposed to a non-lethal bacterial inoculum coincided with a transient decrease in bacterial loads, and we provide strong evidence that the effect of priming requires the IMD-responsive antimicrobial-peptide Diptericin-B in the fat body. Further, we show that while Diptericin B is the main effector of bacterial clearance, it is not sufficient for immune priming, which requires regulation of IMD by peptidoglycan recognition proteins. This work underscores the plasticity and complexity of invertebrate responses to infection, providing novel experimental evidence for the effects of innate immune priming on population-level epidemiological outcomes.},
	language = {en},
	number = {6},
	urldate = {2024-06-10},
	journal = {PLOS Pathogens},
	author = {Prakash, Arun and Fenner, Florence and Shit, Biswajit and Salminen, Tiina S. and Monteith, Katy M. and Khan, Imroze and Vale, Pedro F.},
	month = jun,
	year = {2024},
	note = {Publisher: Public Library of Science},
	pages = {e1012308},
}

Invertebrates lack the immune machinery underlying vertebrate-like acquired immunity. However, in many insects past infection by the same pathogen can ‘prime’ the immune response, resulting in improved survival upon reinfection. Here, we investigated the mechanistic basis and epidemiological consequences of innate immune priming in the fruit fly Drosophila melanogaster when infected with the gram-negative bacterial pathogen Providencia rettgeri. We find that priming in response to P. rettgeri infection is long-lasting and sexually dimorphic response. We further explore the epidemiological consequences of immune priming and find it has the potential to curtail pathogen transmission by reducing pathogen shedding and spread. The enhanced survival of individuals previously exposed to a non-lethal bacterial inoculum coincided with a transient decrease in bacterial loads, and we provide strong evidence that the effect of priming requires the IMD-responsive antimicrobial-peptide Diptericin-B in the fat body. Further, we show that while Diptericin B is the main effector of bacterial clearance, it is not sufficient for immune priming, which requires regulation of IMD by peptidoglycan recognition proteins. This work underscores the plasticity and complexity of invertebrate responses to infection, providing novel experimental evidence for the effects of innate immune priming on population-level epidemiological outcomes.

@article{vesala_mitochondrial_2024,
	title = {Mitochondrial perturbation in immune cells enhances cell-mediated innate immunity in {Drosophila}},
	volume = {22},
	copyright = {All rights reserved},
	issn = {1741-7007},
	url = {https://doi.org/10.1186/s12915-024-01858-5},
	doi = {10.1186/s12915-024-01858-5},
	abstract = {Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, production of reactive oxygen species, stress responses, inflammation and immunity. However, the role of mitochondrial metabolism in immune cells and tissues shaping the innate immune responses are not yet fully understood. We investigated the effects of tissue-specific mitochondrial perturbation on the immune responses at the organismal level. Genes for oxidative phosphorylation (OXPHOS) complexes cI-cV were knocked down in the fruit fly Drosophila melanogaster, targeting the two main immune tissues, the fat body and the immune cells (hemocytes).},
	number = {1},
	urldate = {2024-03-13},
	journal = {BMC Biology},
	author = {Vesala, Laura and Basikhina, Yuliya and Tuomela, Tea and Nurminen, Anssi and Siukola, Emilia and Vale, Pedro F. and Salminen, Tiina S.},
	month = mar,
	year = {2024},
	pages = {60},
}

Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, production of reactive oxygen species, stress responses, inflammation and immunity. However, the role of mitochondrial metabolism in immune cells and tissues shaping the innate immune responses are not yet fully understood. We investigated the effects of tissue-specific mitochondrial perturbation on the immune responses at the organismal level. Genes for oxidative phosphorylation (OXPHOS) complexes cI-cV were knocked down in the fruit fly Drosophila melanogaster, targeting the two main immune tissues, the fat body and the immune cells (hemocytes).

@misc{prakash_negative_2023,
	title = {Negative immune regulation contributes to disease tolerance in {Drosophila}},
	copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2021.09.23.461574v3},
	doi = {10.1101/2021.09.23.461574},
	abstract = {Disease tolerance is an infection phenotype where hosts show relatively high health despite harbouring elevated pathogen loads. Variation in the ability to reduce immunopathology may explain why some hosts can tolerate higher pathogen burdens with reduced pathology. Negative immune regulation would therefore appear to be a clear candidate for a mechanism underlying disease tolerance. Here, we examined how the negative regulation of the immune deficiency (IMD) pathway affects disease tolerance in Drosophila melanogaster when infected with four doses of the gram-negative bacterial pathogen Pseudomonas entomophila. We find that while flies unable to regulate the IMD response exhibited higher expression of antimicrobial peptides and lower bacterial loads as expected, this was not accompanied by a proportional reduction in mortality. Instead, UAS-RNAi knockdown of negative regulators of IMD (pirk and caudal) substantially increased the per-pathogen-mortality in both males and females across all tested infectious doses. Our results therefore highlight that in addition to regulating an efficient pathogen clearance response, negative regulators of IMD also contribute to disease tolerance.},
	language = {en},
	urldate = {2024-06-04},
	publisher = {bioRxiv},
	author = {Prakash, Arun and Monteith, Katy M. and Vale, Pedro F.},
	month = may,
	year = {2023},
	note = {Pages: 2021.09.23.461574
Section: New Results},
}

Disease tolerance is an infection phenotype where hosts show relatively high health despite harbouring elevated pathogen loads. Variation in the ability to reduce immunopathology may explain why some hosts can tolerate higher pathogen burdens with reduced pathology. Negative immune regulation would therefore appear to be a clear candidate for a mechanism underlying disease tolerance. Here, we examined how the negative regulation of the immune deficiency (IMD) pathway affects disease tolerance in Drosophila melanogaster when infected with four doses of the gram-negative bacterial pathogen Pseudomonas entomophila. We find that while flies unable to regulate the IMD response exhibited higher expression of antimicrobial peptides and lower bacterial loads as expected, this was not accompanied by a proportional reduction in mortality. Instead, UAS-RNAi knockdown of negative regulators of IMD (pirk and caudal) substantially increased the per-pathogen-mortality in both males and females across all tested infectious doses. Our results therefore highlight that in addition to regulating an efficient pathogen clearance response, negative regulators of IMD also contribute to disease tolerance.

@article{prakash_duox_2023,
	title = {Duox and {Jak}/{Stat} signalling influence disease tolerance in {Drosophila} during {Pseudomonas} entomophila infection},
	copyright = {All rights reserved},
	issn = {0145-305X},
	url = {https://www.sciencedirect.com/science/article/pii/S0145305X2300126X},
	doi = {10.1016/j.dci.2023.104756},
	abstract = {Disease tolerance describes an infected host's ability to maintain health independently of the ability to clear microbe loads. The Jak/Stat pathway plays a pivotal role in humoral innate immunity by detecting tissue damage and triggering cellular renewal, making it a candidate tolerance mechanism. Here, we find that in Drosophila melanogaster infected with Pseudomonas entomophila disrupting ROS-producing dual oxidase (duox) or the negative regulator of Jak/Stat Socs36E, render male flies less tolerant. Another negative regulator of Jak/Stat, G9a - which has previously been associated with variable tolerance of viral infections – did not affect the rate of mortality with increasing microbe loads compared to flies with functional G9a, suggesting it does not affect tolerance of bacterial infection as in viral infection. Our findings highlight that ROS production and Jak/Stat signalling influence the ability of flies to tolerate bacterial infection sex-specifically and may therefore contribute to sexually dimorphic infection outcomes in Drosophila.},
	language = {en},
	urldate = {2023-06-12},
	journal = {Developmental \& Comparative Immunology},
	author = {Prakash, Arun and Monteith, Katy M. and Bonnet, Mickael and Vale, Pedro F.},
	month = jun,
	year = {2023},
	pages = {104756},
}

Disease tolerance describes an infected host's ability to maintain health independently of the ability to clear microbe loads. The Jak/Stat pathway plays a pivotal role in humoral innate immunity by detecting tissue damage and triggering cellular renewal, making it a candidate tolerance mechanism. Here, we find that in Drosophila melanogaster infected with Pseudomonas entomophila disrupting ROS-producing dual oxidase (duox) or the negative regulator of Jak/Stat Socs36E, render male flies less tolerant. Another negative regulator of Jak/Stat, G9a - which has previously been associated with variable tolerance of viral infections – did not affect the rate of mortality with increasing microbe loads compared to flies with functional G9a, suggesting it does not affect tolerance of bacterial infection as in viral infection. Our findings highlight that ROS production and Jak/Stat signalling influence the ability of flies to tolerate bacterial infection sex-specifically and may therefore contribute to sexually dimorphic infection outcomes in Drosophila.

@article{kutzer_intraspecific_2023,
	title = {Intraspecific genetic variation in host vigour, viral load and disease tolerance during {Drosophila} {C} virus infection},
	volume = {13},
	copyright = {All rights reserved},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsob.230025},
	doi = {10.1098/rsob.230025},
	abstract = {Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible (S) or resistant (R) pst allele. We find among-line variation in fly survival, viral load and disease tolerance measured both as the ability to maintain survival (mortality tolerance) and reproduction (fecundity tolerance). We further uncover novel effects of pst on host vigour, as flies carrying the R allele exhibited higher survival and fecundity even in the absence of infection. Finally, we found significant genetic variation in the expression of the JAK-STAT ligand upd3 and the epigenetic regulator of JAK-STAT G9a. However, while G9a has been previously shown to mediate tolerance of DCV infection, we found no correlation between the expression of either upd3 or G9a on fly tolerance or resistance. Our work highlights the importance of both resistance and tolerance in viral defence.},
	number = {3},
	urldate = {2023-03-01},
	journal = {Open Biology},
	author = {Kutzer, Megan A. M. and Gupta, Vanika and Neophytou, Kyriaki and Doublet, Vincent and Monteith, Katy M. and Vale, Pedro F.},
	month = mar,
	year = {2023},
	note = {Publisher: Royal Society},
	pages = {230025},
}

Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible (S) or resistant (R) pst allele. We find among-line variation in fly survival, viral load and disease tolerance measured both as the ability to maintain survival (mortality tolerance) and reproduction (fecundity tolerance). We further uncover novel effects of pst on host vigour, as flies carrying the R allele exhibited higher survival and fecundity even in the absence of infection. Finally, we found significant genetic variation in the expression of the JAK-STAT ligand upd3 and the epigenetic regulator of JAK-STAT G9a. However, while G9a has been previously shown to mediate tolerance of DCV infection, we found no correlation between the expression of either upd3 or G9a on fly tolerance or resistance. Our work highlights the importance of both resistance and tolerance in viral defence.

@article{anderson_variation_2022,
	title = {Variation in mitochondrial {DNA} affects locomotor activity and sleep in {Drosophila} melanogaster},
	copyright = {2022 The Author(s)},
	issn = {1365-2540},
	url = {https://www.nature.com/articles/s41437-022-00554-w},
	doi = {10.1038/s41437-022-00554-w},
	abstract = {Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved among many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. Our results demonstrate that Drosophila strains from different locations differ in sleep and activity, and that females are generally more active than males. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we were able to quantify the among-line variance attributable to mitochondrial DNA, and we establish that mtDNA variation affects both activity and sleep, in a sex-specific manner. Altogether our study highlights the important role that mitochondrial genome variation plays on organismal physiology and behaviour.},
	language = {en},
	urldate = {2022-06-29},
	journal = {Heredity},
	author = {Anderson, Lucy and Camus, M. Florencia and Monteith, Katy M. and Salminen, Tiina S. and Vale, Pedro F.},
	month = jun,
	year = {2022},
	pages = {1--8},
}

Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved among many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. Our results demonstrate that Drosophila strains from different locations differ in sleep and activity, and that females are generally more active than males. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we were able to quantify the among-line variance attributable to mitochondrial DNA, and we establish that mtDNA variation affects both activity and sleep, in a sex-specific manner. Altogether our study highlights the important role that mitochondrial genome variation plays on organismal physiology and behaviour.

@article{prakash_mechanisms_2022,
	title = {Mechanisms of damage prevention, signalling and repair impact disease tolerance},
	volume = {289},
	copyright = {All rights reserved},
	url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2022.0837},
	doi = {10.1098/rspb.2022.0837},
	abstract = {The insect gut is frequently exposed to pathogenic threats and must not only clear these potential infections, but also tolerate relatively high microbe loads. In contrast to the mechanisms that eliminate pathogens, we currently know less about the mechanisms of disease tolerance. We investigated how well-described mechanisms that prevent, signal, control or repair damage during infection contribute to the phenotype of disease tolerance. We established enteric infections with the bacterial pathogen Pseudomonas entomophila in transgenic lines of Drosophila melanogaster fruit flies affecting dcy (a major component of the peritrophic matrix), upd3 (a cytokine-like molecule), irc (a negative regulator of reactive oxygen species) and egfr1 (epithelial growth factor receptor). Flies lacking dcy experienced the highest mortality, while loss of function of either irc or upd3 reduced tolerance in both sexes. The disruption of egfr1 resulted in a severe loss in tolerance in male flies but had no substantial effect on the ability of female flies to tolerate P. entomophila infection, despite carrying greater microbe loads than males. Together, our findings provide evidence for the role of damage limitation mechanisms in disease tolerance and highlight how sexual dimorphism in these mechanisms could generate sex differences in infection outcomes.},
	number = {1981},
	urldate = {2022-08-18},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Prakash, Arun and Monteith, Katy M. and Vale, Pedro F.},
	month = aug,
	year = {2022},
	pages = {20220837},
}

The insect gut is frequently exposed to pathogenic threats and must not only clear these potential infections, but also tolerate relatively high microbe loads. In contrast to the mechanisms that eliminate pathogens, we currently know less about the mechanisms of disease tolerance. We investigated how well-described mechanisms that prevent, signal, control or repair damage during infection contribute to the phenotype of disease tolerance. We established enteric infections with the bacterial pathogen Pseudomonas entomophila in transgenic lines of Drosophila melanogaster fruit flies affecting dcy (a major component of the peritrophic matrix), upd3 (a cytokine-like molecule), irc (a negative regulator of reactive oxygen species) and egfr1 (epithelial growth factor receptor). Flies lacking dcy experienced the highest mortality, while loss of function of either irc or upd3 reduced tolerance in both sexes. The disruption of egfr1 resulted in a severe loss in tolerance in male flies but had no substantial effect on the ability of female flies to tolerate P. entomophila infection, despite carrying greater microbe loads than males. Together, our findings provide evidence for the role of damage limitation mechanisms in disease tolerance and highlight how sexual dimorphism in these mechanisms could generate sex differences in infection outcomes.

@article{savola_larval_2022,
	title = {Larval diet affects adult reproduction, but not survival, independent of the effect of injury and infection in {Drosophila} melanogaster},
	copyright = {All rights reserved},
	issn = {0022-1910},
	url = {https://www.sciencedirect.com/science/article/pii/S0022191022000749},
	doi = {10.1016/j.jinsphys.2022.104428},
	abstract = {Early-life conditions have profound effects on many life-history traits, where early-life diet affects both juvenile development, and adult survival and reproduction. Early-life diet also has consequences for the ability of adults to withstand environmental challenges such as starvation, temperature and desiccation. However, it is less well known how early-life diet influences the consequences of infection in adults. Here we test whether varying the larval diet of female Drosophila melanogaster (through altering protein to carbohydrate ratio, P:C) influences the long-term consequences of injury and infection with the bacterial pathogen Pseudomonasentomophila. Given previous work manipulating adult dietary P:C, we predicted that adults from larvae raised on higher P:C diets would have increased reproduction, but shorter lifespans and an increased rate of ageing, and that the lowest larval P:C diets would be particularly detrimental for adult survival in infected individuals. For larval development, we predicted that low P:C would lead to a longer development time and lower viability. We found that early-life and lifetime egg production were highest at intermediate to high larval P:C diets, but this was independent of injury and infection. There was no effect of larval P:C on adult survival. Larval development was quickest on intermediate P:C and egg-to-pupae and egg-to-adult viability were slightly higher on higher P:C. Overall, despite larval P:C affecting several measured traits, we saw no evidence that larval P:C altered the consequence of infection or injury for adult survival or early-life and lifetime reproduction. Taken together, these data suggest that larval diets appear to have a limited impact on the adult life history consequences of infection.},
	language = {en},
	urldate = {2022-08-03},
	journal = {Journal of Insect Physiology},
	author = {Savola, Eevi and Vale, Pedro and Walling, Craig},
	month = aug,
	year = {2022},
	pages = {104428},
}

Early-life conditions have profound effects on many life-history traits, where early-life diet affects both juvenile development, and adult survival and reproduction. Early-life diet also has consequences for the ability of adults to withstand environmental challenges such as starvation, temperature and desiccation. However, it is less well known how early-life diet influences the consequences of infection in adults. Here we test whether varying the larval diet of female Drosophila melanogaster (through altering protein to carbohydrate ratio, P:C) influences the long-term consequences of injury and infection with the bacterial pathogen Pseudomonasentomophila. Given previous work manipulating adult dietary P:C, we predicted that adults from larvae raised on higher P:C diets would have increased reproduction, but shorter lifespans and an increased rate of ageing, and that the lowest larval P:C diets would be particularly detrimental for adult survival in infected individuals. For larval development, we predicted that low P:C would lead to a longer development time and lower viability. We found that early-life and lifetime egg production were highest at intermediate to high larval P:C diets, but this was independent of injury and infection. There was no effect of larval P:C on adult survival. Larval development was quickest on intermediate P:C and egg-to-pupae and egg-to-adult viability were slightly higher on higher P:C. Overall, despite larval P:C affecting several measured traits, we saw no evidence that larval P:C altered the consequence of infection or injury for adult survival or early-life and lifetime reproduction. Taken together, these data suggest that larval diets appear to have a limited impact on the adult life history consequences of infection.

@article{romano_host_2022,
	title = {Host genetics and pathogen species modulate infection-induced changes in social aggregation behaviour},
	volume = {18},
	copyright = {All rights reserved},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsbl.2022.0233},
	doi = {10.1098/rsbl.2022.0233},
	abstract = {Identifying how infection modifies host behaviours that determine social contact networks is important for understanding heterogeneity in infectious disease dynamics. Here, we investigate whether group social behaviour is modified during bacterial infection in fruit flies (Drosophila melanogaster) according to pathogen species, infectious dose, host genetic background and sex. In one experiment, we find that systemic infection with four different bacterial species results in a reduction in the mean pairwise distance within infected female flies, and that the extent of this change depends on pathogen species. However, susceptible flies did not show any evidence of avoidance in the presence of infected flies. In a separate experiment, we observed genetic- and sex-based variation in social aggregation within infected, same-sex groups, with infected female flies aggregating more closely than infected males. In general, our results confirm that bacterial infection induces changes in fruit fly behaviour across a range of pathogen species, but also highlight that these effects vary between fly genetic backgrounds and can be sex-specific. We discuss possible explanations for sex differences in social aggregation and their consequences for individual variation in pathogen transmission.},
	number = {8},
	urldate = {2023-09-18},
	journal = {Biology Letters},
	author = {Romano, Valéria and Lussiana, Amy and Monteith, Katy M. and MacIntosh, Andrew J. J. and Vale, Pedro F.},
	month = aug,
	year = {2022},
	note = {Publisher: Royal Society},
	pages = {20220233},
}

Identifying how infection modifies host behaviours that determine social contact networks is important for understanding heterogeneity in infectious disease dynamics. Here, we investigate whether group social behaviour is modified during bacterial infection in fruit flies (Drosophila melanogaster) according to pathogen species, infectious dose, host genetic background and sex. In one experiment, we find that systemic infection with four different bacterial species results in a reduction in the mean pairwise distance within infected female flies, and that the extent of this change depends on pathogen species. However, susceptible flies did not show any evidence of avoidance in the presence of infected flies. In a separate experiment, we observed genetic- and sex-based variation in social aggregation within infected, same-sex groups, with infected female flies aggregating more closely than infected males. In general, our results confirm that bacterial infection induces changes in fruit fly behaviour across a range of pathogen species, but also highlight that these effects vary between fly genetic backgrounds and can be sex-specific. We discuss possible explanations for sex differences in social aggregation and their consequences for individual variation in pathogen transmission.

@article{shit_ageing_2022,
	title = {Ageing leads to reduced specificity of antimicrobial peptide responses in {Drosophila} melanogaster},
	volume = {289},
	copyright = {All rights reserved},
	url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2022.1642},
	doi = {10.1098/rspb.2022.1642},
	abstract = {Evolutionary theory predicts a late-life decline in the force of natural selection, possibly leading to late-life deregulations of the immune system. A potential outcome of such deregulations is the inability to produce specific immunity against target pathogens. We tested this possibility by infecting multiple Drosophila melanogaster lines (with bacterial pathogens) across age groups, where either individual or different combinations of Imd- and Toll-inducible antimicrobial peptides (AMPs) were deleted using CRISPR gene editing. We show a high degree of non-redundancy and pathogen-specificity of AMPs in young flies: in some cases, even a single AMP could confer complete resistance. However, ageing led to drastic reductions in such specificity to target pathogens, warranting the action of multiple AMPs across Imd and Toll pathways. Moreover, use of diverse AMPs either lacked survival benefits or even accompanied survival costs post-infection. These features were also sexually dimorphic: females required a larger repertoire of AMPs than males but extracted equivalent survival benefits. Finally, age-specific expansion of the AMP-repertoire was accompanied with ageing-induced downregulation of negative-regulators of the Imd pathway and damage to renal function post-infection, as features of poorly regulated immunity. Overall, we could highlight the potentially non-adaptive role of ageing in producing less-specific AMP responses, across sexes and pathogens.},
	number = {1987},
	urldate = {2022-11-16},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Shit, Biswajit and Prakash, Arun and Sarkar, Saubhik and Vale, Pedro F. and Khan, Imroze},
	month = nov,
	year = {2022},
	note = {0 citations (Semantic Scholar/DOI) [2023-02-08]
0 citations (Crossref) [2023-02-08]
Publisher: Royal Society},
	pages = {20221642},
}

Evolutionary theory predicts a late-life decline in the force of natural selection, possibly leading to late-life deregulations of the immune system. A potential outcome of such deregulations is the inability to produce specific immunity against target pathogens. We tested this possibility by infecting multiple Drosophila melanogaster lines (with bacterial pathogens) across age groups, where either individual or different combinations of Imd- and Toll-inducible antimicrobial peptides (AMPs) were deleted using CRISPR gene editing. We show a high degree of non-redundancy and pathogen-specificity of AMPs in young flies: in some cases, even a single AMP could confer complete resistance. However, ageing led to drastic reductions in such specificity to target pathogens, warranting the action of multiple AMPs across Imd and Toll pathways. Moreover, use of diverse AMPs either lacked survival benefits or even accompanied survival costs post-infection. These features were also sexually dimorphic: females required a larger repertoire of AMPs than males but extracted equivalent survival benefits. Finally, age-specific expansion of the AMP-repertoire was accompanied with ageing-induced downregulation of negative-regulators of the Imd pathway and damage to renal function post-infection, as features of poorly regulated immunity. Overall, we could highlight the potentially non-adaptive role of ageing in producing less-specific AMP responses, across sexes and pathogens.

@misc{listmann_epidemiological_2021,
	title = {Epidemiological dynamics of viral infection in a marine picoeukaryote},
	copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	url = {https://www.biorxiv.org/content/10.1101/2021.03.23.436719v1},
	doi = {10.1101/2021.03.23.436719},
	abstract = {Ostreococcus tauri is a ubiquitous marine pico-eukaryote that is susceptible to lysis upon infection by its species specific Ostreococcus tauri viruses (OtVs). In natural populations of O. tauri, costs of resistance are usually invoked to explain the persistence or reappearance of susceptible individuals in resistant populations. Given the low costs of resistance measured in laboratory experiments with the O. tauri/OtV system to date, the question remains of why susceptible individuals persist in the wild at all. Epidemiological models of host and pathogen population dynamics are one useful approach to understand the conditions that can allow the coexistence of susceptible and resistant hosts. We used a SIR (Susceptible-Infected-Resistant) model to investigate epidemiological dynamics under different laboratory culturing regimes that are commonly used in the O.tauri/OtV system. When taking into account serial transfer (i.e. batchcycle lengths) and dilution rates as well as different resistance costs, our model predicts that no susceptible cells should be detected under any of the simulated conditions – this is consistent with laboratory findings. We thus considered an alternative model that is not used in laboratory experiments, but which incorporates one key process in natural populations: host populations are periodically re-seeded with new infective viruses. In this model, susceptible individuals re-occurred in the population, despite low costs of resistance. This suggests that periodic attack by new viruses, rather than (or in addition to) costs of resistance, may explain the high proportion of susceptible hosts in natural populations, and underlie the discrepancy between laboratory studies and observations of fresh isolates.
Importance In natural samples of Ostreococcus sp. and its associated viruses, susceptible hosts are common. However, in laboratory experiments, fully resistant host populations readily and irreversibly evolve. Laboratory experiments are powerful methods for studying process because they offer a stripped-down simplification of a complex system, but this simplification may be an oversimplification for some questions. For example, laboratory and field systems of marine microbes and their viruses differ in population sizes and dynamics, mixing or migration rates, and species diversity, all of which can dramatically alter process outcomes. We demonstrate the utility of using epidemiological models to explore experimental design and to understand mechanisms underlying host-virus population dynamics. We highlight that such models can be used to form strong, testable hypotheses about which key elements of natural systems need to be included in laboratory systems to make them simplified, rather than oversimplified, versions of the processes we use them to study.},
	language = {en},
	urldate = {2024-06-04},
	publisher = {bioRxiv},
	author = {Listmann, Luisa and Heath, Sarah and Vale, Pedro F. and Schaum, C. Elisa and Collins, Sinead},
	month = mar,
	year = {2021},
	note = {Pages: 2021.03.23.436719
Section: New Results},
}

Ostreococcus tauri is a ubiquitous marine pico-eukaryote that is susceptible to lysis upon infection by its species specific Ostreococcus tauri viruses (OtVs). In natural populations of O. tauri, costs of resistance are usually invoked to explain the persistence or reappearance of susceptible individuals in resistant populations. Given the low costs of resistance measured in laboratory experiments with the O. tauri/OtV system to date, the question remains of why susceptible individuals persist in the wild at all. Epidemiological models of host and pathogen population dynamics are one useful approach to understand the conditions that can allow the coexistence of susceptible and resistant hosts. We used a SIR (Susceptible-Infected-Resistant) model to investigate epidemiological dynamics under different laboratory culturing regimes that are commonly used in the O.tauri/OtV system. When taking into account serial transfer (i.e. batchcycle lengths) and dilution rates as well as different resistance costs, our model predicts that no susceptible cells should be detected under any of the simulated conditions – this is consistent with laboratory findings. We thus considered an alternative model that is not used in laboratory experiments, but which incorporates one key process in natural populations: host populations are periodically re-seeded with new infective viruses. In this model, susceptible individuals re-occurred in the population, despite low costs of resistance. This suggests that periodic attack by new viruses, rather than (or in addition to) costs of resistance, may explain the high proportion of susceptible hosts in natural populations, and underlie the discrepancy between laboratory studies and observations of fresh isolates. Importance In natural samples of Ostreococcus sp. and its associated viruses, susceptible hosts are common. However, in laboratory experiments, fully resistant host populations readily and irreversibly evolve. Laboratory experiments are powerful methods for studying process because they offer a stripped-down simplification of a complex system, but this simplification may be an oversimplification for some questions. For example, laboratory and field systems of marine microbes and their viruses differ in population sizes and dynamics, mixing or migration rates, and species diversity, all of which can dramatically alter process outcomes. We demonstrate the utility of using epidemiological models to explore experimental design and to understand mechanisms underlying host-virus population dynamics. We highlight that such models can be used to form strong, testable hypotheses about which key elements of natural systems need to be included in laboratory systems to make them simplified, rather than oversimplified, versions of the processes we use them to study.

@article{savola_testing_2021,
	title = {Testing evolutionary explanations for the lifespan benefit of dietary restriction in fruit flies ({Drosophila} melanogaster)},
	volume = {75},
	copyright = {All rights reserved},
	issn = {1558-5646},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/evo.14146},
	doi = {10.1111/evo.14146},
	abstract = {Dietary restriction (DR), limiting calories or specific nutrients without malnutrition, extends lifespan across diverse taxa. Traditionally, this lifespan extension has been explained as a result of diet-mediated changes in the trade-off between lifespan and reproduction, with survival favored when resources are scarce. However, a recently proposed alternative suggests that the selective benefit of the response to DR is the maintenance of reproduction. This hypothesis predicts that lifespan extension is a side effect of benign laboratory conditions, and DR individuals would be frailer and unable to deal with additional stressors, and thus lifespan extension should disappear under more stressful conditions. We tested this by rearing outbred female fruit flies (Drosophila melanogaster) on 10 different protein:carbohydrate diets. Flies were either infected with a bacterial pathogen (Pseudomonas entomophila), injured with a sterile pinprick, or unstressed. We monitored lifespan, fecundity, and measures of aging. DR extended lifespan and reduced reproduction irrespective of injury and infection. Infected flies on lower protein diets had particularly poor survival. Exposure to infection and injury did not substantially alter the relationship between diet and aging patterns. These results do not provide support for lifespan extension under DR being a side effect of benign laboratory conditions.},
	language = {en},
	number = {2},
	urldate = {2021-09-17},
	journal = {Evolution},
	author = {Savola, Eevi and Montgomery, Clara and Waldron, Fergal M. and Monteith, Katy M. and Vale, Pedro and Walling, Craig},
	year = {2021},
	pages = {450--463},
}

Dietary restriction (DR), limiting calories or specific nutrients without malnutrition, extends lifespan across diverse taxa. Traditionally, this lifespan extension has been explained as a result of diet-mediated changes in the trade-off between lifespan and reproduction, with survival favored when resources are scarce. However, a recently proposed alternative suggests that the selective benefit of the response to DR is the maintenance of reproduction. This hypothesis predicts that lifespan extension is a side effect of benign laboratory conditions, and DR individuals would be frailer and unable to deal with additional stressors, and thus lifespan extension should disappear under more stressful conditions. We tested this by rearing outbred female fruit flies (Drosophila melanogaster) on 10 different protein:carbohydrate diets. Flies were either infected with a bacterial pathogen (Pseudomonas entomophila), injured with a sterile pinprick, or unstressed. We monitored lifespan, fecundity, and measures of aging. DR extended lifespan and reduced reproduction irrespective of injury and infection. Infected flies on lower protein diets had particularly poor survival. Exposure to infection and injury did not substantially alter the relationship between diet and aging patterns. These results do not provide support for lifespan extension under DR being a side effect of benign laboratory conditions.

@article{siva-jothy_dissecting_2021,
	title = {Dissecting genetic and sex-specific sources of host heterogeneity in pathogen shedding and spread},
	volume = {17},
	copyright = {All rights reserved},
	issn = {1553-7374},
	url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009196},
	doi = {10.1371/journal.ppat.1009196},
	abstract = {Host heterogeneity in disease transmission is widespread but precisely how different host traits drive this heterogeneity remains poorly understood. Part of the difficulty in linking individual variation to population-scale outcomes is that individual hosts can differ on multiple behavioral, physiological and immunological axes, which will together impact their transmission potential. Moreover, we lack well-characterized, empirical systems that enable the quantification of individual variation in key host traits, while also characterizing genetic or sex-based sources of such variation. Here we used Drosophila melanogaster and Drosophila C Virus as a host-pathogen model system to dissect the genetic and sex-specific sources of variation in multiple host traits that are central to pathogen transmission. Our findings show complex interactions between genetic background, sex, and female mating status accounting for a substantial proportion of variance in lifespan following infection, viral load, virus shedding, and viral load at death. Two notable findings include the interaction between genetic background and sex accounting for nearly 20\% of the variance in viral load, and genetic background alone accounting for {\textasciitilde}10\% of the variance in viral shedding and in lifespan following infection. To understand how variation in these traits could generate heterogeneity in individual pathogen transmission potential, we combined measures of lifespan following infection, virus shedding, and previously published data on fly social aggregation. We found that the interaction between genetic background and sex explained {\textasciitilde}12\% of the variance in individual transmission potential. Our results highlight the importance of characterising the sources of variation in multiple host traits to understand the drivers of heterogeneity in disease transmission.},
	language = {en},
	number = {1},
	urldate = {2021-04-20},
	journal = {PLOS Pathogens},
	author = {Siva-Jothy, Jonathon A. and Vale, Pedro F.},
	month = jan,
	year = {2021},
	pages = {e1009196},
}

Host heterogeneity in disease transmission is widespread but precisely how different host traits drive this heterogeneity remains poorly understood. Part of the difficulty in linking individual variation to population-scale outcomes is that individual hosts can differ on multiple behavioral, physiological and immunological axes, which will together impact their transmission potential. Moreover, we lack well-characterized, empirical systems that enable the quantification of individual variation in key host traits, while also characterizing genetic or sex-based sources of such variation. Here we used Drosophila melanogaster and Drosophila C Virus as a host-pathogen model system to dissect the genetic and sex-specific sources of variation in multiple host traits that are central to pathogen transmission. Our findings show complex interactions between genetic background, sex, and female mating status accounting for a substantial proportion of variance in lifespan following infection, viral load, virus shedding, and viral load at death. Two notable findings include the interaction between genetic background and sex accounting for nearly 20% of the variance in viral load, and genetic background alone accounting for ~10% of the variance in viral shedding and in lifespan following infection. To understand how variation in these traits could generate heterogeneity in individual pathogen transmission potential, we combined measures of lifespan following infection, virus shedding, and previously published data on fly social aggregation. We found that the interaction between genetic background and sex explained ~12% of the variance in individual transmission potential. Our results highlight the importance of characterising the sources of variation in multiple host traits to understand the drivers of heterogeneity in disease transmission.

@article{ratz_carry_2021,
	title = {Carry on caring: infected females maintain their parental care despite high mortality},
	copyright = {All rights reserved},
	issn = {1045-2249},
	shorttitle = {Carry on caring},
	url = {https://doi.org/10.1093/beheco/arab028},
	doi = {10.1093/beheco/arab028},
	abstract = {Parental care is a key component of an organism’s reproductive strategy that is thought to trade-off with allocation toward immunity. Yet, it is unclear how caring parents respond to pathogens: do infected parents reduce care as a sickness behavior or simply from being ill or do they prioritize their offspring by maintaining high levels of care? To address this issue, we investigated the consequences of infection by the pathogen Serratia marcescens on mortality, time spent providing care, reproductive output, and expression of immune genes of female parents in the burying beetle Nicrophorus vespilloides. We compared untreated control females with infected females that were inoculated with live bacteria, immune-challenged females that were inoculated with heat-killed bacteria, and injured females that were injected with buffer. We found that infected and immune-challenged females changed their immune gene expression and that infected females suffered increased mortality. Nevertheless, infected and immune-challenged females maintained their normal level of care and reproductive output. There was thus no evidence that infection led to either a decrease or an increase in parental care or reproductive output. Our results show that parental care, which is generally highly flexible, can remain remarkably robust and consistent despite the elevated mortality caused by infection by pathogens. Overall, these findings suggest that infected females maintain a high level of parental care, a strategy that may ensure that offspring receive the necessary amount of care but that might be detrimental to the parents’ own survival or that may even facilitate disease transmission to offspring.},
	urldate = {2021-04-21},
	journal = {Behavioral Ecology},
	author = {Ratz, Tom and Monteith, Katy M and Vale, Pedro F and Smiseth, Per T},
	month = apr,
	year = {2021},
}

Parental care is a key component of an organism’s reproductive strategy that is thought to trade-off with allocation toward immunity. Yet, it is unclear how caring parents respond to pathogens: do infected parents reduce care as a sickness behavior or simply from being ill or do they prioritize their offspring by maintaining high levels of care? To address this issue, we investigated the consequences of infection by the pathogen Serratia marcescens on mortality, time spent providing care, reproductive output, and expression of immune genes of female parents in the burying beetle Nicrophorus vespilloides. We compared untreated control females with infected females that were inoculated with live bacteria, immune-challenged females that were inoculated with heat-killed bacteria, and injured females that were injected with buffer. We found that infected and immune-challenged females changed their immune gene expression and that infected females suffered increased mortality. Nevertheless, infected and immune-challenged females maintained their normal level of care and reproductive output. There was thus no evidence that infection led to either a decrease or an increase in parental care or reproductive output. Our results show that parental care, which is generally highly flexible, can remain remarkably robust and consistent despite the elevated mortality caused by infection by pathogens. Overall, these findings suggest that infected females maintain a high level of parental care, a strategy that may ensure that offspring receive the necessary amount of care but that might be detrimental to the parents’ own survival or that may even facilitate disease transmission to offspring.

@article{siva-jothy_v_2020,
	title = {To {V}, {R0} to {V} ?},
	copyright = {All rights reserved},
	url = {https://era.ed.ac.uk/handle/1842/36740},
	doi = {10.7488/era/47},
	abstract = {Outbreaks of infectious disease can be caused by only a few highly infectious 
individuals. These individuals are produced by variation in traits affecting contact 
between infected and susceptible individuals, the likelihood that contact results in 
infection and the duration of infection. High-risk individuals are difficult to predict 
because traditional assessments of disease transmission, such as R0, rely on 
population averages that conceal the variation that produces high transmission-risk 
phenotypes. Contact rate between infected and susceptible individuals, is primarily 
determined by behaviour whereas physiological immunity is the main determinant 
of the likelihood that contact causes infection and infection duration. I characterise 
variation in traits affecting the determinants of disease transmission and use this to 
predict individual variation in disease transmission, V. Using the fruit fly, Drosophila 
melanogaster, and its viral pathogen Drosophila C Virus, I have found pervasive and 
complex effects of genetic and sex-specific variation, mating, and infection on suites 
of behaviours, physiological traits and outcomes of infection. Many of my results 
point to an individual’s disease transmission potential being determined by genetic 
background and sex. Males, for example, typically survive DCV infection longer than 
females, however the amount of virus they shed is also determined by their genetic 
background. To predict how this variation could affect disease transmission 
dynamics, I simulated outbreaks of DCV in theoretical populations. These 
populations exhibited genetic and sex-specific variation based on my experiments 
and significantly affected population-level outbreak dynamics. Differences in these 
dynamics highlight potentially high-risk transmission classes of individuals, defined 
by their genetic background and sex.},
	language = {en},
	urldate = {2020-02-12},
	journal = {University of Edinburgh},
	author = {Siva-Jothy, Jonathon Arumugam},
	month = jan,
	year = {2020},
}

Outbreaks of infectious disease can be caused by only a few highly infectious individuals. These individuals are produced by variation in traits affecting contact between infected and susceptible individuals, the likelihood that contact results in infection and the duration of infection. High-risk individuals are difficult to predict because traditional assessments of disease transmission, such as R0, rely on population averages that conceal the variation that produces high transmission-risk phenotypes. Contact rate between infected and susceptible individuals, is primarily determined by behaviour whereas physiological immunity is the main determinant of the likelihood that contact causes infection and infection duration. I characterise variation in traits affecting the determinants of disease transmission and use this to predict individual variation in disease transmission, V. Using the fruit fly, Drosophila melanogaster, and its viral pathogen Drosophila C Virus, I have found pervasive and complex effects of genetic and sex-specific variation, mating, and infection on suites of behaviours, physiological traits and outcomes of infection. Many of my results point to an individual’s disease transmission potential being determined by genetic background and sex. Males, for example, typically survive DCV infection longer than females, however the amount of virus they shed is also determined by their genetic background. To predict how this variation could affect disease transmission dynamics, I simulated outbreaks of DCV in theoretical populations. These populations exhibited genetic and sex-specific variation based on my experiments and significantly affected population-level outbreak dynamics. Differences in these dynamics highlight potentially high-risk transmission classes of individuals, defined by their genetic background and sex.

@article{salminen_drosophila_2020,
	title = {Drosophila as a {Model} {System} to {Investigate} the {Effects} of {Mitochondrial} {Variation} on {Innate} {Immunity}},
	volume = {11},
	copyright = {All rights reserved},
	issn = {1664-3224},
	url = {https://www.frontiersin.org/articles/10.3389/fimmu.2020.00521},
	doi = {10.3389/fimmu.2020.00521},
	abstract = {Understanding why the response to infection varies between individuals remains one of the major challenges in immunology and infection biology. A substantial proportion of this heterogeneity can be explained by individual genetic differences which result in variable immune responses, and there are many examples of polymorphisms in nuclear-encoded genes that alter immunocompetence. However, how immunity is affected by genetic polymorphism in an additional genome, inherited maternally inside mitochondria (mtDNA), has been relatively understudied. Mitochondria are increasingly recognized as important mediators of innate immune responses, not only because they are the main source of energy required for costly immune responses, but also because by-products of mitochondrial metabolism, such as reactive oxygen species (ROS), may have direct microbicidal action. Yet, it is currently unclear how naturally occurring variation in mtDNA contributes to heterogeneity in infection outcomes. In this review article, we describe potential sources of variation in mitochondrial function that may arise due to mutations in vital nuclear and mitochondrial components of energy production or due to a disruption in mito-nuclear crosstalk. We then highlight how these changes in mitochondrial function can impact immune responses, focusing on their effects on ATP- and ROS-generating pathways, as well as immune signaling. Finally, we outline how being a powerful and genetically tractable model of infection, immunity and mitochondrial genetics makes the fruit fly Drosophila melanogaster ideally suited to dissect mitochondrial effects on innate immune responses to infection.},
	urldate = {2023-04-14},
	journal = {Frontiers in Immunology},
	author = {Salminen, Tiina S. and Vale, Pedro F.},
	year = {2020},
}

Understanding why the response to infection varies between individuals remains one of the major challenges in immunology and infection biology. A substantial proportion of this heterogeneity can be explained by individual genetic differences which result in variable immune responses, and there are many examples of polymorphisms in nuclear-encoded genes that alter immunocompetence. However, how immunity is affected by genetic polymorphism in an additional genome, inherited maternally inside mitochondria (mtDNA), has been relatively understudied. Mitochondria are increasingly recognized as important mediators of innate immune responses, not only because they are the main source of energy required for costly immune responses, but also because by-products of mitochondrial metabolism, such as reactive oxygen species (ROS), may have direct microbicidal action. Yet, it is currently unclear how naturally occurring variation in mtDNA contributes to heterogeneity in infection outcomes. In this review article, we describe potential sources of variation in mitochondrial function that may arise due to mutations in vital nuclear and mitochondrial components of energy production or due to a disruption in mito-nuclear crosstalk. We then highlight how these changes in mitochondrial function can impact immune responses, focusing on their effects on ATP- and ROS-generating pathways, as well as immune signaling. Finally, we outline how being a powerful and genetically tractable model of infection, immunity and mitochondrial genetics makes the fruit fly Drosophila melanogaster ideally suited to dissect mitochondrial effects on innate immune responses to infection.

@article{hudson_terminal_2020,
	title = {Terminal investment strategies following infection are dependent on diet},
	volume = {33},
	copyright = {© 2019 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2019 European Society For Evolutionary Biology},
	issn = {1420-9101},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jeb.13566},
	doi = {10.1111/jeb.13566},
	abstract = {When future reproductive potential is threatened, for example following infection, the terminal investment hypothesis predicts that individuals will respond by investing preferentially in current reproduction. Terminal investment involves reallocating resources to current reproductive effort, so it is likely to be influenced by the quantity and quality of resources acquired through diet. Dietary protein specifically has been shown to impact both immunity and reproduction in a range of organisms, but its impact on terminal investment is unclear. We challenged females from ten naturally derived fruit fly (Drosophila melanogaster) genotypes with the bacterial pathogen Pseudomonas aeruginosa. We then placed these on either a standard or isocaloric high-protein diet, and measured multiple components of reproductive investment. As oogenesis requires protein, and flies increase egg production with protein intake, we hypothesized that terminal investment would be easier to observe if protein was not already limiting. Oral exposure to the pathogen triggered an increase in reproductive investment. However, whereas flies feeding on a high-protein diet increased the number of eggs laid when exposed to P. aeruginosa, those fed the standard diet did not increase the number of eggs laid but increased egg-to-adult viability following infection. This suggests that the specific routes through which flies terminally invest are influenced by the protein content of the maternal diet. We discuss the importance of considering diet and natural routes of infection when measuring nonimmunological defences.},
	language = {en},
	number = {3},
	urldate = {2023-09-28},
	journal = {Journal of Evolutionary Biology},
	author = {Hudson, Ali L. and Moatt, Joshua P. and Vale, Pedro F.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jeb.13566},
	pages = {309--317},
}

When future reproductive potential is threatened, for example following infection, the terminal investment hypothesis predicts that individuals will respond by investing preferentially in current reproduction. Terminal investment involves reallocating resources to current reproductive effort, so it is likely to be influenced by the quantity and quality of resources acquired through diet. Dietary protein specifically has been shown to impact both immunity and reproduction in a range of organisms, but its impact on terminal investment is unclear. We challenged females from ten naturally derived fruit fly (Drosophila melanogaster) genotypes with the bacterial pathogen Pseudomonas aeruginosa. We then placed these on either a standard or isocaloric high-protein diet, and measured multiple components of reproductive investment. As oogenesis requires protein, and flies increase egg production with protein intake, we hypothesized that terminal investment would be easier to observe if protein was not already limiting. Oral exposure to the pathogen triggered an increase in reproductive investment. However, whereas flies feeding on a high-protein diet increased the number of eggs laid when exposed to P. aeruginosa, those fed the standard diet did not increase the number of eggs laid but increased egg-to-adult viability following infection. This suggests that the specific routes through which flies terminally invest are influenced by the protein content of the maternal diet. We discuss the importance of considering diet and natural routes of infection when measuring nonimmunological defences.

@article{oliveira_how_2020,
	title = {How are arbovirus vectors able to tolerate infection?},
	volume = {103},
	copyright = {All rights reserved},
	issn = {0145-305X},
	url = {http://www.sciencedirect.com/science/article/pii/S0145305X19303799},
	doi = {10.1016/j.dci.2019.103514},
	abstract = {One of the defining features of mosquito vectors of arboviruses such as Dengue and Zika is their ability to tolerate high levels of virus proliferation without suffering significant pathology. This adaptation is central to vector competence and disease spread. The molecular mechanisms, pathways, cellular and metabolic adaptations responsible for mosquito disease tolerance are still largely unknown and may represent effective ways to control mosquito populations and prevent arboviral diseases. In this review article, we describe the key link between disease tolerance and pathogen transmission, and how vector control methods may benefit by focusing efforts on dissecting the mechanisms underlying mosquito tolerance of arboviral infections. We briefly review recent work investigating tolerance mechanisms in other insects, describe the state of the art regarding the mechanisms of disease tolerance in mosquitos, and highlight the emerging role of gut microbiota in mosquito immunity and disease tolerance.},
	language = {en},
	urldate = {2019-10-18},
	journal = {Developmental \& Comparative Immunology},
	author = {Oliveira, José Henrique and Bahia, Ana Cristina and Vale, Pedro F.},
	month = feb,
	year = {2020},
	pages = {103514},
}

One of the defining features of mosquito vectors of arboviruses such as Dengue and Zika is their ability to tolerate high levels of virus proliferation without suffering significant pathology. This adaptation is central to vector competence and disease spread. The molecular mechanisms, pathways, cellular and metabolic adaptations responsible for mosquito disease tolerance are still largely unknown and may represent effective ways to control mosquito populations and prevent arboviral diseases. In this review article, we describe the key link between disease tolerance and pathogen transmission, and how vector control methods may benefit by focusing efforts on dissecting the mechanisms underlying mosquito tolerance of arboviral infections. We briefly review recent work investigating tolerance mechanisms in other insects, describe the state of the art regarding the mechanisms of disease tolerance in mosquitos, and highlight the emerging role of gut microbiota in mosquito immunity and disease tolerance.

@article{white_genotype_2020,
	title = {Genotype and sex-based host variation in behaviour and susceptibility drives population disease dynamics},
	volume = {287},
	copyright = {All rights reserved},
	url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2020.1653},
	doi = {10.1098/rspb.2020.1653},
	abstract = {Host heterogeneity in pathogen transmission is widespread and presents a major hurdle to predicting and minimizing disease outbreaks. Using Drosophila melanogaster infected with Drosophila C virus as a model system, we integrated experimental measurements of social aggregation, virus shedding, and disease-induced mortality from different genetic lines and sexes into a disease modelling framework. The experimentally measured host heterogeneity produced substantial differences in simulated disease outbreaks, providing evidence for genetic and sex-specific effects on disease dynamics at a population level. While this was true for homogeneous populations of single sex/genetic line, the genetic background or sex of the index case did not alter outbreak dynamics in simulated, heterogeneous populations. Finally, to explore the relative effects of social aggregation, viral shedding and mortality, we compared simulations where we allowed these traits to vary, as measured experimentally, to simulations where we constrained variation in these traits to the population mean. In this context, variation in infectiousness, followed by social aggregation, was the most influential component of transmission. Overall, we show that host heterogeneity in three host traits dramatically affects population-level transmission, but the relative impact of this variation depends on both the susceptible population diversity and the distribution of population-level variation.},
	number = {1938},
	urldate = {2020-11-11},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {White, Lauren A. and Siva-Jothy, Jonathon A. and Craft, Meggan E. and Vale, Pedro F.},
	month = nov,
	year = {2020},
	pages = {20201653},
}

Host heterogeneity in pathogen transmission is widespread and presents a major hurdle to predicting and minimizing disease outbreaks. Using Drosophila melanogaster infected with Drosophila C virus as a model system, we integrated experimental measurements of social aggregation, virus shedding, and disease-induced mortality from different genetic lines and sexes into a disease modelling framework. The experimentally measured host heterogeneity produced substantial differences in simulated disease outbreaks, providing evidence for genetic and sex-specific effects on disease dynamics at a population level. While this was true for homogeneous populations of single sex/genetic line, the genetic background or sex of the index case did not alter outbreak dynamics in simulated, heterogeneous populations. Finally, to explore the relative effects of social aggregation, viral shedding and mortality, we compared simulations where we allowed these traits to vary, as measured experimentally, to simulations where we constrained variation in these traits to the population mean. In this context, variation in infectiousness, followed by social aggregation, was the most influential component of transmission. Overall, we show that host heterogeneity in three host traits dramatically affects population-level transmission, but the relative impact of this variation depends on both the susceptible population diversity and the distribution of population-level variation.

@article{listmann_epidemiological_2020,
	title = {Epidemiological dynamics of viral infection in a marine pico-eukaryote},
	copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	url = {https://www.biorxiv.org/content/10.1101/2021.03.23.436719v1},
	doi = {10.1101/2021.03.23.436719},
	abstract = {{\textless}p{\textgreater}\textit{Ostreococcus tauri} is a ubiquitous marine pico-eukaryote that is susceptible to lysis upon infection by its specific \textit{Ostreococcus tauri} viruses (OtVs). In natural populations of \textit{O. tauri}, costs of resistance are usually invoked to explain the persistence or reappearance of susceptible individuals in resistant populations. Given the low costs of resistance measured in laboratory experiments with the \textit{O. tauri}/OtV system to date, the question remains of why susceptible individuals persist in the wild at all. Epidemiological models of host and pathogen population dynamics are one useful approach to understand the conditions that can allow the coexistence of susceptible and resistant hosts. We used a SIR (Susceptible-Infected-Resistant) model to investigate epidemiological dynamics under different laboratory culturing regimes that are commonly used in the \textit{O. tauri}/OtV system. When taking into account serial transfer (i.e. batchcycle lengths) and dilution rates as well as different resistance costs, our model predicts that no susceptible cells should be detected under any of the simulated conditions – this is consistent with laboratory findings. We thus considered an alternative model that is not used in laboratory experiments, but which incorporates one key process in natural populations: host populations are periodically re-seeded with new infective viruses. In this model, susceptible individuals re-occurred in the population, despite low costs of resistance. This suggests that periodic attack by new viruses, rather than (or in addition to) costs of resistance, may explain the high proportion of susceptible hosts in natural populations, and underlie the discrepancy between laboratory studies and observations of fresh isolates.{\textless}/p{\textgreater}},
	language = {en},
	urldate = {2021-03-25},
	journal = {bioRxiv},
	author = {Listmann, Luisa and Heath, Sarah and Vale, Pedro F. and Schaum, Elisa and Collins, Sinead},
	year = {2020},
	note = {0 citations (Semantic Scholar/DOI) [2023-02-08]
0 citations (Crossref) [2023-02-08]
Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {2021.03.23.436719},
}

\textlessp\textgreaterOstreococcus tauri is a ubiquitous marine pico-eukaryote that is susceptible to lysis upon infection by its specific Ostreococcus tauri viruses (OtVs). In natural populations of O. tauri, costs of resistance are usually invoked to explain the persistence or reappearance of susceptible individuals in resistant populations. Given the low costs of resistance measured in laboratory experiments with the O. tauri/OtV system to date, the question remains of why susceptible individuals persist in the wild at all. Epidemiological models of host and pathogen population dynamics are one useful approach to understand the conditions that can allow the coexistence of susceptible and resistant hosts. We used a SIR (Susceptible-Infected-Resistant) model to investigate epidemiological dynamics under different laboratory culturing regimes that are commonly used in the O. tauri/OtV system. When taking into account serial transfer (i.e. batchcycle lengths) and dilution rates as well as different resistance costs, our model predicts that no susceptible cells should be detected under any of the simulated conditions – this is consistent with laboratory findings. We thus considered an alternative model that is not used in laboratory experiments, but which incorporates one key process in natural populations: host populations are periodically re-seeded with new infective viruses. In this model, susceptible individuals re-occurred in the population, despite low costs of resistance. This suggests that periodic attack by new viruses, rather than (or in addition to) costs of resistance, may explain the high proportion of susceptible hosts in natural populations, and underlie the discrepancy between laboratory studies and observations of fresh isolates.\textless/p\textgreater

@misc{siva-jothy_population-level_2019,
	title = {Population-{Level} {Disease} {Dynamics} {Reflect} {Individual} {Heterogeneities} in {Transmission}},
	copyright = {© 2019, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/735480v1},
	doi = {10.1101/735480},
	abstract = {Host heterogeneity in disease transmission is widespread and presents a major hurdle to predicting and minimizing pathogen spread. Using the Drosophila melanogaster model system infected with Drosophila C virus, we integrate experimental measurements of individual host heterogeneity in social aggregation, virus shedding, and disease-induced mortality into an epidemiological framework that simulates outbreaks of infectious disease. We use these simulations to calculate individual variation in disease transmission and apportion this variation to specific components of transmission: social network degree distribution, infectiousness, and infection duration. The experimentally-observed variation produces substantial differences in individual transmission potential, providing evidence for genetic and sex-specific effects on disease dynamics at a population level. Manipulating variation in social network connectivity, infectiousness, and infection duration in simulated populations reveals that these components affect disease transmission in clear and distinct ways. We consider the implications of this genetic and sex-specific variation in disease transmission and discuss implications for appropriate control methods given the relative contributions made by social aggregation, virus shedding, and infection duration to transmission in other host-pathogen systems.},
	language = {en},
	urldate = {2024-06-04},
	publisher = {bioRxiv},
	author = {Siva-Jothy, Jonathon A. and White, Lauren A. and Craft, Meggan E. and Vale, Pedro F.},
	month = aug,
	year = {2019},
	note = {Pages: 735480
Section: New Results},
}

Host heterogeneity in disease transmission is widespread and presents a major hurdle to predicting and minimizing pathogen spread. Using the Drosophila melanogaster model system infected with Drosophila C virus, we integrate experimental measurements of individual host heterogeneity in social aggregation, virus shedding, and disease-induced mortality into an epidemiological framework that simulates outbreaks of infectious disease. We use these simulations to calculate individual variation in disease transmission and apportion this variation to specific components of transmission: social network degree distribution, infectiousness, and infection duration. The experimentally-observed variation produces substantial differences in individual transmission potential, providing evidence for genetic and sex-specific effects on disease dynamics at a population level. Manipulating variation in social network connectivity, infectiousness, and infection duration in simulated populations reveals that these components affect disease transmission in clear and distinct ways. We consider the implications of this genetic and sex-specific variation in disease transmission and discuss implications for appropriate control methods given the relative contributions made by social aggregation, virus shedding, and infection duration to transmission in other host-pathogen systems.

@article{siva-jothy_viral_2019,
	title = {Viral infection causes sex-specific changes in fruit fly social aggregation behaviour},
	volume = {15},
	copyright = {All rights reserved},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsbl.2019.0344},
	doi = {10.1098/rsbl.2019.0344},
	abstract = {Host behavioural changes following infection are common and could be important determinants of host behavioural competence to transmit pathogens. Identifying potential sources of variation in sickness behaviours is therefore central to our understanding of disease transmission. Here, we test how group social aggregation and individual locomotor activity vary between different genotypes of male and female fruit flies (Drosophila melanogaster) following septic infection with Drosophila C virus (DCV). We find genetic-based variation in both locomotor activity and social aggregation, but we did not detect an effect of DCV infection on fly activity or sleep patterns within the initial days following infection. However, DCV infection caused sex-specific effects on social aggregation, as male flies in most genetic backgrounds increased the distance to their nearest neighbour when infected. We discuss possible causes for these differences in the context of individual variation in immunity and their potential consequences for disease transmission.},
	number = {9},
	urldate = {2019-10-18},
	journal = {Biology Letters},
	author = {Siva-Jothy, Jonathon A. and Vale, Pedro F.},
	month = sep,
	year = {2019},
	pages = {20190344},
}

Host behavioural changes following infection are common and could be important determinants of host behavioural competence to transmit pathogens. Identifying potential sources of variation in sickness behaviours is therefore central to our understanding of disease transmission. Here, we test how group social aggregation and individual locomotor activity vary between different genotypes of male and female fruit flies (Drosophila melanogaster) following septic infection with Drosophila C virus (DCV). We find genetic-based variation in both locomotor activity and social aggregation, but we did not detect an effect of DCV infection on fly activity or sleep patterns within the initial days following infection. However, DCV infection caused sex-specific effects on social aggregation, as male flies in most genetic backgrounds increased the distance to their nearest neighbour when infected. We discuss possible causes for these differences in the context of individual variation in immunity and their potential consequences for disease transmission.

@article{vale_influence_2018,
	title = {The influence of parasites on insect behavior},
	volume = {1},
	copyright = {All rights reserved},
	url = {https://www.oxfordscholarship.com/view/10.1093/oso/9780198797500.001.0001/oso-9780198797500-chapter-18},
	abstract = {This chapter discusses insect behavioral responses to parasites. Dividing behaviors conceptually into those that occur before and after infection, we start by reviewing the evidence that insects identify and avoid potentially infectious environments to minimize negative consequences of infection. Behavioral responses following infection according to their adaptive value to either the insect host or to the parasite will then be considered. One section covers sickness behaviors proposed to benefit the host by conserving energetic resources during infection; another section discusses evidence for altered host behavior as a parasite adaptation enhancing parasite survival or transmission. The mechanistic link between behavior and immunity in insects is briefly discussed, and provide a summary of methods and techniques becoming standard to studying behavior of model insect species in the context of infection. The chapter concludes by discussing future directions in the study of insect behavioral responses to parasites.},
	language = {en},
	urldate = {2019-10-19},
	journal = {Insect Behavior: from mechanisms to ecological and evolutionary consequences},
	author = {Vale, Pedro F. and Siva-Jothy, Jonathon A. and Morrill, André and Forbes, Mark R.},
	month = sep,
	year = {2018},
	note = {Oxford University Press},
}

This chapter discusses insect behavioral responses to parasites. Dividing behaviors conceptually into those that occur before and after infection, we start by reviewing the evidence that insects identify and avoid potentially infectious environments to minimize negative consequences of infection. Behavioral responses following infection according to their adaptive value to either the insect host or to the parasite will then be considered. One section covers sickness behaviors proposed to benefit the host by conserving energetic resources during infection; another section discusses evidence for altered host behavior as a parasite adaptation enhancing parasite survival or transmission. The mechanistic link between behavior and immunity in insects is briefly discussed, and provide a summary of methods and techniques becoming standard to studying behavior of model insect species in the context of infection. The chapter concludes by discussing future directions in the study of insect behavioral responses to parasites.

@article{siva-jothy_oral_2018,
	title = {Oral {Bacterial} {Infection} and {Shedding} in {Drosophila} melanogaster},
	copyright = {All rights reserved},
	issn = {1940-087X},
	url = {https://app.jove.com/t/57676/oral-bacterial-infection-and-shedding-in-drosophila-melanogaster},
	doi = {10.3791/57676},
	abstract = {The fruit fly Drosophila melanogaster is one of the best developed model systems of infection and innate immunity. While most work has focused on systemic infections, there has been a recent increase of interest in the mechanisms of gut immunocompetence to pathogens, which require methods to orally infect flies. Here we present a protocol to orally expose individual flies to an opportunistic bacterial pathogen (Pseudomonas aeruginosa) and a natural bacterial pathogen of D. melanogaster (Pseudomonas entomophila). The goal of this protocol is to provide a robust method to expose male and female flies to these pathogens. We provide representative results showing survival phenotypes, microbe loads, and bacterial shedding, which is relevant for the study of heterogeneity in pathogen transmission. Finally, we confirm that Dcy mutants (lacking the protective peritrophic matrix in the gut epithelium) and Relish mutants (lacking a functional immune deficiency (IMD) pathway), show increased susceptibility to bacterial oral infection. This protocol, therefore, describes a robust method to infect flies using the oral route of infection, which can be extended to the study of a variety genetic and environmental sources of variation in gut infection outcomes and bacterial transmission.},
	language = {eng},
	number = {135},
	journal = {Journal of Visualized Experiments: JoVE},
	author = {Siva-Jothy, Jonathon A. and Prakash, Arun and Vasanthakrishnan, Radhakrishnan B. and Monteith, Katy M. and Vale, Pedro F.},
	year = {2018},
	pmid = {29912178},
	pmcid = {PMC6101445},
	note = {23 citations (Semantic Scholar/DOI) [2023-02-08]
9 citations (Crossref) [2023-02-08]},
}

The fruit fly Drosophila melanogaster is one of the best developed model systems of infection and innate immunity. While most work has focused on systemic infections, there has been a recent increase of interest in the mechanisms of gut immunocompetence to pathogens, which require methods to orally infect flies. Here we present a protocol to orally expose individual flies to an opportunistic bacterial pathogen (Pseudomonas aeruginosa) and a natural bacterial pathogen of D. melanogaster (Pseudomonas entomophila). The goal of this protocol is to provide a robust method to expose male and female flies to these pathogens. We provide representative results showing survival phenotypes, microbe loads, and bacterial shedding, which is relevant for the study of heterogeneity in pathogen transmission. Finally, we confirm that Dcy mutants (lacking the protective peritrophic matrix in the gut epithelium) and Relish mutants (lacking a functional immune deficiency (IMD) pathway), show increased susceptibility to bacterial oral infection. This protocol, therefore, describes a robust method to infect flies using the oral route of infection, which can be extended to the study of a variety genetic and environmental sources of variation in gut infection outcomes and bacterial transmission.

@article{siva-jothy_navigating_2018,
	title = {Navigating infection risk during oviposition and cannibalistic foraging in a holometabolous insect},
	volume = {29},
	copyright = {All rights reserved},
	issn = {1045-2249},
	url = {https://watermark.silverchair.com/ary106.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAl4wggJaBgkqhkiG9w0BBwagggJLMIICRwIBADCCAkAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMndhfZ_4oDYOqNb79AgEQgIICEQq3nOxYAd2EMTFEfRO1anZZIVtKIQhoTXihkbydsjeICRto4dKwRduzCyU2NSL1fpYdGm1ZPteISUwHAPMI2PTqu_kDhy3_yYWhcnwQBBdaF5-BXc1a6OogJncLLSO_N-VYVXdVhpiebtyOG5LaxfZR01ZtJPGtWn3VcZ3WReO527KXxE1TzKa1nURN0JsBfwIATWBJFgE7nWxdDttozo3MfZfQJAyFD43kF7nmNkUJDrbRJLosGYw08gcDrw9KrVxa4rVrrvk7whh23jSM2Ks_2WasbMVC-X4E9lTuuf3z8sF1e0x6o21ePTx6otanyQ7qtORQBdoP6ECo8ptgE4BsFt34Z5ngu8QdA3_Uk5bpk32ayW_I2PCxBpR3YBHyJDggj_pYMP3wvFaaAyMfJpRYDpPZ4riL4nlStVwpuVQtrgoRfHdJTH6-Kf18j8a_FYzXcadO4tGTUcRq6pEpjrPfA2F_T_YZvUze_CHvNMPOGTJEHGjyM0r-I-HdCBBzNg1Op01CYXAA2oArzcnNkYd8u9oPpVztu1nz3DCJH6p9P4I8mT4OGAFlsiqsOsinEQPQxb6ynwGrMhrpykiNWQzD_YtCYhLKA_gzNjZxhVgfbCCi-jsBoGTmObgmik7zSqpKQF3ySS55i3TKefS3GKXIns3K0_0QNmbRMKkXW-DDm-eCT5Crty_KBPuPApnNe7I},
	doi = {10.1093/beheco/ary106},
	abstract = {Deciding where to eat and raise offspring carries important fitness consequences for all animals, especially if foraging, feeding, and reproduction increase pathogen exposure. In insects with complete metamorphosis, foraging mainly occurs during the larval stage, while oviposition decisions are made by adult females. Selection for infection avoidance behaviors may therefore be developmentally uncoupled. Using a combination of experimental infections and behavioral choice assays, we tested if Drosophila melanogaster fruit flies avoid infectious environments at distinct developmental stages. When given conspecific fly carcasses as a food source, larvae did not discriminate between carcasses that were clean or infected with the pathogenic Drosophila C Virus (DCV), even though cannibalism was a viable route of DCV transmission. When laying eggs, DCV-infected females did not discriminate between infectious and noninfectious carcasses, and laying eggs near potentially infectious carcasses was always preferred to sites containing only fly food. Healthy mothers, however, laid more eggs near a clean rather than an infectious carcass. Avoidance during oviposition changed over time: after an initial oviposition period, healthy mothers stopped avoiding infectious carcasses. We interpret this result as a possible trade-off between managing infection risk and maximizing reproduction. Our findings suggest infection avoidance contributes to how mothers provision their offspring and underline the need to consider infection avoidance behaviors at multiple life-stages.},
	language = {eng},
	number = {6},
	journal = {Behavioral Ecology: Official Journal of the International Society for Behavioral Ecology},
	author = {Siva-Jothy, Jonathon A. and Monteith, Katy M. and Vale, Pedro F.},
	month = dec,
	year = {2018},
	pages = {1426--1435},
}

Deciding where to eat and raise offspring carries important fitness consequences for all animals, especially if foraging, feeding, and reproduction increase pathogen exposure. In insects with complete metamorphosis, foraging mainly occurs during the larval stage, while oviposition decisions are made by adult females. Selection for infection avoidance behaviors may therefore be developmentally uncoupled. Using a combination of experimental infections and behavioral choice assays, we tested if Drosophila melanogaster fruit flies avoid infectious environments at distinct developmental stages. When given conspecific fly carcasses as a food source, larvae did not discriminate between carcasses that were clean or infected with the pathogenic Drosophila C Virus (DCV), even though cannibalism was a viable route of DCV transmission. When laying eggs, DCV-infected females did not discriminate between infectious and noninfectious carcasses, and laying eggs near potentially infectious carcasses was always preferred to sites containing only fly food. Healthy mothers, however, laid more eggs near a clean rather than an infectious carcass. Avoidance during oviposition changed over time: after an initial oviposition period, healthy mothers stopped avoiding infectious carcasses. We interpret this result as a possible trade-off between managing infection risk and maximizing reproduction. Our findings suggest infection avoidance contributes to how mothers provision their offspring and underline the need to consider infection avoidance behaviors at multiple life-stages.

@article{vale_disease_2018,
	title = {Disease {Tolerance}: {Linking} {Sickness} {Behaviours} to {Metabolism} {Helps} {Mitigate} {Malaria}},
	volume = {28},
	copyright = {All rights reserved},
	issn = {1879-0445},
	shorttitle = {Disease {Tolerance}},
	url = {https://www.researchgate.net/publication/325276717_Disease_Tolerance_Linking_Sickness_Behaviours_to_Metabolism_Helps_Mitigate_Malaria},
	doi = {10.1016/j.cub.2018.04.031},
	abstract = {Malaria-infected mice exhibit a range of sickness behaviours, and experience metabolic shifts and physiological pathologies that result in reduced energy expenditure. Treating sick mice with glucose increases disease tolerance by improving the physiological and behavioural symptoms of malaria infection without affecting parasite loads.},
	language = {eng},
	number = {10},
	journal = {Current biology: CB},
	author = {Vale, Pedro F.},
	year = {2018},
	pages = {R606--R607},
}

Malaria-infected mice exhibit a range of sickness behaviours, and experience metabolic shifts and physiological pathologies that result in reduced energy expenditure. Treating sick mice with glucose increases disease tolerance by improving the physiological and behavioural symptoms of malaria infection without affecting parasite loads.

@article{gupta_route_2017,
	title = {The route of infection determines {Wolbachia} antibacterial protection in {Drosophila}},
	volume = {284},
	copyright = {All rights reserved},
	issn = {1471-2954},
	url = {https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2017.0809},
	doi = {10.1098/rspb.2017.0809},
	abstract = {Bacterial symbionts are widespread among metazoans and provide a range of beneficial functions. Wolbachia-mediated protection against viral infection has been extensively demonstrated in Drosophila. In mosquitoes that are artificially transinfected with Drosophila melanogaster Wolbachia (wMel), protection from both viral and bacterial infections has been demonstrated. However, no evidence for Wolbachia-mediated antibacterial protection has been demonstrated in Drosophila to date. Here, we show that the route of infection is key for Wolbachia-mediated antibacterial protection. Drosophila melanogaster carrying Wolbachia showed reduced mortality during enteric-but not systemic-infection with the opportunist pathogen Pseudomonas aeruginosaWolbachia-mediated protection was more pronounced in male flies and is associated with increased early expression of the antimicrobial peptide Attacin A, and also increased expression of a reactive oxygen species detoxification gene (Gst D8). These results highlight that the route of infection is important for symbiont-mediated protection from infection, that Wolbachia can protect hosts by eliciting a combination of resistance and disease tolerance mechanisms, and that these effects are sexually dimorphic. We discuss the importance of using ecologically relevant routes of infection to gain a better understanding of symbiont-mediated protection.},
	language = {eng},
	number = {1856},
	journal = {Proceedings of the Royal Society B},
	author = {Gupta, Vanika and Vasanthakrishnan, Radhakrishnan B. and Siva-Jothy, Jonathon and Monteith, Katy M. and Brown, Sam P. and Vale, Pedro F.},
	month = jun,
	year = {2017},
}

Bacterial symbionts are widespread among metazoans and provide a range of beneficial functions. Wolbachia-mediated protection against viral infection has been extensively demonstrated in Drosophila. In mosquitoes that are artificially transinfected with Drosophila melanogaster Wolbachia (wMel), protection from both viral and bacterial infections has been demonstrated. However, no evidence for Wolbachia-mediated antibacterial protection has been demonstrated in Drosophila to date. Here, we show that the route of infection is key for Wolbachia-mediated antibacterial protection. Drosophila melanogaster carrying Wolbachia showed reduced mortality during enteric-but not systemic-infection with the opportunist pathogen Pseudomonas aeruginosaWolbachia-mediated protection was more pronounced in male flies and is associated with increased early expression of the antimicrobial peptide Attacin A, and also increased expression of a reactive oxygen species detoxification gene (Gst D8). These results highlight that the route of infection is important for symbiont-mediated protection from infection, that Wolbachia can protect hosts by eliciting a combination of resistance and disease tolerance mechanisms, and that these effects are sexually dimorphic. We discuss the importance of using ecologically relevant routes of infection to gain a better understanding of symbiont-mediated protection.

@article{gupta_costs_2017,
	title = {Costs and benefits of sublethal {Drosophila} {C} virus infection},
	volume = {30},
	copyright = {All rights reserved},
	issn = {1420-9101},
	url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/jeb.13096},
	doi = {10.1111/jeb.13096},
	abstract = {Viruses are major evolutionary drivers of insect immune systems. Much of our knowledge of insect immune responses derives from experimental infections using the fruit fly Drosophila melanogaster. Most experiments, however, employ lethal pathogen doses through septic injury, frequently overwhelming host physiology. While this approach has revealed several immune mechanisms, it is less informative about the fitness costs hosts may experience during infection in the wild. Using both systemic and oral infection routes, we find that even apparently benign, sublethal infections with the horizontally transmitted Drosophila C virus (DCV) can cause significant physiological and behavioural morbidity that is relevant for host fitness. We describe DCV-induced effects on fly reproductive output, digestive health and locomotor activity, and we find that viral morbidity varies according to the concentration of pathogen inoculum, host genetic background and sex. Notably, sublethal DCV infection resulted in a significant increase in fly reproduction, but this effect depended on host genotype. We discuss the relevance of sublethal morbidity for Drosophila ecology and evolution, and more broadly, we remark on the implications of deleterious and beneficial infections for the evolution of insect immunity.},
	language = {eng},
	number = {7},
	journal = {Journal of Evolutionary Biology},
	author = {Gupta, V. and Stewart, C. O. and Rund, S. S. C. and Monteith, K. and Vale, P. F.},
	year = {2017},
	pages = {1325--1335},
}

Viruses are major evolutionary drivers of insect immune systems. Much of our knowledge of insect immune responses derives from experimental infections using the fruit fly Drosophila melanogaster. Most experiments, however, employ lethal pathogen doses through septic injury, frequently overwhelming host physiology. While this approach has revealed several immune mechanisms, it is less informative about the fitness costs hosts may experience during infection in the wild. Using both systemic and oral infection routes, we find that even apparently benign, sublethal infections with the horizontally transmitted Drosophila C virus (DCV) can cause significant physiological and behavioural morbidity that is relevant for host fitness. We describe DCV-induced effects on fly reproductive output, digestive health and locomotor activity, and we find that viral morbidity varies according to the concentration of pathogen inoculum, host genetic background and sex. Notably, sublethal DCV infection resulted in a significant increase in fly reproduction, but this effect depended on host genotype. We discuss the relevance of sublethal morbidity for Drosophila ecology and evolution, and more broadly, we remark on the implications of deleterious and beneficial infections for the evolution of insect immunity.

@article{gupta_nonlinear_2017,
	title = {Nonlinear disease tolerance curves reveal distinct components of host responses to viral infection},
	volume = {4},
	copyright = {All rights reserved},
	issn = {2054-5703},
	url = {https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.170342},
	doi = {10.1098/rsos.170342},
	abstract = {The ability to tolerate infection is a key component of host defence and offers potential novel therapeutic approaches for infectious diseases. To yield successful targets for therapeutic intervention, it is important that the analytical tools employed to measure disease tolerance are able to capture distinct host responses to infection. Here, we show that commonly used methods that estimate tolerance as a linear relationship should be complemented with more flexible, nonlinear estimates of this relationship which may reveal variation in distinct components such as host vigour, sensitivity to increases in pathogen loads, and the severity of the infection. To illustrate this, we measured the survival of Drosophila melanogaster carrying either a functional or non-functional regulator of the JAK-STAT immune pathway (G9a) when challenged with a range of concentrations of Drosophila C virus (DCV). While classical linear model analyses indicated that G9a affected tolerance only in females, a more powerful nonlinear logistic model showed that G9a mediates viral tolerance to different extents in both sexes. This analysis also revealed that G9a acts by changing the sensitivity to increasing pathogen burdens, but does not reduce the ultimate severity of disease. These results indicate that fitting nonlinear models to host health-pathogen burden relationships may offer better and more detailed estimates of disease tolerance.},
	language = {eng},
	number = {7},
	journal = {Royal Society Open Science},
	author = {Gupta, Vanika and Vale, Pedro F.},
	month = jul,
	year = {2017},
	pages = {170342},
}

The ability to tolerate infection is a key component of host defence and offers potential novel therapeutic approaches for infectious diseases. To yield successful targets for therapeutic intervention, it is important that the analytical tools employed to measure disease tolerance are able to capture distinct host responses to infection. Here, we show that commonly used methods that estimate tolerance as a linear relationship should be complemented with more flexible, nonlinear estimates of this relationship which may reveal variation in distinct components such as host vigour, sensitivity to increases in pathogen loads, and the severity of the infection. To illustrate this, we measured the survival of Drosophila melanogaster carrying either a functional or non-functional regulator of the JAK-STAT immune pathway (G9a) when challenged with a range of concentrations of Drosophila C virus (DCV). While classical linear model analyses indicated that G9a affected tolerance only in females, a more powerful nonlinear logistic model showed that G9a mediates viral tolerance to different extents in both sexes. This analysis also revealed that G9a acts by changing the sensitivity to increasing pathogen burdens, but does not reduce the ultimate severity of disease. These results indicate that fitting nonlinear models to host health-pathogen burden relationships may offer better and more detailed estimates of disease tolerance.

@article{heath_virus_2017,
	title = {Virus {Resistance} {Is} {Not} {Costly} in a {Marine} {Alga} {Evolving} under {Multiple} {Environmental} {Stressors}},
	volume = {9},
	copyright = {All rights reserved},
	issn = {1999-4915},
	url = {https://www.mdpi.com/1999-4915/9/3/39/pdf},
	doi = {10.3390/v9030039},
	abstract = {Viruses are important evolutionary drivers of host ecology and evolution. The marine picoplankton Ostreococcus tauri has three known resistance types that arise in response to infection with the Phycodnavirus OtV5: susceptible cells (S) that lyse following viral entry and replication; resistant cells (R) that are refractory to viral entry; and resistant producers (RP) that do not all lyse but maintain some viruses within the population. To test for evolutionary costs of maintaining antiviral resistance, we examined whether O. tauri populations composed of each resistance type differed in their evolutionary responses to several environmental drivers (lower light, lower salt, lower phosphate and a changing environment) in the absence of viruses for approximately 200 generations. We did not detect a cost of resistance as measured by life-history traits (population growth rate, cell size and cell chlorophyll content) and competitive ability. Specifically, all R and RP populations remained resistant to OtV5 lysis for the entire 200-generation experiment, whereas lysis occurred in all S populations, suggesting that resistance is not costly to maintain even when direct selection for resistance was removed, or that there could be a genetic constraint preventing return to a susceptible resistance type. Following evolution, all S population densities dropped when inoculated with OtV5, but not to zero, indicating that lysis was incomplete, and that some cells may have gained a resistance mutation over the evolution experiment. These findings suggest that maintaining resistance in the absence of viruses was not costly.},
	language = {eng},
	number = {3},
	journal = {Viruses},
	author = {Heath, Sarah E. and Knox, Kirsten and Vale, Pedro F. and Collins, Sinead},
	month = mar,
	year = {2017},
}

Viruses are important evolutionary drivers of host ecology and evolution. The marine picoplankton Ostreococcus tauri has three known resistance types that arise in response to infection with the Phycodnavirus OtV5: susceptible cells (S) that lyse following viral entry and replication; resistant cells (R) that are refractory to viral entry; and resistant producers (RP) that do not all lyse but maintain some viruses within the population. To test for evolutionary costs of maintaining antiviral resistance, we examined whether O. tauri populations composed of each resistance type differed in their evolutionary responses to several environmental drivers (lower light, lower salt, lower phosphate and a changing environment) in the absence of viruses for approximately 200 generations. We did not detect a cost of resistance as measured by life-history traits (population growth rate, cell size and cell chlorophyll content) and competitive ability. Specifically, all R and RP populations remained resistant to OtV5 lysis for the entire 200-generation experiment, whereas lysis occurred in all S populations, suggesting that resistance is not costly to maintain even when direct selection for resistance was removed, or that there could be a genetic constraint preventing return to a susceptible resistance type. Following evolution, all S population densities dropped when inoculated with OtV5, but not to zero, indicating that lysis was incomplete, and that some cells may have gained a resistance mutation over the evolution experiment. These findings suggest that maintaining resistance in the absence of viruses was not costly.

@article{vale_infection_2017,
	title = {Infection avoidance behavior: {Viral} exposure reduces the motivation to forage in female {Drosophila} melanogaster},
	volume = {11},
	copyright = {All rights reserved},
	issn = {1933-6942},
	shorttitle = {Infection avoidance behavior},
	url = {https://www.tandfonline.com/doi/full/10.1080/19336934.2016.1207029#aHR0cHM6Ly93d3cudGFuZGZvbmxpbmUuY29tL2RvaS9wZGYvMTAuMTA4MC8xOTMzNjkzNC4yMDE2LjEyMDcwMjk/bmVlZEFjY2Vzcz10cnVlQEBAMA==},
	doi = {10.1080/19336934.2016.1207029},
	abstract = {Infection avoidance behaviors are the first line of defense against pathogenic encounters. Behavioral plasticity in response to internal or external cues of infection can therefore generate potentially significant heterogeneity in infection. We tested whether Drosophila melanogaster exhibits infection avoidance behavior, and whether this behavior is modified by prior exposure to Drosophila C Virus (DCV) and by the risk of DCV encounter. We examined 2 measures of infection avoidance: (1) the motivation to seek out food sources in the presence of an infection risk and (2) the preference to land on a clean food source over a potentially infectious source. While we found no evidence for preference of clean food sources over potentially infectious ones, previously exposed female flies showed lower motivation to pick a food source when presented with a risk of encountering DCV. We discuss the relevance of behavioral plasticity during foraging for host fitness and pathogen spread.},
	language = {eng},
	number = {1},
	journal = {Fly},
	author = {Vale, Pedro F. and Jardine, Michael D.},
	year = {2017},
	pages = {3--9},
}

Infection avoidance behaviors are the first line of defense against pathogenic encounters. Behavioral plasticity in response to internal or external cues of infection can therefore generate potentially significant heterogeneity in infection. We tested whether Drosophila melanogaster exhibits infection avoidance behavior, and whether this behavior is modified by prior exposure to Drosophila C Virus (DCV) and by the risk of DCV encounter. We examined 2 measures of infection avoidance: (1) the motivation to seek out food sources in the presence of an infection risk and (2) the preference to land on a clean food source over a potentially infectious source. While we found no evidence for preference of clean food sources over potentially infectious ones, previously exposed female flies showed lower motivation to pick a food source when presented with a risk of encountering DCV. We discuss the relevance of behavioral plasticity during foraging for host fitness and pathogen spread.

@article{vale_beyond_2016,
	title = {Beyond killing: {Can} we find new ways to manage infection?},
	volume = {2016},
	copyright = {All rights reserved},
	url = {https://academic.oup.com/emph/article/2016/1/148/2802627},
	doi = {10.1093/emph/eow012},
	abstract = {The antibiotic pipeline is running dry and infectious disease remains a major threat to public health. An efficient strategy to stay ahead of rapidly},
	language = {en},
	number = {1},
	urldate = {2018-05-21},
	journal = {Evolution, Medicine, and Public Health},
	author = {Vale, Pedro F. and McNally, Luke and Doeschl-Wilson, Andrea and King, Kayla C. and Popat, Roman and Domingo-Sananes, Maria R. and Allen, Judith E. and Soares, Miguel P. and Kümmerli, Rolf},
	month = jan,
	year = {2016},
	pages = {148--157},
}

The antibiotic pipeline is running dry and infectious disease remains a major threat to public health. An efficient strategy to stay ahead of rapidly

@misc{mcnally_microbiome_2015,
	title = {Microbiome engineering could select for more virulent pathogens},
	copyright = {© 2015, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	url = {https://www.biorxiv.org/content/10.1101/027854v1},
	doi = {10.1101/027854},
	abstract = {Recent insights into the human microbiome offer the hope of manipulating its composition to help fight infectious diseases1–7. While this strategy has shown huge potential, its consequences for pathogen evolution have not been explored. Here we show that manipulating the microbiome to increase the competition that pathogens face could lead to the evolution of increased production of virulence factors that pathogens use to combat commensals, an evolutionary response that can increase total disease induced mortality in the long-term. However, if treatment with microbiome engineering is sufficiently aggressive this evolutionary response can be avoided and the pathogen eradicated. Furthermore, we show that using damage limitation therapies8 (e.g. antivirulence and anti-inflammatory drugs) in combination with microbiome manipulation increases the potential for pathogen eradication. While manipulating our microbiota offers a promising alternative to antibiotics, our results show that these treatments must be designed with careful consideration of the potential evolutionary responses of target pathogens.},
	language = {en},
	urldate = {2024-06-04},
	publisher = {bioRxiv},
	author = {McNally, Luke and Vale, Pedro F. and Brown, Sam P.},
	month = sep,
	year = {2015},
	note = {Pages: 027854
Section: New Results},
}

Recent insights into the human microbiome offer the hope of manipulating its composition to help fight infectious diseases1–7. While this strategy has shown huge potential, its consequences for pathogen evolution have not been explored. Here we show that manipulating the microbiome to increase the competition that pathogens face could lead to the evolution of increased production of virulence factors that pathogens use to combat commensals, an evolutionary response that can increase total disease induced mortality in the long-term. However, if treatment with microbiome engineering is sufficiently aggressive this evolutionary response can be avoided and the pathogen eradicated. Furthermore, we show that using damage limitation therapies8 (e.g. antivirulence and anti-inflammatory drugs) in combination with microbiome manipulation increases the potential for pathogen eradication. While manipulating our microbiota offers a promising alternative to antibiotics, our results show that these treatments must be designed with careful consideration of the potential evolutionary responses of target pathogens.

@article{susi_co-infection_2015,
	title = {Co-infection alters population dynamics of infectious disease},
	volume = {6},
	copyright = {All rights reserved},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/ncomms6975.pdf},
	doi = {10.1038/ncomms6975},
	abstract = {Co-infections by multiple pathogen strains are common in the wild. Theory predicts co-infections to have major consequences for both within- and between-host disease dynamics, but data are currently scarce. Here, using common garden populations of Plantago lanceolata infected by two strains of the pathogen Podosphaera plantaginis, either singly or under co-infection, we find the highest disease prevalence in co-infected treatments both at the host genotype and population levels. A spore-trapping experiment demonstrates that co-infected hosts shed more transmission propagules than singly infected hosts, thereby explaining the observed change in epidemiological dynamics. Our experimental findings are confirmed in natural pathogen populations-more devastating epidemics were measured in populations with higher levels of co-infection. Jointly, our results confirm the predictions made by theoretical and experimental studies for the potential of co-infection to alter disease dynamics across a large host-pathogen metapopulation.},
	language = {eng},
	journal = {Nature Communications},
	author = {Susi, Hanna and Barrès, Benoit and Vale, Pedro F. and Laine, Anna-Liisa},
	month = jan,
	year = {2015},
	pages = {5975},
}

Co-infections by multiple pathogen strains are common in the wild. Theory predicts co-infections to have major consequences for both within- and between-host disease dynamics, but data are currently scarce. Here, using common garden populations of Plantago lanceolata infected by two strains of the pathogen Podosphaera plantaginis, either singly or under co-infection, we find the highest disease prevalence in co-infected treatments both at the host genotype and population levels. A spore-trapping experiment demonstrates that co-infected hosts shed more transmission propagules than singly infected hosts, thereby explaining the observed change in epidemiological dynamics. Our experimental findings are confirmed in natural pathogen populations-more devastating epidemics were measured in populations with higher levels of co-infection. Jointly, our results confirm the predictions made by theoretical and experimental studies for the potential of co-infection to alter disease dynamics across a large host-pathogen metapopulation.

@article{susi_host_2015,
	title = {Host {Genotype} and {Coinfection} {Modify} the {Relationship} of within and between {Host} {Transmission}},
	volume = {186},
	copyright = {All rights reserved},
	issn = {1537-5323},
	url = {https://www.journals.uchicago.edu/doi/pdfplus/10.1086/682069},
	doi = {10.1086/682069},
	abstract = {Variation in individual-level disease transmission is well documented, but the underlying causes of this variation are challenging to disentangle in natural epidemics. In general, within-host replication is critical in determining the extent to which infected hosts shed transmission propagules, but which factors cause variation in this relationship are poorly understood. Here, using a plant host, Plantago lanceolata, and the powdery mildew fungus Podosphaera plantaginis, we quantify how the distinct stages of within-host spread (autoinfection), spore release, and successful transmission to new hosts (alloinfection) are influenced by host genotype, pathogen genotype, and the coinfection status of the host. We find that within-host spread alone fails to predict transmission rates, as this relationship is modified by genetic variation in hosts and pathogens. Their contributions change throughout the course of the epidemic. Host genotype and coinfection had particularly pronounced effects on the dynamics of spore release from infected hosts. Confidently predicting disease spread from local levels of individual transmission, therefore, requires a more nuanced understanding of genotype-specific infection outcomes. This knowledge is key to better understanding the drivers of epidemiological dynamics and the resulting evolutionary trajectories of infectious disease.},
	language = {eng},
	number = {2},
	journal = {The American Naturalist},
	author = {Susi, Hanna and Vale, Pedro F. and Laine, Anna-Liisa},
	month = aug,
	year = {2015},
	pages = {252--263},
}

Variation in individual-level disease transmission is well documented, but the underlying causes of this variation are challenging to disentangle in natural epidemics. In general, within-host replication is critical in determining the extent to which infected hosts shed transmission propagules, but which factors cause variation in this relationship are poorly understood. Here, using a plant host, Plantago lanceolata, and the powdery mildew fungus Podosphaera plantaginis, we quantify how the distinct stages of within-host spread (autoinfection), spore release, and successful transmission to new hosts (alloinfection) are influenced by host genotype, pathogen genotype, and the coinfection status of the host. We find that within-host spread alone fails to predict transmission rates, as this relationship is modified by genetic variation in hosts and pathogens. Their contributions change throughout the course of the epidemic. Host genotype and coinfection had particularly pronounced effects on the dynamics of spore release from infected hosts. Confidently predicting disease spread from local levels of individual transmission, therefore, requires a more nuanced understanding of genotype-specific infection outcomes. This knowledge is key to better understanding the drivers of epidemiological dynamics and the resulting evolutionary trajectories of infectious disease.

@article{vale_sex-specific_2015,
	title = {Sex-specific behavioural symptoms of viral gut infection and {Wolbachia} in {Drosophila} melanogaster},
	volume = {82},
	copyright = {All rights reserved},
	issn = {1879-1611},
	url = {https://www.sciencedirect.com/science/article/pii/S002219101500178X/pdfft?md5=876000defbcf20f0a95ed162e787001e&pid=1-s2.0-S002219101500178X-main.pdf},
	doi = {10.1016/j.jinsphys.2015.08.005},
	abstract = {All organisms are infected with a range of symbionts spanning the spectrum of beneficial mutualists to detrimental parasites. The fruit fly Drosophila melanogaster is a good example, as both endosymbiotic Wolbachia, and pathogenic Drosophila C Virus (DCV) commonly infect it. While the pathophysiology and immune responses against both symbionts are the focus of intense study, the behavioural effects of these infections have received less attention. Here we report sex-specific behavioural responses to these infections in D. melanogaster. DCV infection caused increased sleep in female flies, but had no detectable effect in male flies. The presence of Wolbachia did not reduce this behavioural response to viral infection. We also found evidence for a sex-specific cost of Wolbachia, as male flies infected with the endosymbiont became more lethargic when awake. We discuss these behavioural symptoms as potentially adaptive sickness behaviours.},
	language = {eng},
	journal = {Journal of Insect Physiology},
	author = {Vale, Pedro F. and Jardine, Michael D.},
	month = nov,
	year = {2015},
	pages = {28--32},
}

All organisms are infected with a range of symbionts spanning the spectrum of beneficial mutualists to detrimental parasites. The fruit fly Drosophila melanogaster is a good example, as both endosymbiotic Wolbachia, and pathogenic Drosophila C Virus (DCV) commonly infect it. While the pathophysiology and immune responses against both symbionts are the focus of intense study, the behavioural effects of these infections have received less attention. Here we report sex-specific behavioural responses to these infections in D. melanogaster. DCV infection caused increased sleep in female flies, but had no detectable effect in male flies. The presence of Wolbachia did not reduce this behavioural response to viral infection. We also found evidence for a sex-specific cost of Wolbachia, as male flies infected with the endosymbiont became more lethargic when awake. We discuss these behavioural symptoms as potentially adaptive sickness behaviours.

@article{vale_costs_2015,
	title = {Costs of {CRISPR}-{Cas}-mediated resistance in {Streptococcus} thermophilus},
	volume = {282},
	copyright = {All rights reserved},
	issn = {1471-2954},
	url = {https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2015.1270},
	doi = {10.1098/rspb.2015.1270},
	abstract = {CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.},
	language = {eng},
	number = {1812},
	journal = {Proceedings. Biological Sciences},
	author = {Vale, Pedro F. and Lafforgue, Guillaume and Gatchitch, Francois and Gardan, Rozenn and Moineau, Sylvain and Gandon, Sylvain},
	month = aug,
	year = {2015},
	pages = {20151270},
}

CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.

@article{gandon_evolution_2014,
	title = {The evolution of resistance against good and bad infections},
	volume = {27},
	copyright = {All rights reserved},
	issn = {1420-9101},
	url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/jeb.12291},
	doi = {10.1111/jeb.12291},
	abstract = {Opportunities for genetic exchange are abundant between bacteria and foreign genetic elements (FGEs) such as conjugative plasmids, transposable elements and bacteriophages. The genetic novelty that may arise from these forms of genetic exchange is potentially beneficial to bacterial hosts, but there are also potential costs, which may be considerable in the case of phage infection. Some bacterial resistance mechanisms target both beneficial and deleterious forms of genetic exchange. Using a general epidemiological model, we explored under which conditions such resistance mechanisms may evolve. We considered a population of hosts that may be infected by FGEs that either confer a benefit or are deleterious to host fitness, and we analysed the epidemiological and evolutionary outcomes of resistance evolving under different cost/benefit scenarios. We show that the degree of co-infection between these two types of infection is particularly important in determining the evolutionarily stable level of host resistance. We explore these results using the example of CRISPR-Cas, a form of bacterial immunity that targets a variety of FGEs, and we show the potential role of bacteriophage infection in selecting for resistance mechanisms that in turn limit the acquisition of plasmid-borne antibiotic resistance. Finally, beyond microbes, we discuss how endosymbiotic associations may have shaped the evolution of host immune responses to pathogens.},
	language = {eng},
	number = {2},
	journal = {Journal of Evolutionary Biology},
	author = {Gandon, S. and Vale, P. F.},
	month = feb,
	year = {2014},
	pages = {303--312},
}

Opportunities for genetic exchange are abundant between bacteria and foreign genetic elements (FGEs) such as conjugative plasmids, transposable elements and bacteriophages. The genetic novelty that may arise from these forms of genetic exchange is potentially beneficial to bacterial hosts, but there are also potential costs, which may be considerable in the case of phage infection. Some bacterial resistance mechanisms target both beneficial and deleterious forms of genetic exchange. Using a general epidemiological model, we explored under which conditions such resistance mechanisms may evolve. We considered a population of hosts that may be infected by FGEs that either confer a benefit or are deleterious to host fitness, and we analysed the epidemiological and evolutionary outcomes of resistance evolving under different cost/benefit scenarios. We show that the degree of co-infection between these two types of infection is particularly important in determining the evolutionarily stable level of host resistance. We explore these results using the example of CRISPR-Cas, a form of bacterial immunity that targets a variety of FGEs, and we show the potential role of bacteriophage infection in selecting for resistance mechanisms that in turn limit the acquisition of plasmid-borne antibiotic resistance. Finally, beyond microbes, we discuss how endosymbiotic associations may have shaped the evolution of host immune responses to pathogens.

@article{vale_limiting_2014,
	title = {Limiting damage during infection: lessons from infection tolerance for novel therapeutics},
	volume = {12},
	copyright = {All rights reserved},
	issn = {1545-7885},
	shorttitle = {Limiting damage during infection},
	url = {https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1001769&type=printable},
	doi = {10.1371/journal.pbio.1001769},
	abstract = {The distinction between pathogen elimination and damage limitation during infection is beginning to change perspectives on infectious disease control, and has recently led to the development of novel therapies that focus on reducing the illness caused by pathogens (‘‘damage limitation’’)rather than reducing pathogen burdens directly (‘‘pathogen elimination’’). While beneficial at the individual host level, the population consequences of these interventions remain unclear. To address this issue,we present a simple conceptual framework for damage limitation during infection that distinguishes between therapies that are either host-centric (pro-tolerance) or pathogen-centric (anti-virulence). We then draw on recent developments from the evolutionary ecology of disease tolerance to highlight some potential epidemiological and evolutionary responses of pathogens to medical interventions that target the symptoms of infection. Just as pathogens are known to evolve in response to antimicrobial and vaccination therapies, we caution that claims of ‘‘evolution-proof’’ anti-virulence interventions may be premature, and further, that in infections where virulence and transmission are linked, reducing illness without reducing pathogen burden could have non-trivial epidemiological and evolutionary consequences that require careful examination.},
	language = {eng},
	number = {1},
	journal = {PLoS biology},
	author = {Vale, Pedro F. and Fenton, Andy and Brown, Sam P.},
	month = jan,
	year = {2014},
	pages = {e1001769},
}

The distinction between pathogen elimination and damage limitation during infection is beginning to change perspectives on infectious disease control, and has recently led to the development of novel therapies that focus on reducing the illness caused by pathogens (‘‘damage limitation’’)rather than reducing pathogen burdens directly (‘‘pathogen elimination’’). While beneficial at the individual host level, the population consequences of these interventions remain unclear. To address this issue,we present a simple conceptual framework for damage limitation during infection that distinguishes between therapies that are either host-centric (pro-tolerance) or pathogen-centric (anti-virulence). We then draw on recent developments from the evolutionary ecology of disease tolerance to highlight some potential epidemiological and evolutionary responses of pathogens to medical interventions that target the symptoms of infection. Just as pathogens are known to evolve in response to antimicrobial and vaccination therapies, we caution that claims of ‘‘evolution-proof’’ anti-virulence interventions may be premature, and further, that in infections where virulence and transmission are linked, reducing illness without reducing pathogen burden could have non-trivial epidemiological and evolutionary consequences that require careful examination.

@article{vale_killing_2013,
	title = {Killing them softly: managing pathogen polymorphism and virulence in spatially variable environments},
	volume = {29},
	copyright = {All rights reserved},
	issn = {1471-5007},
	shorttitle = {Killing them softly},
	url = {https://www.sciencedirect.com/science/article/pii/S1471492213001074/pdfft?md5=165d7b3988a7b32987888a2b5f0ae856&pid=1-s2.0-S1471492213001074-main.pdf},
	doi = {10.1016/j.pt.2013.07.002},
	abstract = {Understanding why pathogen populations are genetically variable is vital because genetic variation fuels evolution, which often hampers disease control efforts. Here I argue that classical models of evolution in spatially variable environments - specifically, models of hard and soft selection - provide a useful framework to understand the maintenance of pathogen polymorphism and the evolution of virulence. First, the similarities between models of hard and soft selection and pathogen life cycles are described, highlighting how the type and timing of pathogen control measures impose density regulation that may affect both the level of pathogen polymorphism and virulence. The article concludes with an outline of potential lines of future theoretical and experimental work.},
	language = {eng},
	number = {9},
	journal = {Trends in Parasitology},
	author = {Vale, Pedro F.},
	month = sep,
	year = {2013},
	pages = {417--422},
}

Understanding why pathogen populations are genetically variable is vital because genetic variation fuels evolution, which often hampers disease control efforts. Here I argue that classical models of evolution in spatially variable environments - specifically, models of hard and soft selection - provide a useful framework to understand the maintenance of pathogen polymorphism and the evolution of virulence. First, the similarities between models of hard and soft selection and pathogen life cycles are described, highlighting how the type and timing of pathogen control measures impose density regulation that may affect both the level of pathogen polymorphism and virulence. The article concludes with an outline of potential lines of future theoretical and experimental work.

@article{vale_host_2013,
	title = {Host nutrition alters the variance in parasite transmission potential},
	volume = {9},
	copyright = {All rights reserved},
	issn = {1744-957X},
	url = {https://royalsocietypublishing.org/doi/pdf/10.1098/rsbl.2012.1145},
	doi = {10.1098/rsbl.2012.1145},
	abstract = {The environmental conditions experienced by hosts are known to affect their mean parasite transmission potential. How different conditions may affect the variance of transmission potential has received less attention, but is an important question for disease management, especially if specific ecological contexts are more likely to foster a few extremely infectious hosts. Using the obligate-killing bacterium Pasteuria ramosa and its crustacean host Daphnia magna, we analysed how host nutrition affected the variance of individual parasite loads, and, therefore, transmission potential. Under low food, individual parasite loads showed similar mean and variance, following a Poisson distribution. By contrast, among well-nourished hosts, parasite loads were right-skewed and overdispersed, following a negative binomial distribution. Abundant food may, therefore, yield individuals causing potentially more transmission than the population average. Measuring both the mean and variance of individual parasite loads in controlled experimental infections may offer a useful way of revealing risk factors for potential highly infectious hosts.},
	language = {eng},
	number = {2},
	journal = {Biology Letters},
	author = {Vale, Pedro F. and Choisy, Marc and Little, Tom J.},
	month = apr,
	year = {2013},
	pages = {20121145},
}

The environmental conditions experienced by hosts are known to affect their mean parasite transmission potential. How different conditions may affect the variance of transmission potential has received less attention, but is an important question for disease management, especially if specific ecological contexts are more likely to foster a few extremely infectious hosts. Using the obligate-killing bacterium Pasteuria ramosa and its crustacean host Daphnia magna, we analysed how host nutrition affected the variance of individual parasite loads, and, therefore, transmission potential. Under low food, individual parasite loads showed similar mean and variance, following a Poisson distribution. By contrast, among well-nourished hosts, parasite loads were right-skewed and overdispersed, following a negative binomial distribution. Abundant food may, therefore, yield individuals causing potentially more transmission than the population average. Measuring both the mean and variance of individual parasite loads in controlled experimental infections may offer a useful way of revealing risk factors for potential highly infectious hosts.

@article{garbutt_elevated_2013,
	title = {Elevated maternal temperature enhances offspring disease resistance in {Daphnia} magna},
	copyright = {© 2013 The Authors. Functional Ecology © 2013 British Ecological Society},
	issn = {1365-2435},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12197/abstract},
	doi = {10.1111/1365-2435.12197},
	abstract = {* Maternal effects are increasingly recognized to impact upon infectious diseases. Stressful environmental conditions that coincide with high infection prevalence are potential cues for adaptive maternal effects on offspring resistance to infection. * We studied how maternal temperature (15 °C, 20 °C and 25 °C), as well as maternal food availability (high and low food) influenced the ability of the crustacean, Daphnia magna, to resist its bacterial parasite, Pasteuria ramosa. * Mothers held at a higher temperature and mothers fed a restricted diet produced offspring that were more resistant to P. ramosa infection. * Maternal temperature also influenced the progression of disease in infected offspring. Parasite spore production and host reproduction were affected by maternal temperature, but these effects differed in the two genotypes used. * As Daphnia populations experience regular summer epidemics of P. ramosa, temperature may be an environmental signal of infection risk. Thus, the enhanced resistance we observed under stressful food and temperature is conceivably an adaptation to looming epidemics. * Thus, this study identifies novel ways in which the maternal environment impacts upon disease resistance and indicates how phenotypic plasticity might both alter co-evolution and mitigate epidemics driven by environmental change in a wide range of taxa.},
	language = {en},
	urldate = {2014-01-25},
	journal = {Functional Ecology},
	author = {Garbutt, Jennie S. and Scholefield, Jennifer A. and Vale, Pedro F. and Little, Tom J.},
	year = {2013},
	pages = {n/a--n/a},
}

* Maternal effects are increasingly recognized to impact upon infectious diseases. Stressful environmental conditions that coincide with high infection prevalence are potential cues for adaptive maternal effects on offspring resistance to infection. * We studied how maternal temperature (15 °C, 20 °C and 25 °C), as well as maternal food availability (high and low food) influenced the ability of the crustacean, Daphnia magna, to resist its bacterial parasite, Pasteuria ramosa. * Mothers held at a higher temperature and mothers fed a restricted diet produced offspring that were more resistant to P. ramosa infection. * Maternal temperature also influenced the progression of disease in infected offspring. Parasite spore production and host reproduction were affected by maternal temperature, but these effects differed in the two genotypes used. * As Daphnia populations experience regular summer epidemics of P. ramosa, temperature may be an environmental signal of infection risk. Thus, the enhanced resistance we observed under stressful food and temperature is conceivably an adaptation to looming epidemics. * Thus, this study identifies novel ways in which the maternal environment impacts upon disease resistance and indicates how phenotypic plasticity might both alter co-evolution and mitigate epidemics driven by environmental change in a wide range of taxa.

@article{fellous_genetic_2012,
	title = {Genetic influence on disease spread following arrival of infected carriers},
	volume = {15},
	copyright = {All rights reserved},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1461-0248.2011.01723.x},
	doi = {10.1111/j.1461-0248.2011.01723.x},
	abstract = {Epidemiology in host meta-populations depends on parasite ability to disperse between, establish and persist in distinct sub-populations of hosts. We studied the genetic factors determining the short-term establishment, and long-term maintenance, of pathogens introduced by infected hosts (i.e. carriers) into recipient populations. We used experimental populations of the freshwater ciliate Paramecium caudatum and its bacterial parasite Holospora undulata. Parasite short-term spread (approximately one horizontal transmission cycle) was affected mainly by carrier genotype, and its interactions with parasite and recipient genotypes. By contrast, parasite longer term spread (2-3 horizontal transmission cycles) was mostly determined by parasite isolate. Importantly, measures of parasite short-term success (reproductive number, R) were not good predictors for longer term prevalence, probably because of the specific interactions between host and parasite genotypes. Analogous to variation in vectorial capacity and super-spreader occurrence, two crucial components of epidemiology, we show that carrier genotype can also affect disease spread within meta-populations.},
	language = {eng},
	number = {3},
	journal = {Ecology Letters},
	author = {Fellous, Simon and Duncan, Alison B. and Quillery, Elsa and Vale, Pedro F. and Kaltz, Oliver},
	month = mar,
	year = {2012},
	pages = {186--192},
}

Epidemiology in host meta-populations depends on parasite ability to disperse between, establish and persist in distinct sub-populations of hosts. We studied the genetic factors determining the short-term establishment, and long-term maintenance, of pathogens introduced by infected hosts (i.e. carriers) into recipient populations. We used experimental populations of the freshwater ciliate Paramecium caudatum and its bacterial parasite Holospora undulata. Parasite short-term spread (approximately one horizontal transmission cycle) was affected mainly by carrier genotype, and its interactions with parasite and recipient genotypes. By contrast, parasite longer term spread (2-3 horizontal transmission cycles) was mostly determined by parasite isolate. Importantly, measures of parasite short-term success (reproductive number, R) were not good predictors for longer term prevalence, probably because of the specific interactions between host and parasite genotypes. Analogous to variation in vectorial capacity and super-spreader occurrence, two crucial components of epidemiology, we show that carrier genotype can also affect disease spread within meta-populations.

@article{vale_fecundity_2012,
	title = {Fecundity compensation and tolerance to a sterilizing pathogen in {Daphnia}},
	volume = {25},
	copyright = {All rights reserved},
	issn = {1420-9101},
	url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1420-9101.2012.02579.x},
	doi = {10.1111/j.1420-9101.2012.02579.x},
	abstract = {Hosts are armed with several lines of defence in the battle against parasites: they may prevent the establishment of infection, reduce parasite growth once infected or persevere through mechanisms that reduce the damage caused by infection, called tolerance. Studies on tolerance in animals have focused on mortality, and sterility tolerance has not been investigated experimentally. Here, we tested for genetic variation in the multiple steps of defence when the invertebrate Daphnia magna is infected with the sterilizing bacterial pathogen Pasteuria ramosa: anti-infection resistance, anti-growth resistance and the ability to tolerate sterilization once infected. When exposed to nine doses of a genetically diverse pathogen inoculum, six host genotypes varied in their average susceptibility to infection and in their parasite loads once infected. How host fecundity changed with increasing parasite loads did not vary between genotypes, indicating that there was no genetic variation for this measure of fecundity tolerance. However, genotypes differed in their level of fecundity compensation under infection, and we discuss how, by increasing host fitness without targeting parasite densities, fecundity compensation is consistent with the functional definition of tolerance. Such infection-induced life-history shifts are not traditionally considered to be part of the immune response, but may crucially reduce harm (in terms of fitness loss) caused by disease, and are a distinct source of selection on pathogens.},
	language = {eng},
	number = {9},
	journal = {Journal of Evolutionary Biology},
	author = {Vale, P. F. and Little, T. J.},
	month = sep,
	year = {2012},
	pages = {1888--1896},
}

Hosts are armed with several lines of defence in the battle against parasites: they may prevent the establishment of infection, reduce parasite growth once infected or persevere through mechanisms that reduce the damage caused by infection, called tolerance. Studies on tolerance in animals have focused on mortality, and sterility tolerance has not been investigated experimentally. Here, we tested for genetic variation in the multiple steps of defence when the invertebrate Daphnia magna is infected with the sterilizing bacterial pathogen Pasteuria ramosa: anti-infection resistance, anti-growth resistance and the ability to tolerate sterilization once infected. When exposed to nine doses of a genetically diverse pathogen inoculum, six host genotypes varied in their average susceptibility to infection and in their parasite loads once infected. How host fecundity changed with increasing parasite loads did not vary between genotypes, indicating that there was no genetic variation for this measure of fecundity tolerance. However, genotypes differed in their level of fecundity compensation under infection, and we discuss how, by increasing host fitness without targeting parasite densities, fecundity compensation is consistent with the functional definition of tolerance. Such infection-induced life-history shifts are not traditionally considered to be part of the immune response, but may crucially reduce harm (in terms of fitness loss) caused by disease, and are a distinct source of selection on pathogens.

@article{vale_distribution_2012,
	title = {The distribution of mutational fitness effects of phage φ{X174} on different hosts},
	volume = {66},
	copyright = {All rights reserved},
	issn = {1558-5646},
	doi = {10.1111/j.1558-5646.2012.01691.x},
	abstract = {Adaptation depends greatly on the distribution of mutation fitness effects (DMFE), but the phenotypic expression of mutations is often environment dependent. The environments faced by multihost pathogens are mostly governed by their hosts and therefore measuring the DMFE on multiple hosts can inform on the likelihood of short-term establishment and longer term adaptation of emerging pathogens. We explored this by measuring the growth rate of 36 mutants of the lytic bacteriophage φX174 on two host backgrounds, Escherichia coli (EcC) and Salmonella typhimurium (StGal). The DMFE showed higher mean and variance on EcC than on StGal. Most mutations were either deleterious or neutral on both hosts, but a greater proportion of mutations were deleterious on StGal. We identified two mutations with beneficial fitness effects on EcC that were neutral on StGal. Host-specific differences in fitness were associated with particular functional classes of genes involved in the initial stages of infection in accordance with previous studies of host specificity. Overall, there was a positive correlation between the effects of mutations on each host, suggesting that most new mutations will have general, rather than host-specific fitness effects. We consider these results in light of simple fitness landscape models of adaptation and discuss the relevance of context-dependent DMFE for multihost pathogens.},
	language = {eng},
	number = {11},
	journal = {Evolution; International Journal of Organic Evolution},
	author = {Vale, Pedro F. and Choisy, Marc and Froissart, Rémy and Sanjuán, Rafael and Gandon, Sylvain},
	month = nov,
	year = {2012},
	pages = {3495--3507},
}

Adaptation depends greatly on the distribution of mutation fitness effects (DMFE), but the phenotypic expression of mutations is often environment dependent. The environments faced by multihost pathogens are mostly governed by their hosts and therefore measuring the DMFE on multiple hosts can inform on the likelihood of short-term establishment and longer term adaptation of emerging pathogens. We explored this by measuring the growth rate of 36 mutants of the lytic bacteriophage φX174 on two host backgrounds, Escherichia coli (EcC) and Salmonella typhimurium (StGal). The DMFE showed higher mean and variance on EcC than on StGal. Most mutations were either deleterious or neutral on both hosts, but a greater proportion of mutations were deleterious on StGal. We identified two mutations with beneficial fitness effects on EcC that were neutral on StGal. Host-specific differences in fitness were associated with particular functional classes of genes involved in the initial stages of infection in accordance with previous studies of host specificity. Overall, there was a positive correlation between the effects of mutations on each host, suggesting that most new mutations will have general, rather than host-specific fitness effects. We consider these results in light of simple fitness landscape models of adaptation and discuss the relevance of context-dependent DMFE for multihost pathogens.

@article{vale_epidemiological_2011,
	title = {Epidemiological, evolutionary, and coevolutionary implications of context-dependent parasitism},
	volume = {177},
	copyright = {All rights reserved},
	issn = {1537-5323},
	url = {http://www.journals.uchicago.edu/doi/pdfplus/10.1086/659002},
	doi = {10.1086/659002},
	abstract = {Abstract Victims of infection are expected to suffer increasingly as parasite population growth increases. Yet, under some conditions, faster-growing parasites do not appear to cause more damage, and infections can be quite tolerable. We studied these conditions by assessing how the relationship between parasite population growth and host health is sensitive to environmental variation. In experimental infections of the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa, we show how easily an interaction can shift from a severe interaction, that is, when host fitness declines substantially with each unit of parasite growth, to a tolerable relationship by changing only simple environmental variables: temperature and food availability. We explored the evolutionary and epidemiological implications of such a shift by modeling pathogen evolution and disease spread under different levels of infection severity and found that environmental shifts that promote tolerance ultimately result in populations harboring more parasitized individuals. We also find that the opportunity for selection, as indicated by the variance around traits, varied considerably with the environmental treatment. Thus, our results suggest two mechanisms that could underlie coevolutionary hotspots and coldspots: spatial variation in tolerance and spatial variation in the opportunity for selection.},
	language = {eng},
	number = {4},
	journal = {The American Naturalist},
	author = {Vale, Pedro F. and Wilson, Alastair J. and Best, Alex and Boots, Mike and Little, Tom J.},
	month = apr,
	year = {2011},
	pages = {510--521},
}

Abstract Victims of infection are expected to suffer increasingly as parasite population growth increases. Yet, under some conditions, faster-growing parasites do not appear to cause more damage, and infections can be quite tolerable. We studied these conditions by assessing how the relationship between parasite population growth and host health is sensitive to environmental variation. In experimental infections of the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa, we show how easily an interaction can shift from a severe interaction, that is, when host fitness declines substantially with each unit of parasite growth, to a tolerable relationship by changing only simple environmental variables: temperature and food availability. We explored the evolutionary and epidemiological implications of such a shift by modeling pathogen evolution and disease spread under different levels of infection severity and found that environmental shifts that promote tolerance ultimately result in populations harboring more parasitized individuals. We also find that the opportunity for selection, as indicated by the variance around traits, varied considerably with the environmental treatment. Thus, our results suggest two mechanisms that could underlie coevolutionary hotspots and coldspots: spatial variation in tolerance and spatial variation in the opportunity for selection.

@article{vale_crispr-mediated_2010,
	title = {{CRISPR}-mediated phage resistance and the ghost of coevolution past},
	volume = {277},
	copyright = {All rights reserved},
	doi = {10.1098/rspb.2010.0055},
	number = {1691},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Vale, Pedro F and Little, Tom J},
	year = {2010},
	pages = {2097--2103},
}

@article{labbe_successfully_2010,
	title = {Successfully resisting a pathogen is rarely costly in {Daphnia} magna},
	volume = {10},
	copyright = {All rights reserved},
	issn = {1471-2148},
	url = {https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-10-355},
	doi = {10.1186/1471-2148-10-355},
	abstract = {BACKGROUND: A central hypothesis in the evolutionary ecology of parasitism is that trade-offs exist between resistance to parasites and other fitness components such as fecundity, growth, survival, and predator avoidance, or resistance to other parasites. These trade-offs are called costs of resistance. These costs fall into two broad categories: constitutive costs of resistance, which arise from a negative genetic covariance between immunity and other fitness-related traits, and inducible costs of resistance, which are the physiological costs incurred by hosts when mounting an immune response. We sought to study inducible costs in depth using the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa.
RESULTS: We designed specific experiments to study the costs induced by exposure to this parasite, and we re-analysed previously published data in an effort to determine the generality of such costs. However, despite the variety of genetic backgrounds of both hosts and parasites, and the different exposure protocols and environmental conditions used in these experiment, this work showed that costs of exposure can only rarely be detected in the D. magna-P. ramosa system.
CONCLUSIONS: We discuss possible reasons for this lack of detectable costs, including scenarios where costs of resistance to parasites might not play a major role in the co-evolution of hosts and parasites.},
	language = {eng},
	journal = {BMC evolutionary biology},
	author = {Labbé, Pierrick and Vale, Pedro F. and Little, Tom J.},
	month = nov,
	year = {2010},
	pages = {355},
}

BACKGROUND: A central hypothesis in the evolutionary ecology of parasitism is that trade-offs exist between resistance to parasites and other fitness components such as fecundity, growth, survival, and predator avoidance, or resistance to other parasites. These trade-offs are called costs of resistance. These costs fall into two broad categories: constitutive costs of resistance, which arise from a negative genetic covariance between immunity and other fitness-related traits, and inducible costs of resistance, which are the physiological costs incurred by hosts when mounting an immune response. We sought to study inducible costs in depth using the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa. RESULTS: We designed specific experiments to study the costs induced by exposure to this parasite, and we re-analysed previously published data in an effort to determine the generality of such costs. However, despite the variety of genetic backgrounds of both hosts and parasites, and the different exposure protocols and environmental conditions used in these experiment, this work showed that costs of exposure can only rarely be detected in the D. magna-P. ramosa system. CONCLUSIONS: We discuss possible reasons for this lack of detectable costs, including scenarios where costs of resistance to parasites might not play a major role in the co-evolution of hosts and parasites.

@article{vale_measuring_2009,
	title = {Measuring parasite fitness under genetic and thermal variation},
	volume = {103},
	copyright = {All rights reserved},
	doi = {10.1038/hdy.2009.54},
	number = {2},
	journal = {Heredity},
	author = {Vale, PF and Little, TJ},
	year = {2009},
	pages = {102--109},
}

@phdthesis{vale_infection_2009,
	address = {Edinburgh, UK},
	type = {{PhD}},
	title = {Infection outcomes under genetic and environmental variation in a host-parasite system: {Implications} for maintenance of polymorphism and the evolution of virulence},
	copyright = {All rights reserved},
	shorttitle = {Infection outcomes under genetic and environmental variation in a host-parasite system},
	url = {https://www.era.lib.ed.ac.uk/handle/1842/3189},
	abstract = {Virulence (the harm to the host during infection) is the outcome of continuous coevolution
between hosts and parasites. This thesis adds to a growing body of work on host-parasite
interactions, and describes experiments that study the effects of variation in the genetic and
the environmental contexts of infection. All of them focus on interaction between the
planktonic freshwater crustacean Daphnia magna and a naturally occurring parasite, the
spore-forming bacterium Pasteuria ramosa. I show that elevated minimum temperatures that
facilitate parasite growth drive natural epidemics of this parasite. I also demonstrate that the
expression of infection traits in P. ramosa is temperature-dependent in a genotype-specific
manner [genotype-by-environment (GxE) interactions]. These GxE interactions could
maintain polymorphism through environment-dependent selection. Next, I test if GxG
interactions for infectivity can be altered by environmental variation (GxGxE interactions),
and find that this trait is quite robust to thermal variation. Infectivity is also more important
in determining parasite fitness relative to the production of transmission stages, highlighting
the importance of considering natural infection routes, an aspect sometimes overlooked in
studies of host-parasite systems. Another experiment under different food and temperature
regimes showed evidence for environment-dependent virulence-transmission relationships, a
fundamental component of virulence evolution models. Lastly, I show that variation in
temperature does not increase the cost to the host of resisting infection.},
	language = {en},
	urldate = {2016-11-08},
	school = {University of Edinburgh},
	author = {Vale, Pedro F.},
	year = {2009},
}

Virulence (the harm to the host during infection) is the outcome of continuous coevolution between hosts and parasites. This thesis adds to a growing body of work on host-parasite interactions, and describes experiments that study the effects of variation in the genetic and the environmental contexts of infection. All of them focus on interaction between the planktonic freshwater crustacean Daphnia magna and a naturally occurring parasite, the spore-forming bacterium Pasteuria ramosa. I show that elevated minimum temperatures that facilitate parasite growth drive natural epidemics of this parasite. I also demonstrate that the expression of infection traits in P. ramosa is temperature-dependent in a genotype-specific manner [genotype-by-environment (GxE) interactions]. These GxE interactions could maintain polymorphism through environment-dependent selection. Next, I test if GxG interactions for infectivity can be altered by environmental variation (GxGxE interactions), and find that this trait is quite robust to thermal variation. Infectivity is also more important in determining parasite fitness relative to the production of transmission stages, highlighting the importance of considering natural infection routes, an aspect sometimes overlooked in studies of host-parasite systems. Another experiment under different food and temperature regimes showed evidence for environment-dependent virulence-transmission relationships, a fundamental component of virulence evolution models. Lastly, I show that variation in temperature does not increase the cost to the host of resisting infection.

@article{vale_temperature-dependent_2008,
	title = {Temperature-dependent costs of parasitism and maintenance of polymorphism under genotype-by-environment interactions},
	volume = {21},
	copyright = {All rights reserved},
	issn = {1420-9101},
	url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1420-9101.2008.01555.x},
	doi = {10.1111/j.1420-9101.2008.01555.x},
	abstract = {The maintenance of genetic variation for infection-related traits is often attributed to coevolution between hosts and parasites, but it can also be maintained by environmental variation if the relative fitness of different genotypes changes with environmental variation. To gain insight into how infection-related traits are sensitive to environmental variation, we exposed a single host genotype of the freshwater crustacean Daphnia magna to four parasite isolates (which we assume to represent different genotypes) of its naturally co-occurring parasite Pasteuria ramosa at 15, 20 and 25 degrees C. We found that the cost to the host of becoming infected varied with temperature, but the magnitude of this cost did not depend on the parasite isolate. Temperature influenced parasite fitness traits; we found parasite genotype-by-environment (G x E) interactions for parasite transmission stage production, suggesting the potential for temperature variation to maintain genetic variation in this trait. Finally, we tested for temperature-dependent relationships between host and parasite fitness traits that form a key component of models of virulence evolution, and we found them to be stable across temperatures.},
	language = {eng},
	number = {5},
	journal = {Journal of Evolutionary Biology},
	author = {Vale, P. F. and Stjernman, M. and Little, T. J.},
	month = sep,
	year = {2008},
	pages = {1418--1427},
}

The maintenance of genetic variation for infection-related traits is often attributed to coevolution between hosts and parasites, but it can also be maintained by environmental variation if the relative fitness of different genotypes changes with environmental variation. To gain insight into how infection-related traits are sensitive to environmental variation, we exposed a single host genotype of the freshwater crustacean Daphnia magna to four parasite isolates (which we assume to represent different genotypes) of its naturally co-occurring parasite Pasteuria ramosa at 15, 20 and 25 degrees C. We found that the cost to the host of becoming infected varied with temperature, but the magnitude of this cost did not depend on the parasite isolate. Temperature influenced parasite fitness traits; we found parasite genotype-by-environment (G x E) interactions for parasite transmission stage production, suggesting the potential for temperature variation to maintain genetic variation in this trait. Finally, we tested for temperature-dependent relationships between host and parasite fitness traits that form a key component of models of virulence evolution, and we found them to be stable across temperatures.

@article{vale_role_2008,
	title = {The role of the environment in the evolutionary ecology of host parasite interactions},
	volume = {8},
	copyright = {All rights reserved},
	issn = {1567-1348},
	shorttitle = {The role of the environment in the evolutionary ecology of host parasite interactions},
	doi = {10.1016/j.meegid.2008.01.011},
	language = {eng},
	number = {3},
	journal = {Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases},
	author = {Vale, Pedro F. and Salvaudon, Lucie and Kaltz, Oliver and Fellous, Simon},
	month = may,
	year = {2008},
	pages = {302--305},
}

@article{little_parasite_2007,
	title = {Parasite transgenerational effects on infection},
	volume = {9},
	copyright = {All rights reserved},
	issn = {1522-0613},
	url = {http://www.evolutionary-ecology.com/abstracts/v09/2135.html},
	language = {English},
	number = {3},
	urldate = {2019-10-18},
	journal = {Evolutionary Ecology Research},
	author = {Little, Tom and Birch, * Jane and Vale, Pedro and Tseng, Michelle},
	year = {2007},
	pages = {459--469},
}

@unpublished{vale_comportamento_2004,
	address = {Universidade de Évora},
	title = {Comportamento social em bactérias. {O} papel dos cheaters na evolução da resistência a antibióticos},
	copyright = {All rights reserved},
	url = {https://catalogo.bib.uevora.pt/cgi-bin/koha/opac-detail.pl?biblionumber=150442},
	abstract = {Licenciatura em Biologia apresentada à Universidade de Évora},
	language = {por},
	author = {Vale, Pedro F},
	year = {2004},
}

Licenciatura em Biologia apresentada à Universidade de Évora

@article{costa_transplantes_2003,
	title = {Transplantes e {Rejeição}},
	copyright = {All rights reserved},
	author = {Costa, Helena and Vale, Pedro and Águas, Ricardo},
	year = {2003},
}