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Boyd RJ, Denommé MR, Grieves LA, MacDougall-Shackleton EA. Stronger population differentiation at infection-sensing than infection-clearing innate immune loci in songbirds: Different selective regimes for different defenses. Evolution 2021; 75:2736-2746. [PMID: 34596241 DOI: 10.1111/evo.14368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Parasite-mediated selection is widespread at loci involved in immune defense, but different defenses may experience different selective regimes. For defenses involved in clearing infections, purifying selection favoring a single most efficacious allele likely predominates. However, for defenses involved in sensing and recognizing infections, evolutionary arms races may make positive selection particularly important. This could manifest primarily within populations (e.g., balancing selection maintaining variation) or among them (e.g., spatially varying selection enhancing population differences in allele frequencies). We genotyped three toll-like receptors (TLR; involved in sensing infections) and three avian beta-defensins (involved in clearing infections) in 96 song sparrows (Melospiza melodia) from three breeding populations that differ in disease resistance. Variation-based indicators of selection (proportion of variable sites, proportion of nonsynonymous SNPs, proportion of sites bearing signatures of positive or purifying selection, rare allele frequencies) did not differ appreciably between the two locus types. However, differentiation was generally higher at infection-sensing than infection-clearing loci. Allele frequencies differed markedly at TLR3, driven by a variant predicted to alter protein function. Geographically structured variants at infection-sensing loci may reflect local adaptation to spatially heterogeneous parasite communities. Selective regimes experienced by infection-sensing versus infection-clearing loci may differ primarily due to parasite-mediated population differentiation.
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Affiliation(s)
- Rachel J Boyd
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Melanie R Denommé
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Biological Sciences, Brock University Faculty of Mathematics & Science, St. Catherines, Ontario, L2S 3A1, Canada
| | - Leanne A Grieves
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ontario, L8S 4M4, Canada
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Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. Sci Rep 2019; 9:15849. [PMID: 31676844 PMCID: PMC6825141 DOI: 10.1038/s41598-019-52312-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird and advance our understanding of fundamental questions in evolutionary and organismal biology.
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Affiliation(s)
- Alexandra B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA. .,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Kimberly A Rosvall
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
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Garant D, Bourret A, Schmitt C, Turcotte A, Pelletier F, Bélisle M. Effects of blood parasite infection and innate immune genetic diversity on mating patterns in a passerine bird breeding in contrasted habitats. PeerJ 2018; 6:e6004. [PMID: 30505637 PMCID: PMC6254242 DOI: 10.7717/peerj.6004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/26/2018] [Indexed: 11/20/2022] Open
Abstract
Genetic diversity at immune genes and levels of parasitism are known to affect patterns of (dis)assortative mating in several species. Heterozygote advantage and/or good genes should shape mate choice originating from pathogen/parasite-driven selection at immune genes. However, the stability of these associations, and whether they vary with environmental conditions, are still rarely documented. In this study, we describe mating patterns in a wild population of tree swallows (Tachycineta bicolor) over 4 years and assess the effects of haemosporidian parasite infection and immune genetic diversity at β-defensin genes on those patterns within two habitats of contrasting environmental quality, in southern Québec, Canada. We first show that mating patterns were only very weakly related to individual status of infection by haemosporidian parasites. However, we found a difference between habitats in mating patterns related to infection status, which was likely due to a non-random distribution of individuals, as non-infected mating pairs were more frequent in lower quality habitats. Mating patterns also differed depending on β-defensin heterozygosity at AvBD2, but only for genetic partners outside of the social couple, with heterozygous individuals pairing together. Our study underlines the importance of considering habitat heterogeneity in studies of sexual selection.
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Affiliation(s)
- Dany Garant
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Audrey Bourret
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Clarence Schmitt
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Sorbonne Universités, UPMC Univ Paris 06, UPEC, Paris 7, CNRS, INRA, IRD, Paris, France
| | - Audrey Turcotte
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Fanie Pelletier
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marc Bélisle
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
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