Figure - available from: Conservation Genetics
This content is subject to copyright. Terms and conditions apply.
Phylogenetic tree for all AvBD loci across avian lineages. The evolutionary history was inferred using the Neighbour-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the number of differences method and are in the units of the number of base differences per sequence. All positions containing gaps and missing data were eliminated. Only bootstrap values above 50 % are presented. There were a total of 35 positions in the final dataset
Source publication
β-defensins are important components of the vertebrate innate immune system responsible for encoding a variety of anti-microbial peptides. Pathogen-mediated selection is thought to act on immune genes and potentially maintain allelic variation in the face of genetic drift. The Seychelles warbler, Acrocephalus sechellensis, is an endemic passerine t...
Citations
... In most MSAs available in the literature, monodomain AvBDs are aligned with the N-terminal domain of AvBD11 when full-length AvBD11 (with both domains) is used. Our findings are in agreement with most published phylogenetic studies on AvBDs, showing that AvBD11 is primarily related to either AvBD9 [42][43][44][45][46][47], AvBD10 [6,48], or AvBD13/AvBD14/AvBD9 [49], while some publications rather reveal relationships with AvBD5 [50], AvBD8 [51], or AvBD5/AvBD4/AvBD8/AvBD10/AvBD1/AvBD2 [52]. The type of sequences (nucleotide, protein) and the methods used to build up the alignments and trees may explain, in part, the discrepancies of these data. ...
Beta-defensins are an essential group of cysteine-rich host-defence peptides involved in vertebrate innate immunity and are generally monodomain. Among bird defensins, the avian β-defensin 11 (AvBD11) is unique because of its peculiar structure composed of two β-defensin domains. The reasons for the appearance of such ‘polydefensins’ during the evolution of several, but not all branches of vertebrates, still remain an open question. In this study, we aimed at exploring the origin and evolution of the bird AvBD11 using a phylogenetic approach. Although they are homologous, the N- and C-terminal domains of AvBD11 share low protein sequence similarity and possess different cysteine spacing patterns. Interestingly, strong variations in charge properties can be observed on the C-terminal domain depending on bird species but, despite this feature, no positive selection was detected on the AvBD11 gene (neither on site nor on branches). The comparison of AvBD11 protein sequences in different bird species, however, suggests that some amino acid residues may have undergone convergent evolution. The phylogenetic tree of avian defensins revealed that each domain of AvBD11 is distant from ovodefensins (OvoDs) and may have arisen from different ancestral defensins. Strikingly, our phylogenetic analysis demonstrated that each domain of AvBD11 has common ancestors with different putative monodomain β-defensins from crocodiles and turtles and are even more closely related with these reptilian defensins than with their avian paralogs. Our findings support that AvBD11′s domains, which differ in their cysteine spacing and charge distribution, do not result from a recent internal duplication but most likely originate from a fusion of two different ancestral genes or from an ancestral double-defensin arisen before the Testudines-Archosauria split.
... Little information is available about levels of variation at AvBD loci within songbird populations. However, we observed comparable nucleotide and haplotype diversities at locus AvBD7 to those reported for nonbottlenecked populations of Acrocephalus warblers in mainland Europe (Gilroy et al. 2016). By contrast, locus AvBD12 appears invariant in song sparrows, despite nonsynonymous variation at this locus within other songbird species (Hellgren and Sheldon 2011). ...
Parasite-mediated selection is widespread at loci involved in immune defence, but different defences may experience different selective regimes. For defences involved in clearing infections, purifying selection favouring a single most efficacious allele likely predominates. However, for defences 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.
This article is protected by copyright. All rights reserved
... Likewise, backwards extrapolation suggests that both TLR3 alleles were at roughly equal frequency in the mid-1970s. It has been possible to use museum samples from 26 warblers to examine pre-bottleneck diversity of microsatellite markers, MHC class I alleles (Spurgin et al., 2014), and avian β-defensin genes (Gilroy, van Oosterhout, Komdeur, & Richardson, 2016). In the future, we hope to gain more DNA and sequence these samples to determine what TLR3 variation existed prior to the bottleneck. ...
Understanding where and how genetic variation is maintained within populations is important from an evolutionary and conservation perspective. Signatures of past selection suggest that pathogen-mediated balancing selection is a key driver of immunogenetic variation, but studies tracking contemporary evolution are needed to help resolve the evolutionary forces and mechanism at play. Previous work in a bottlenecked population of Seychelles warblers (Acrocephalus sechellensis) show that functional variation has been maintained at the viral-sensing Toll-like receptor 3 (TLR3) gene. Here, we characterise evolution at this TLR3 locus over a 25-year period within the original remnant population of the Seychelles warbler, and in four other derived, contained populations. Results show a significant and consistent temporal decline in the frequency of the TLR3C allele in the original population, and that similar declines in the TLR3C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3CC genotype had lower survival, and males - but not females - that carry the TLR3C allele had significantly lower lifetime reproductive success than those with only the TLR3A allele. These results indicate that positive selection, caused by an as yet unknown agent, is driving TLR3 evolution in the Seychelles warblers. No evidence of heterozygote advantage was detected. However, whether the positive selection observed is part of a longer-term pattern of balancing selection (through fluctuating selection or rare-allele advantage) cannot be resolved without tracking the TLR3C allele in the populations over an extended period of time.
... I focused on the PBR of class I and class II loci as candidate regions for local adaptation and locally-protective alleles, because protein-sequence variation at these loci determines the repertoire of antigen peptides that can be bound and presented to T-cells. I do not exclude the possibility that locally-protective alleles could be operating at other loci related to immunity (e.g., innate defenses such as β-defensins; Gilroy et al. 2016 Miller and Lambert 2004) and thus the potential for local adaptation at these loci. However, the high levels of variation I observed at both class I and class II, together with both sites' apparently large population sizes and lack of physical isolation make this latter explanation unlikely. ...
In recent years, sexual selection theory has redefined genetic quality to consider not only additive genetic effects on fitness but also non-additive genetic effects, such as heterozygote advantage or disadvantage. In jawed vertebrates, the major histocompatibility complex (MHC) gene family has been shown to exhibit both additive and non-additive genetic effects on fitness. MHC gene products are involved in initiating adaptive immune responses, and MHC genotype determines the range of pathogens to which an individual can respond. Therefore, parasite-mediated selection at MHC may favour locally-adapted, rare, or particular combination of alleles. Because heterozygote advantage at MHC is widespread, sexual selection should favour mechanisms by which individuals assess the MHC genotypes of potential mates, and mate non-randomly. Studies exploring the role of MHC in immunity and sexual selection are widespread amongst mammals and fish, but in birds (especially songbirds) there is relatively scant evidence for MHC-mediated mating and the mechanism by which this might be accomplished remains unknown. First, I assessed differentiation at MHC class I and II that might underlie locally-good gene effects in two populations of song sparrows (Melospiza melodia) previously shown to exhibit higher resistance to sympatric malaria (Plasmodium) strains. I found no population differentiation, suggesting no locally-good gene effects at MHC, but individuals with higher class I diversity were less likely to be infected when experimentally inoculated with Plasmodium. Second, I explored whether song sparrows convey information on MHC class II genotype through chemical (preen oil) or auditory (birdsong) cues. Pairwise similarity at MHC was related to pairwise similarity of preen oil chemical composition, but not to pairwise similarity in song repertoire content. Song repertoire size, a sexually selected trait in this species, was nonlinearly related to MHC diversity, such that males with intermediate MHC diversity sang the most songs. Finally, to investigate MHC-mediated mate choice, I compared MHC similarity of socially mated pairs of free-living song sparrows to random expectations. Contrary to my prediction of MHC-disassortative mating, social pairs were more similar at MHC than expected by chance. This work emphasizes the importance of considering mate choice in the context of fitness effects at MHC.
... Considering the genetic background of the Seychelles warbler, there is considerably more variation within the TLR gene group than was observed in another innate immune gene group of arguably equal importance, avian beta-defensins (AvBDs). Our previous study showed high levels of conservation and monomorphism across AvBD loci (Table S1; Gilroy et al., 2016b), which emphasizes the significance of our findings particularly at TLR15. As the most polymorphic TLR locus in the Seychelles warbler, TLR15 is predicted to maintain a considerable amount of heterozygosity with a relatively small selection coefficient (S = 0.03). ...
Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations.
... We focused on the PBR of class I and class II loci as candidate regions for local adaptation and locally protective alleles, because protein-sequence variation at these loci determines the repertoire of antigen peptides that can be bound and presented to T cells. We do not exclude the possibility that locally protective alleles could be operating at other loci related to immunity (e.g., innate defenses such as β-defensins; Gilroy et al. 2016), or at portions of MHC not sequenced in our study. Locally protective allele effects at MHC have been described mainly in inhabitants of relatively small-scale environments (e.g., river-dwelling Atlantic salmon Salmo salar, Dionne et al. 2009; Chinook salmon Oncorhynchus tshawytscha, Neff 2009, Evans et al. 2010; yellow-necked mouse Apodemus flavicollis, Meyer-Lucht and Sommer 2005), and could be less pronounced in highly mobile animals such as migratory birds that encounter multiple environments, and multiple parasite fauna, each year. ...
Infectious disease represents an emerging threat to natural populations, particularly when hosts are more susceptible to novel parasites (allopatric) than to parasites from the local area (sympatric). This pattern could arise through evolutionary processes (host populations become adapted to their local parasites and genetically differentiated from other populations at immune-related loci) and/or through ecological interactions (host individuals develop resistance to local parasites through previous exposure). The relative importance of these candidate mechanisms remains unclear. In jawed vertebrates, genes of the major histocompatibility complex (MHC) play a fundamental role in immunity and are compelling candidates for spatially varying selection. We recently showed that song sparrows (Melospiza melodia) are more susceptible to allopatric than to sympatric strains of malaria (Plasmodium). In the current study, to determine whether population differences at MHC explain this pattern, we characterized the peptide-binding regions of MHC (classes I and II) of birds that did or did not become infected in the previous experiment. We recovered up to four alleles per individual at class I, implying at least two loci, and up to 26 alleles per individual at class II, implying at least 13 loci. Individuals with more class I alleles were less likely to become infected by Plasmodium, consistent with parasite-mediated balancing selection. However, we found no evidence for population genetic differentiation at either class of MHC, based on 36 individuals sequenced. Resistance to sympatric parasites previously described for this system likely stems from individuals' prior immune experience, not from population differentiation and locally-protective alleles at MHC.
... While research on adaptive evolution and speciation theory has historically focused on the MHC, there are many other multigene families in the immune genome of birds that show high levels of polymorphism and strong signatures of positive selection, perhaps most notably the avian β-defensins (AvBDs) and Toll-like receptor (TLRs) [55,56]. Further analyses of these immune gene families and comparisons with the MHC are warranted to examine whether the unique expansion of the MHC has indeed been instrumental in the evolutionary success of passerines. ...
A key characteristic of MHC genes is the persistence of allelic lineages over macroevolutionary periods, often through multiple speciation events. This phenomenon, known as trans-species polymorphism (TSP), is well documented in several major taxonomic groups, but has less frequently been observed in birds. The order Passeriformes is arguably the most successful terrestrial vertebrate order in terms of diversity of species and ecological range, but the reasons for this success remain unclear. Passerines exhibit the most highly duplicated MHC genes of any major vertebrate taxonomic group, which may generate increased immune response relative to other avian orders with fewer MHC loci. Here, we describe phylogenetic patterns of the MHC IIB in the passerine family Corvidae. Our results indicate wide-spread TSP within this family, with at least four supported MHC IIB allelic lineages that predate speciation by many millions of years. Markov chain Monte Carlo simulations indicate that divergence of these lineages occurred near the time of the divergence of the Passeriformes and other avian orders. We suggest that the current MHC diversity observed in passerines is due in part to the multiple duplication of a single MHC locus, DAB1, early in passerine evolution and that subsequent duplications of these paralogues have contributed to the enormous success of this order by increasing their ability to recognize and mount immune responses to novel pathogens.
Understanding where genetic variation exists, and how it influences fitness within populations is important from an evolutionary and conservation perspective. Signatures of past selection suggest that pathogen‐mediated balancing selection is a key driver of immunogenetic variation, but studies tracking contemporary evolution are needed to help resolve the evolutionary forces and mechanism at play. Previous work in a bottlenecked population of Seychelles warblers (Acrocephalus sechellensis) show that functional variation has been maintained at the viral‐sensing Toll‐like receptor 3 (TLR3) gene, including one nonsynonymous SNP, resulting in two alleles. Here, we characterise evolution at this TLR3 locus over a 25‐year period within the original remnant population of the Seychelles warbler, and in four other derived, populations. Results show a significant and consistent temporal decline in the frequency of the TLR3C allele in the original population, and that similar declines in the TLR3C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3CC genotype had lower survival, and males ‐ but not females ‐ that carry the TLR3C allele had significantly lower lifetime reproductive success than those with only the TLR3A allele. These results indicate that positive selection on the TLR3A allele, caused by an as yet unknown agent, is driving TLR3 evolution in the Seychelles warbler. No evidence of heterozygote advantage was detected. However, whether the positive selection observed is part of a longer‐term pattern of balancing selection (through fluctuating selection or rare‐allele advantage) cannot be resolved without tracking the TLR3C allele over an extended time period.
Unravelling the genetic basis of phenotypic variation among individuals is an important step in our understanding of evolution. Recent studies of innate immune genes, such as β -defensins, revealed that these genes had high levels of polymorphism. However, researchers have yet to quantify the effects of such variability on immune responses and fitness-related traits in wild populations. In this study, we assessed how the variability at six avian β -defensin (AvBD) genes was linked to an immune function and reproductive success in adult tree swallows (Tachycineta bicolor). We investigated the links between genetic variations using single nucleotide polymorphisms at AvBD genes, immune function as the bacterial killing ability (BKA) and fledging success. We assessed how female immunogenetics were linked to the presence of eggshell bacteria in their clutches and hatching success. We found weak associations between the presence of AvBD genes, BKA and eggshell bacteria. Our results suggested that homozygosity at some loci may be advantageous for defence against bacteria. Variability at β -defensin genes was not related to either hatching or fledging success. BKA of parents was positively linked with fledging success. More studies are needed to assess whether or not β -defensin genes are significantly affecting fitness-related traits in wild populations.
