Avian β-defensin variation in bottlenecked populations: the Seychelles warbler and other congeners

The Two Domains of the Avian Double-β-Defensin AvBD11 Have Different Ancestors, Common with Potential Monodomain Crocodile and Turtle Defensins

Simple Summary

Vertebrate defensins are a multigene family of antimicrobial peptides that evolved following a series of gene duplication and divergence events during the expansion of vertebrates. In birds, the repertoire of avian defensins contains an atypical defensin, namely AvBD11 (avian beta-defensin 11), which consists of two repeated but divergent defensin units (or domains) while most vertebrate defensins only possess one unit. In this study, we investigated the evolutionary scenario leading to the formation of this double defensin in birds by comparing each defensin unit of AvBD11 with other defensins from birds and closely related reptiles (crocodile, turtles) predicted to have a single defensin unit. Our most outstanding results suggest that the double defensin AvBD11 probably appeared following a fusion of two ancestral genes or from an ancestral double defensin, but not from a recent internal duplication as it can be observed in other types of proteins with domain repeats.

Abstract

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.

Stronger population differentiation at infection-sensing than infection-clearing innate immune loci in songbirds: Different selective regimes for different defenses

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.

Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population

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 TLR3^C allele in the original population, and that similar declines in the TLR3^C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3^CC genotype had lower survival, and males - but not females - that carry the TLR3^C allele had significantly lower lifetime reproductive success than those with only the TLR3^A allele. These results indicate that positive selection on the TLR3^A 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 TLR3^C allele over an extended time period.

Population Differences at MHC Do Not Explain Enhanced Resistance of Song Sparrows to Local Parasites

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 4 alleles per individual at class I, implying at least 2 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.

Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'

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.

Patterns of Diversity and Spatial Variability of β-Defensin Innate Immune Genes in a Declining Wild Population of Tree Swallows

Assessing the genetic variation and distribution of immune genes across heterogeneous environmental conditions in wild species is essential to further our understanding of the role of pathogen pressure and potential resistance or prevalence in hosts. Researchers have recently investigated β-defensin genes in the wild, because their variability suggests that they may play an important role in innate host defense. This study investigated the variation occurring at 6 innate immune genes of the β-defensin family in a declining population of tree swallows (Tachycineta bicolor) in southern Québec, Canada (N = 160). We found that all 6 genes showed synonymous and nonsynonymous single nucleotide polymorphisms (SNPs) within the exon coding for the mature peptide. These results indicated that this group of genes was diverse in tree swallows. Our results suggested a potential interaction of this group of genes with fluctuating pathogen diversity, however, we found no sign of positive or negative selection. We assessed whether or not the distribution of genetic diversity of β-defensin genes in our study population differed between 2 regions that strongly differ in their level of agricultural intensification. Adults are highly philopatric to their breeding sites and their immunological responses differ between these 2 regions. However, we found little evidence that the level and distribution of genetic variability differed between these heterogeneous environmental conditions. Further studies should aim to assess the link between genetic diversity of β-defensin genes and fitness-related traits in wild populations.

Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations

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.