Social and extra-pair mating in relation to major histocompatibility complex variation in common yellowthroats

Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history

The major histocompatibility complex (MHC) multigene family encodes key pathogen-recognition molecules of the vertebrate adaptive immune system. Hyper-polymorphism of MHC genes is de novo generated by point mutations, but new haplotypes may also arise by re-shuffling of existing variation through intra- and inter-locus gene conversion. Although the occurrence of gene conversion at the MHC has been known for decades, we still have limited understanding of its functional importance. Here, I took advantage of extensive genetic resources (~9000 sequences) to investigate broad scale macroevolutionary patterns in gene conversion processes at the MHC across nearly 200 avian species. Gene conversion was found to constitute a universal mechanism in birds, as 83% of species showed footprints of gene conversion at either MHC class and 25% of all allelic variants were attributed to gene conversion. Gene conversion processes were stronger at MHC-II than MHC-I, but inter-specific variation at both MHC classes was explained by similar evolutionary scenarios, reflecting fluctuating selection towards different optima and drift. Gene conversion showed uneven phylogenetic distribution across birds and was driven by gene copy number variation, supporting significant role of inter-locus gene conversion processes in the evolution of the avian MHC. Finally, MHC gene conversion was stronger in species with fast life histories (high fecundity) and in long-distance migrants, likely reflecting variation in population sizes and host-pathogen coevolutionary dynamics. The results provide a robust comparative framework for understanding macroevolutionary variation in gene conversion at the avian MHC and reinforce important contribution of this mechanism to functional MHC diversity.

Limited associations between MHC diversity and reproductive success in a bird species with biparental care

The selective pressure from pathogens on individuals can have direct consequences on reproduction. Genes from the major histocompatibility complex (MHC) are central to the vertebrate adaptive immune system and pathogen resistance. In species with biparental care, each sex has distinct reproductive roles and levels of investment, and due to a trade-off with immunity, one can expect different selective regimes acting upon the MHC of each parent. Here, we addressed whether couples combine each other's variation at MHC loci to increase their breeding success. Specifically, we used a 23-year dataset from a barn owl population (Tyto alba) to understand how MHC class Iα and IIβ functional divergence and supertypes of each parent were associated with clutch size and fledging success. We did not detect associations between MHC diversity and supertypes with the clutch size or with the fledging success. In addition, to understand the relative contribution from the MHC of the genetic parents and the social parents, we analyzed the fledging success using only a cross-fostered dataset. We found several associations of weak-to-moderate effect sizes between the father's MHC and fledging success: (i) lower MHC-Iα divergence in the genetic father increases fledging success, which might improve paternal care during incubation, and (ii) one and two MHC-IIβ DAB2 supertypes in the social father decrease and increase, respectively, fledging success, which may affect the paternal care after hatching. Furthermore, fledging success increased when both parents did not carry MHC-IIβ DAB1 supertype 2, which could suggest conditional effects of this supertype. Although our study relied on a substantial dataset, we showed that the associations between MHC diversity and reproductive success remain scarce and of complex interpretation in the barn owl. Moreover, our results highlighted the need to incorporate more than one proxy of reproductive success and several MHC classes to capture more complex associations.

House sparrows do not exhibit a preference for the scent of potential partners with different MHC-I diversity and genetic distances

MHC genes play a fundamental role in immune recognition of pathogens and parasites. Therefore, females may increase offspring heterozygosity and genetic diversity by selecting males with genetically compatible or heterozygous MHC. In birds, several studies suggest that MHC genes play a role in mate choice, and recent evidence suggests that olfaction may play a role in the MHC-II discrimination. However, whether olfaction is involved in MHC-I discrimination in birds remains unknown. Previous studies indicate that house sparrow females with low allelic diversity prefer males with higher diversity in MHC-I alleles. Here, we directly explored whether female and male house sparrows (Passer domesticus) could estimate by scent MHC-I diversity and/or dissimilarity of potential partners. Our results show that neither females nor males exhibit a preference related to MHC-I diversity or dissimilarity of potential partners, suggesting that MHC-I is not detected through olfaction. Further studies are needed to understand the mechanisms responsible for mate discrimination based on MHC-I in birds.

Using de novo genome assembly and high-throughput sequencing to characterize the MHC region in a non-model bird, the Eurasian coot

Genes of the Major Histocompatibility Complex (MHC) form a key component of vertebrate adaptive immunity, as they code for molecules which bind antigens of intra- and extracellular pathogens (MHC class I and II, respectively) and present them to T cell receptors. In general, MHC genes are hyper-polymorphic and high MHC diversity is often maintained within natural populations (via balancing selection) and within individuals (via gene duplications). Because of its complex architecture with tandems of duplicated genes, characterization of MHC region in non-model vertebrate species still poses a major challenge. Here, we combined de novo genome assembly and high-throughput sequencing to characterize MHC polymorphism in a rallid bird species, the Eurasian coot Fulica atra. An analysis of genome assembly indicated high duplication rate at MHC-I, which was also supported by targeted sequencing of peptide-binding exons (at least five MHC-I loci genotyped). We found high allelic richness at both MHC-I and MHC-II, although signature of diversifying selection and recombination (gene conversion) was much stronger at MHC-II. Our results indicate that Eurasian coot retains extraordinary polymorphism at both MHC classes (when compared to other non-passerine bird species), although they may be subject to different evolutionary mechanism.

Evolution of innate and adaptive immune genes in a non-model waterbird, the common tern

Toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) are the key pathogen-recognition genes of vertebrate immune system and they have a crucial role in the initiation of innate and adaptive immune response, respectively. Recent advancements in sequencing technology sparked research on highly duplicated MHC genes in non-model species, but TLR variation in natural vertebrate populations has remained little studied and comparisons of polymorphism across both TLRs and MHC are scarce. Here, we aimed to compare variation across innate (four TLR loci) and adaptive (MHC class I and class II) immune genes in a non-model avian species, the common tern Sterna hirundo. We detected relatively high allelic richness at TLR genes (9-48 alleles per locus), which was similar to or even higher than the estimated per locus allelic richness at the MHC (24-30 alleles at class I and 13-16 alleles at class II under uniform sample sizes). Despite this, the total number of MHC alleles across all duplicated loci (four class I and three class II) was much higher and MHC alleles showed greater sequence divergence than TLRs. Positive selection targeted relatively more sites at the MHC than TLRs, but the strength of selection (dN/dS ratios) at TLRs was higher when compared to MHC class I. There were also differences in the signature of positive selection and recombination (gene conversion) between MHC class I and II (stronger signature at class II), suggesting that mechanisms maintaining variation at the MHC may vary between both classes. Our study indicates that allelic richness of both innate and adaptive immune receptors may be maintained at relatively high levels in viable avian populations and we recommend a transition from the traditional gene-specific to multi-gene approach in studying molecular evolution of vertebrate immune system.

Avian major histocompatibility complex copy number variation is associated with helminth richness

Genes of the major histocompatibility complex (MHC) play a key role in the adaptive immunity of vertebrates, as they encode receptors responsible for antigen recognition. Evolutionary history of the MHC proceeded through numerous gene duplications, which increase the spectrum of pathogens recognized by individuals. Although pathogen-mediated selection is believed to be a primary driver of MHC expansion over evolutionary times, empirical evidence for this association is virtually lacking. Here, we used an extensive dataset on MHC class II copy number variation in non-passerine birds to test for an evolutionary correlation with helminth parasite richness. As expected, our phylogenetically-informed modelling revealed a positive association between MHC copy number and total helminth richness, even after controlling for a broad spectrum of ecological and life-history traits. Thus, total helminth richness appears to be the most important correlate of MHC copy number, supporting a leading role of pathogen-mediated selection in the evolution of MHC in birds. Our results provide some of the first, although correlative, evidence linking parasitism to interspecific variation in MHC copy number among birds.

Avian MHC Evolution in the Era of Genomics: Phase 1.0

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.

MHC class I diversity predicts non-random mating in Chinese alligators (Alligator sinensis)

The major histocompatibility complex (MHC) has several important roles in kin recognition, pathogen resistance and mate selection. Research in fish, birds and mammals has suggested that individuals optimise MHC diversity, and therefore offspring fitness, when choosing mates. In reptiles, however, it is unclear whether female mate choice is based on genome-wide genetic characteristics such as microsatellite DNA loci, particular functional-trait loci (e.g., MHC) or both, and MHC's effects on mate choice remain relatively understudied. Herein, we used 13 microsatellite loci and two MHC class I loci to investigate female mate choice of Chinese alligators (Alligator sinensis) in the semi-natural condition. We also determined correlations between the MHC genotype of breeding males and male reproductive success. We found that MHC-heterozygous males harbour a greater reproductive success, which probably is the reason that these males are more preferred by the females than MHC-homozygous males. Furthermore, the MHC class I amino-acid distance and functional distance of true mating pairs were higher compared with those of randomly sampled pairs. Analysis of microsatellites revealed that, despite mate choice, females did not completely avoid inbreeding. These findings are the first evidence of MHC-associated mate choice in Chinese alligators, suggesting that females may adopt different mating strategies after assessing the MHC characteristics of potential mates.

"Balancing" balancing selection? Assortative mating at the major histocompatibility complex despite molecular signatures of balancing selection

In vertebrate animals, genes of the major histocompatibility complex (MHC) determine the set of pathogens to which an individual's adaptive immune system can respond. MHC genes are extraordinarily polymorphic, often showing elevated nonsynonymous relative to synonymous sequence variation and sharing presumably ancient polymorphisms between lineages. These patterns likely reflect pathogen-mediated balancing selection, for example, rare-allele or heterozygote advantage. Such selection is often reinforced by disassortative mating at MHC. We characterized exon 2 of MHC class II, corresponding to the hypervariable peptide-binding region, in song sparrows (Melospiza melodia). We compared nonsynonymous to synonymous sequence variation in order to identify positively selected sites; assessed evidence for trans-species polymorphisms indicating ancient balancing selection; and compared MHC similarity of socially mated pairs to expectations under random mating. Six codons showed elevated ratios of nonsynonymous to synonymous variation, consistent with balancing selection, and we characterized several alleles similar to those occurring in at least four other avian families. Despite this evidence for historical balancing selection, mated pairs were significantly more similar at MHC than were randomly generated pairings. Nonrandom mating at MHC thus appears to partially counteract, not reinforce, pathogen-mediated balancing selection in this system. We suggest that in systems where individual fitness does not increase monotonically with MHC diversity, assortative mating may help to avoid excessive offspring heterozygosity that could otherwise arise from long-standing balancing selection.

Allelic diversity and selection at the MHC class I and class II in a bottlenecked bird of prey, the White-tailed Eagle

Background

Genes of the Major Histocompatibility Complex (MHC) are essential for adaptive immune response in vertebrates, as they encode receptors that recognize peptides derived from the processing of intracellular (MHC class I) and extracellular (MHC class II) pathogens. High MHC diversity in natural populations is primarily generated and maintained by pathogen-mediated diversifying and balancing selection. It is, however, debated whether selection at the MHC can counterbalance the effects of drift in bottlenecked populations. The aim of this study was to assess allelic diversity of MHC genes in a recently bottlenecked bird of prey, the White-tailed Eagle Haliaeetus albicilla, as well as to compare mechanisms that shaped the evolution of MHC class I and class II in this species.

Results

We showed that significant levels of MHC diversity were retained in the core Central European (Polish) population of White-tailed Eagles. Ten MHC class I and 17 MHC class II alleles were recovered in total and individual birds showed high average MHC diversity (3.80 and 6.48 MHC class I and class II alleles per individual, respectively). Distribution of alleles within individuals provided evidence for the presence of at least three class I and five class II loci the White-tailed Eagle, which suggests recent duplication events. MHC class II showed greater sequence polymorphism than MHC class I and there was much stronger signature of diversifying selection acting on MHC class II than class I. Phylogenetic analysis provided evidence for trans-species similarity of class II, but not class I, sequences, which is likely consistent with stronger balancing selection at MHC class II.

Conclusions

Relatively high MHC diversity retained in the White-tailed Eagles from northern Poland reinforces high conservation value of local eagle populations. At the same time, our study is the first to demonstrate contrasting patterns of allelic diversity and selection at MHC class I and class II in an accipitrid species, supporting the hypothesis that different mechanisms can shape evolutionary trajectories of MHC class I and class II genes.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1338-3) contains supplementary material, which is available to authorized users.

Evolution of Copy Number at the MHC Varies across the Avian Tree of Life

The evolution of the major histocompatibility complex (MHC) is shaped by frequent gene duplications and deletions, which generate extensive variation in the number of loci (gene copies) between different taxa. Here, we collected estimates of copy number at the MHC for over 250 bird species from 68 families. We found contrasting patterns of copy number evolution between MHC class I and class IIB, which encode receptors for intra- and extracellular pathogens, respectively. Across the avian evolutionary tree, there was evidence of accelerated evolution and stabilizing selection acting on copy number at class I, while copy number at class IIB was primarily influenced by fluctuating selection and drift. Reconstruction of MHC copy number variation showed ancestrally low numbers of MHC loci in nonpasserines and evolution toward larger numbers of loci in passerines. Different passerine lineages had the highest duplication rates for MHC class I (Sylvioidea) and class IIB (Muscicapoidea and Passeroidea). We also found support for the correlated evolution of MHC copy number and life-history traits such as lifespan and migratory behavior. These results suggest that MHC copy number evolution in birds has been driven by life histories and differences in exposure to intra- and extracellular pathogens.

A global analysis of selection at the avian MHC

Recent advancements in sequencing technology have resulted in rapid progress in the study of the major histocompatibility complex (MHC) in non-model avian species. Here, we analyze a global dataset of avian MHC class I and class II sequences (ca. 11,000 sequences from over 250 species) to gain insight into the processes that govern macroevolution of MHC genes in birds. Analysis of substitution rates revealed striking differences in the patterns of diversifying selection between passerine and non-passerine birds. Non-passerines showed stronger selection at MHC class II, which is primarily involved in recognition of extracellular pathogens, while passerines showed stronger selection at MHC class I, which is involved in recognition of intracellular pathogens. Positions of positively selected amino-acid residues showed marked discrepancies with peptide-binding residues (PBRs) of human MHC molecules, suggesting that using a human classification of PBRs to assess selection patterns at the avian MHC may be unjustified. Finally, our analysis provided evidence that indel mutations can make a substantial contribution to adaptive variation at the avian MHC.

Genotyping strategy matters when analyzing hypervariable major histocompatibility complex-Experience from a passerine bird

Genotyping of classical major histocompatibility complex (MHC) genes is challenging when they are hypervariable and occur in multiple copies. In this study, we used several different approaches to genotype the moderately variable MHC class I exon 3 (MHCIe3) and the highly polymorphic MHC class II exon 2 (MHCIIβe2) in the bluethroat (Luscinia svecica). Two family groups (eight individuals) were sequenced in replicates at both markers using Ion Torrent technology with both a single- and a dual-indexed primer structure. Additionally, MHCIIβe2 was sequenced on Illumina MiSeq. Allele calling was conducted by modifications of the pipeline developed by Sommer et al. (BMC Genomics, 14, 2013, 542) and the software AmpliSAS. While the different genotyping strategies gave largely consistent results for MHCIe3, with a maximum of eight alleles per individual, MHCIIβe2 was remarkably complex with a maximum of 56 MHCIIβe2 alleles called for one individual. Each genotyping strategy detected on average 50%-82% of all MHCIIβe2 alleles per individual, but dropouts were largely allele-specific and consistent within families for each strategy. The discrepancies among approaches indicate PCR biases caused by the platform-specific primer tails. Further, AmpliSAS called fewer alleles than the modified Sommer pipeline. Our results demonstrate that allelic dropout is a significant problem when genotyping the hypervariable MHCIIβe2. As these genotyping errors are largely nonrandom and method-specific, we caution against comparing genotypes across different genotyping strategies. Nevertheless, we conclude that high-throughput approaches provide a major advance in the challenging task of genotyping hypervariable MHC loci, even though they may not reveal the complete allelic repertoire.

Age-specific patterns of infection with haemosporidians and trypanosomes in a warbler: implications for sexual selection

Although the selective loss of individuals susceptible to disease can favor the evolution of female preference for older males, the interrelationship between age, infection, longevity, and mating success remains poorly characterized in natural populations. In a longitudinal study of 61 male common yellowthroats (Geothlypis trichas), we found that the probability of infection with hematozoa increased as males aged from 1 to 5 years. Despite a significant, negative association between infection and longevity that partially masked age-effects, the odds that a male was infected with Trypanosoma, Plasmodium, or Leucocytozoon increased 71-212% per year. Nearly 75% of males in their first breeding season were either uninfected or infected with only a single parasite, while 50% of older males were infected with at least two parasites and 16% were infected with all three. No males escaped infection after their second breeding season. Older males were also more likely to sire extra-pair young (EPY) and, as a consequence, infection with multiple parasites was associated with a fourfold increase in the odds of producing EPY. Unlike younger males, 80% of the oldest males had a history of either surviving chronic infection or recovering. Combined with previous work showing higher diversity at the major histocompatibility complex among older males, our results suggest that the song and plumage traits that signal male age in common yellowthroats also, perforce, signal resistance to parasites. By preferring older males, females may obtain good genes for disease resistance even in the absence of any effect of infection on male ornamentation.

Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions

Background

Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population.

Results

The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence.

Conclusions

Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0997-9) contains supplementary material, which is available to authorized users.

Mate choice for neutral and MHC genetic characteristics in Alpine marmots: different targets in different contexts?

Sexual selection through female mate choice for genetic characteristics has been suggested to be an important evolutionary force maintaining genetic variation in animal populations. However, the genetic targets of female mate choice are not clearly identified and whether female mate choice is based on neutral genetic characteristics or on particular functional loci remains an open question. Here, we investigated the genetic targets of female mate choice in Alpine marmots (Marmota marmota), a socially monogamous mammal where extra‐pair paternity (EPP) occurs. We used 16 microsatellites to describe neutral genetic characteristics and two MHC loci belonging to MHC class I and II as functional genetic characteristics. Our results reveal that (1) neutral and MHC genetic characteristics convey different information in this species, (2) social pairs show a higher MHC class II dissimilarity than expected under random mate choice, and (3) the occurrence of EPP increases when social pairs present a high neutral genetic similarity or dissimilarity but also when they present low MHC class II dissimilarity. Thus, female mate choice is based on both neutral and MHC genetic characteristics, and the genetic characteristics targeted seem to be context dependent (i.e., the genes involved in social mate choice and genetic mate choice differ). We emphasize the need for empirical studies of mate choice in the wild using both neutral and MHC genetic characteristics because whether neutral and functional genetic characteristics convey similar information is not universal.

Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

Characterization of major histocompatibility complex class I loci of the lark sparrow (Chondestes grammacus) and insights into avian MHC evolution

The major histocompatibilty complex (MHC) has become increasingly important in the study of the immunocapabilities of non-model vertebrates due to its direct involvement in the immune response. The characterization of MHC class I loci in the lark sparrow (Chondestes grammacus) revealed multiple MHC class I loci with elevated genetic diversity at exon 3, evidence of differential selection between the peptide binding region (PBR) and non-PBR, and the presence of multiple pseudogenes with limited divergence. The minimum number of functional MHC class I loci was estimated at four. Sequence analysis revealed d N /d S ratios significantly less than one at non-PBR sites, indicative of negative selection, whereas PBR sites associated with antigen recognition showed ratios greater than 1 but non-significant. GenBank surveys and phylogenetic analyses of previously reported avian MHC class I sequences revealed variable signatures of evolutionary processes acting upon this gene family, including gene duplication and potential concerted evolution. An increase in the number of class I loci across species coincided with an increase in pseudogene prevalence, revealing the importance of gene duplication in the expansion of multigene families and the creation of pseudogenes.

Multiple paternity does not depend on male genetic diversity

Polyandry is common in many species and it has been suggested that females engage in multiple mating to increase the genetic diversity of their offspring (genetic diversity hypothesis). Multiple paternity occurs in 30% of litters in wild populations of house mice, Mus musculus musculus, and multiple-sired litters are genetically more diverse than single-sired ones. Here, we aimed to test whether female house mice produce multiple-sired litters when they have the opportunity to produce genetically diverse litters. We assessed the rates of multiple paternity when females could choose to mate with two males that were genetically dissimilar to each other (i.e. nonsiblings and MHC dissimilar) compared with when females could choose to mate with two males that were genetically similar to each other (i.e. siblings and shared MHC alleles). Multiple mating may depend upon a female's own condition, and, therefore, we also tested whether inbred (from full-sibling matings) females were more likely to produce multiple-sired progeny than outbred controls. Overall we found that 29% of litters had multiple sires, but we found no evidence that females were more likely to produce multiple-sired litters when they had the opportunity to mate with genetically dissimilar males compared with controls, regardless of whether females were inbred or outbred. Thus, our findings do not support the idea that female mice increase multiple paternity when they have the opportunity to increase the genetic diversity of their offspring, as expected from the genetic diversity hypothesis.

Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae)

The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next-generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (β chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide-binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high-frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non-passerine bird.

Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful tool for the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds.