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

Partial molecular characterization, expression pattern and polymorphism analysis of MHC I genes in Chinese domestic goose (Anser cygnoides)

Major histocompatibility complex (MHC) allelic polymorphism is critically important for mediating antigen presentation in vertebrates. Presently, there are insufficient studies of MHC genetic diversity in domestic Anseriform birds. In this study, we analyzed the expression profile of MHC I genes and screened for MHC I exon 2 polymorphism in one domestic goose population from China using Illumina MiSeq sequencing. The results showed that four MHC I alleles (Ancy-IE2*09/*11/*13/*21) in one goose were identified based on cDNA cloning and sequencing using four primer combinations, and the varying number of cDNA clones implied that these four classical sequences showed differential expression patterns. Through next-generation sequencing, 27 alleles were obtained from 68 geese with 3-10 putative alleles per individual, indicating at least the existence of 5 MHC I loci in the goose. The marked excess of the non-synonymous over the synonymous substitution in the peptide-binding region (PBR) along 27 alleles and five positively selected sites (PSSs) detected around the PBR indicated that balancing selection might be the major force in shaping high MHC variation in the goose. Additionally, IA alleles displaying lower polymorphism were subject to less positive selection pressure than non-IA alleles with a higher level of polymorphism.

Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes)

The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation.

Molecular Characterization of MHC Class I Genes in Four Species of the Turdidae Family to Assess Genetic Diversity and Selection

In vertebrate animals, the molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immunity. MHC class I deals with intracellular pathogens (virus) in birds. MHC class I diversity depends on the consequence of local and global environment selective pressure and gene flow. Here, we evaluated the MHC class I gene in four species of the Turdidae family from a broad geographical area of northeast China. We isolated 77 MHC class I sequences, including 47 putatively functional sequences and 30 pseudosequences from 80 individuals. Using the method based on analysis of cloned amplicons (n = 25) for each species, we found two and seven MHC I sequences per individual indicating more than one MHC I locus identified in all sampled species. Results revealed an overall elevated genetic diversity at MHC class I, evidence of different selection patterns among the domains of PBR and non-PBR. Alleles are found to be divergent with overall polymorphic sites per species ranging between 58 and 70 (out of 291 sites). Moreover, transspecies alleles were evident due to convergent evolution or recent speciation for the genus. Phylogenetic relationships among MHC I show an intermingling of alleles clustering among the Turdidae family rather than between other passerines. Pronounced MHC I gene diversity is essential for the existence of species. Our study signifies a valuable tool for the characterization of evolutionary relevant difference across a population of birds with high conservational concerns.

Evolution of major histocompatibility complex gene copy number

MHC genes, which code for proteins responsible for presenting pathogen-derived antigens to the host immune system, show remarkable copy-number variation both between and within species. However, the evolutionary forces driving this variation are poorly understood. Here, we use computer simulations to investigate whether evolution of the number of MHC variants in the genome can be shaped by the number of pathogen species the host population encounters (pathogen richness). Our model assumed that while increasing a range of pathogens recognised, expressing additional MHC variants also incurs costs such as an increased risk of autoimmunity. We found that pathogen richness selected for high MHC copy number only when the costs were low. Furthermore, the shape of the association was modified by the rate of pathogen evolution, with faster pathogen mutation rates selecting for increased host MHC copy number, but only when pathogen richness was low to moderate. Thus, taking into account factors other than pathogen richness may help explain wide variation between vertebrate species in the number of MHC genes. Within population, variation in the number of unique MHC variants carried by individuals (INV) was observed under most parameter combinations, except at low pathogen richness. This variance gave rise to positive correlations between INV and host immunocompetence (proportion of pathogens recognised). However, within-population variation in host immunocompetence declined with pathogen richness. Thus, counterintuitively, pathogens can contribute more to genetic variance for host fitness in species exposed to fewer pathogen species, with consequences to predictions from “Hamilton-Zuk” theory of sexual selection.

Highly polymorphic genes of the Major Histocompatibility Complex (MHC) code for proteins responsible for presenting antigens to lymphocytes, thus initiating adaptive immune response. The polymorphism is driven by coevolution with parasites which are selected to evade recognition by MHC proteins. Expressing many MHC molecules could ensure that an individual could present antigens of most pathogen species encountered, but this comes at a cost, such as enhanced negative selection on lymphocytes leading to holes in T-cell receptor repertoire. Our simulations showed that evolution of the number of MHC genes in the genome is driven by a complex interaction between three factors we explored: pathogen richness, the intrinsic cost of expressing additional MHC variants, and pathogen mutation rate. In contrast to verbal arguments, our results indicate that pathogen richness does not always selects for MHC gene family expansion. Taking into account factors other than pathogen richness, in particular costs of expressing additional MHC variants which are still poorly understood, may help explain striking interspecific variation in the number of MHC genes. Counterintuitively, our results also demonstrated that opportunity for selection on immunocompetence should decrease with MHC gene family expansion.

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 High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species

Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawaiʻi, the ʻAlalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the ʻAlalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications.

100 million years of multigene family evolution: origin and evolution of the avian MHC class IIB

BACKGROUND

Gene duplication has led to a most remarkable adaptation involved in vertebrates' host-pathogen arms-race, the major histocompatibility complex (MHC). However, MHC duplication history is as yet poorly understood in non-mammalian vertebrates, including birds.

RESULTS

Here, we provide evidence for the evolution of two ancient avian MHC class IIB (MHCIIB) lineages by a duplication event prior to the radiation of all extant birds >100 million years ago, and document the role of concerted evolution in eroding the footprints of the avian MHCIIB duplication history.

CONCLUSIONS

Our results suggest that eroded footprints of gene duplication histories may mimic birth-death evolution and that in the avian MHC the presence of the two lineages may have been masked by elevated rates of concerted evolution in several taxa. Through the presence of a range of intermediate evolutionary stages along the homogenizing process of concerted evolution, the avian MHCIIB provides a remarkable illustration of the erosion of multigene family duplication history.