Diversifying selection is the dominant factor affecting the geographical variation of <scp>MHC</scp> class <scp>II</scp> genes in the Omei tree frog

Li, J.; Shen, Hang; Wang, H.; Zhao, Mo; Luo, Zhenhua; Wu, Hua

doi:10.1111/jzo.12373

Cited by 8 publications

(10 citation statements)

References 39 publications

(83 reference statements)

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“…We probably characterized most of the current MHC class II variability detectable using internal exon primers in B. pachypus , as we sampled a large portion of the species range. The allelic diversity is similar to that of Bufo calamita (38 DAB alleles in 325 individuals in a biogeographical scale study; Zeisset & Beebee, ), but it is considerably lower than in several non‐European anurans, such as Rana omeimontis (130 alleles from 215 individuals in at least three loci; Li et al ., ) and Leiopelma hochstetteri (74 alleles isolated from 121 individuals in a single locus; Lillie et al ., ). Sequence polymorphism is similar to that of B. calamita (Zeisset & Beebee, ) and Rana temporaria (Zeisset & Beebee, ).…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, a similar pattern was detected across Triturus cristatus (Babik et al ., ) and B. calamita ranges (Zeisset & Beebee, ): a loss of both MHC and microsatellites diversity, ascribed to the effects of genetic drift, was observed in the PGE areas. Conversely, in other amphibians, such as R. omeimontis (Li et al ., ) and L. hochstetteri (Lillie et al ., ), diversifying selection is the main force determining MHC variation and leading to high interpopulation differentiation.…”

Section: Discussionmentioning

confidence: 99%

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Genetic drift shaped MHC IIB diversity of an endangered anuran species within the Italian glacial refugium

et al. 2018

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Highly polymorphic genes of the major histocompatibility complex (MHC) encode proteins involved in the immune response that protect vertebrates from parasites and pathogen infections. MHC variation is shaped by a complex and poorly understood interplay of selective and demographic forces. Studies of MHC variation provide biologically meaningful insights useful for conservation of threatened taxa such as amphibians, which are globally declining partly due to the impact of emerging infectious diseases (e.g. chytridiomycosis). Here, we characterized MHC class IIB variation in the Apennine yellow-bellied toad (Bombina pachypus), an endangered anuran, across its whole distribution range within the Italian peninsula. We compared MHC IIB diversity between refugial (REF) and post-glacial expansion (PGE) areas and tested for the correlation between MHC and neutral variation to quantify the role of drift in shaping MHC diversity. Overall MHC polymorphism was limited compared to other amphibian species. Despite the clear evidence of historical positive selection acting on antigen-binding sites, we found a significant correlation between the diversity of MHC and that of putatively neutral microsatellite markers, which suggests that genetic drift has contributed extensively to shaping MHC variation. MHC diversity was higher in the REF populations and decreased northwards into the PGE area, in accordance with the 'southern richness and northern purity' pattern. Past demographic events likely determined the reduction of MHC variation in the PGE area; in particular, the northern populations appeared to survive for a long time with a depleted MHC variation. We discussed recent population declines of B. pachypus in light of our findings. Recent studies based on experiments in semi-natural settings provided evidence that novel alleles are strongly favored (

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genetic drift shaped MHC IIB diversity of an endangered anuran species within the Italian glacial refugium

et al. 2018

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“…Additionally, diversifying selection on broad scales may increase MHC divergence in the form of spatio‐temporally fluctuating selection (Hill, 1991; Spurgin & Richardson, 2010). If there is limited gene flow between populations, this MHC variation may lead to local adaptation of populations to different pathogens (Ekblom et al, 2007; Herdegen et al, 2014; Li et al, 2016; Loiseau et al, 2009; Miller et al, 2010). These vastly different mechanisms produce different characteristics in different parts of the genome.…”

Section: Introductionmentioning

confidence: 99%

Genetic polymorphisms and the independent evolution of major histocompatibility complex class II‐DRBin sibling bat speciesRhinolophus episcopusandRhinolophus siamensis

Liu

et al. 2021

J. Zool. Syst. Evol. Res.

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The relative roles of different microevolutionary forces, like natural selection and demographic processes, in affecting genetic variation are of great scientific interest. In this study, we investigated recent divergence of the sibling bat species Rhinolophus episcopus and R. siamensis, which share a partially sympatric distribution and have different phenotypic characteristics among populations. We combined neutral [microsatellite (SSR)] and adaptive [major histocompatibility complex (MHC) class II‐DRB locus] markers to investigate the evolution of adaptive markers and disentangle the relative effects of neutral and adaptive microevolutionary forces on this MHC gene region. Our results revealed a stronger level of genetic differentiation in SSRs than in MHC genes of both species, which indicates effects of balancing selection on the geographical variation of MHC genes. However, we detected significant correlations in genetic differentiation between MHC and SSRs in R. episcopus, indicating that demographic processes have influenced the level of MHC genetic diversity in this species. In addition, significant moderate genetic differentiation was detected in sympatric populations and no alleles were shared between the two species. Therefore, we speculate that these sibling species have been subject to independent adaptive evolutionary processes.

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“…Such patterns of diversifying selection have been described for MHC class II genes in amphibians (e.g. [ 73 ]), as well as at effector proteins that interact with target host plant defense proteins in the stem rust fungus, Puccinia graminis [ 74 ]. However, despite high allelic divergence and diversity at NLR genes in plants, there is limited evidence for this translating into increased divergence among natural populations [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection

et al. 2018

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BackgroundGenome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome.ResultsWe found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima’s D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested.ConclusionsGenome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4806-7) contains supplementary material, which is available to authorized users.

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Diversifying selection is the dominant factor affecting the geographical variation of MHC class II genes in the Omei tree frog

Cited by 8 publications

References 39 publications

Genetic drift shaped MHC IIB diversity of an endangered anuran species within the Italian glacial refugium

Genetic drift shaped MHC IIB diversity of an endangered anuran species within the Italian glacial refugium

Genetic polymorphisms and the independent evolution of major histocompatibility complex class II‐DRBin sibling bat speciesRhinolophus episcopusandRhinolophus siamensis

Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection

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