PreprintArticleVersion 1Preserved in Portico This version is not peer-reviewed
Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China
Version 1
: Received: 19 July 2023 / Approved: 20 July 2023 / Online: 21 July 2023 (09:13:12 CEST)
How to cite:
Dong, P.; Wang, R.; Abduriyim, S. Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China. Preprints2023, 2023071471. https://doi.org/10.20944/preprints202307.1471.v1
Dong, P.; Wang, R.; Abduriyim, S. Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China. Preprints 2023, 2023071471. https://doi.org/10.20944/preprints202307.1471.v1
Dong, P.; Wang, R.; Abduriyim, S. Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China. Preprints2023, 2023071471. https://doi.org/10.20944/preprints202307.1471.v1
APA Style
Dong, P., Wang, R., & Abduriyim, S. (2023). Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China. Preprints. https://doi.org/10.20944/preprints202307.1471.v1
Chicago/Turabian Style
Dong, P., Rui-Rui Wang and Shamshidin Abduriyim. 2023 "Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China" Preprints. https://doi.org/10.20944/preprints202307.1471.v1
Abstract
The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 came after found in only seven individuals, 14 PFAs occurred once (7 PFAs twice), implying high frequency of rare PFAs. Interestingly, more than half of the (15) PFAs were specific to clade I, only one and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sextual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The way of allele sharing and FST values between three clades were to some extent in agreement with pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed cross-species polymorphisms. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.
Keywords
Mountain ungulate; MHC DRB gene; genetic diversity; population fluctuation
Subject
Biology and Life Sciences, Animal Science, Veterinary Science and Zoology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
