DOI: 10.5061/dryad.h8b93
title: Data from: Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles

description: Background: Rhesus macaques living in western Sichuan, China, have been
 separated into several isolated populations due to habitat fragmentation.
 Previous studies based on the neutral or nearly neutral markers
 (mitochondrial DNA or microsatellites) showed high levels of genetic
 diversity and moderate genetic differentiation in the Sichuan rhesus
 macaques. Variation at the major histocompatibility complex (MHC) loci is
 widely accepted as being maintained by balancing selection, even with a
 low level of neutral variability in some species. However, in small and
 isolated or bottlenecked populations, balancing selection may be
 overwhelmed by genetic drift. To estimate microevolutionary forces acting
 on the isolated rhesus macaque populations, we examined genetic variation
 at MHC-DQB1 loci in 119 wild rhesus macaques from five geographically
 isolated populations in western Sichuan, China, and compared the levels of
 MHC variation and differentiation among populations with that previously
 observed at neutral microsatellite markers. Results: 23 Mamu-DQB1 alleles
 were identified in 119 rhesus macaques in western Sichuan, China. These
 macaques exhibited relatively high levels of genetic diversity at
 Mamu-DQB1. The Hanyuan population presented the highest genetic variation,
 whereas the Heishui population was the lowest. Analysis of molecular
 variance (AMOVA) and pairwise FST values showed moderate genetic
 differentiation occurring among the five populations at the MHC-DQB1
 locus. Non-synonymous substitutions occurred at a higher frequency than
 synonymous substitutions in the peptide binding region. Levels of MHC
 variation within rhesus macaque populations are concordant with
 microsatellite variation. On the phylogenetic tree for the rhesus and
 crab-eating macaques, extensive allele or allelic lineage sharing is
 observed between the two species. Conclusions: Phylogenetic analyses
 confirm the apparent trans-species model of evolution of the MHC-DQB1
 genes in these macaques. Balancing selection plays an important role in
 sharing allelic lineages between species, but genetic drift may share
 balancing selection dominance to maintain MHC diversity. Great divergence
 at neutral or adaptive markers showed that moderate genetic
 differentiation had occurred in rhesus macaque populations in western
 Sichuan, China, due to the habitat fragmentation caused by long-term
 geographic barriers and human activity. The Heishui population should be
 paid more attention for its lowest level of genetic diversity and
 relatively great divergence from others.
description: Phylogenetic tree of the
 MhcMamu- and MhcMafa-DQB1 alleles using Neighbour-joing
 methodsFigure 3 Phylogenetic
 tree of the MhcMamu- and MhcMafa-DQB1 alleles using Neighbour-joing
 methods 23 Mamu-DQB1 sequences detected in this study are shown with a
 solid round spot. 46 Mamu-DQB1 alleles not detected in animals of this
 study are showed with a circle. 85 Mafa-DQB1 sequences are showed without
 anything. 2 Aona-DQB1 (Aona-DQB1*220101 and Aona-DQB1*220102) were
 selected as outgroup. Except for 23 Mamu-DQB1 sequences detected in this
 study, all other DQB1 sequences were retrieved from the IPD-MHC Database
 (http://www.ebi.ac.uk/ipd/mhc/). Numbers at the node are bootstrap value
 in statistic analysis, only values above 50% are showed. software: Mega
 5.05Figure
 3.jpgNJTree
 dataThe phylogenetic tree in
 Figure 3 was constructed for the 156 Mhc-DQB1 gene sequences, including 69
 Mamu-DQB1, 85 Mafa-DQB1 and 2 Aona-DQB1 alleles by using the
 neighbor-joining method, and aona-DQB1 alleles were used as the out-group.
 The 156 sequences can be searched in the IPD-MHC Database
 (http://www.ebi.ac.uk/ipd/mhc/).