DOI: 10.5061/dryad.7ck13
title: Data from: Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus)

description: Levels of adaptive genetic variation influence how species deal with
 environmental and ecological change, but these levels are frequently
 inferred using neutral genetic markers. Major histocompatibility complex
 (MHC) genes play a key role in the adaptive branch of the immune system
 and have been used extensively to estimate levels of adaptive genetic
 variation. Parts of the peptide binding region, sites where MHC molecules
 directly interact with pathogen and self-proteins, were sequenced from a
 MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in
 threatened and non-threatened populations of gopher tortoises (Gopherus
 polyphemus), and adaptive genetic variation at MHC genes was compared to
 neutral genetic variation derived from 10 microsatellite loci (441
 tortoises). Genetic diversity at the MHC class II locus and
 microsatellites was greater in populations in the non-threatened portion
 of the gopher tortoise’s range (MHC class II difference in mean A = 8.11,
 AR = 0.79, HO = 0.51, and HE = 0.16; microsatellite difference in mean A =
 1.05 and AR = 0.47). Only MHC class II sequences showed evidence of
 positive selection (dN/dS &gt; 1, Z = 1.81, P = 0.04). Historical gene
 flow as estimated with Migrate-N was greater than recent migration
 estimated with BayesAss, suggesting that populations were better connected
 in the past when habitat was less fragmented. MHC genetic differentiation
 was correlated with microsatellite differentiation (Mantel r = 0.431, P =
 0.001) suggesting neutral genetic processes are influencing MHC evolution,
 and advantageous MHC alleles could be lost due to genetic drift.
description: GopoMhcIex3S-nexusGopher tortoise MHC class I exon 3 sequences in nexus format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.GopoMhcIIBex2S-nexusGopher tortoise MHC class II B exon 2 sequences in nexus format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.GopoMhcIex3S-arlequinGopher tortoise MHC class I exon 3 alleles in Arlequin format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.GopoMhcIIBex2S-arlequinGopher tortoise MHC class II B exon 2 alleles in Arlequin format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.microsats_GopoMhcIex3S-popsGopher tortoise alleles for 10 microsatellite loci in Arlequin format, detailing which individuals are in which populations those populations being the same as for the MHC class I exon 3 alleles for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.microsats_GopoMhcIIBex2S-popsGopher tortoise alleles for 10 microsatellite loci in Arlequin format, detailing which individuals are in which populations those populations being the same as for the MHC class II B exon 2 alleles for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.