DOI: 10.5061/dryad.7kd74
title: Data from: Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers

description: The role of Pleistocene glacial cycles in forming the contemporary genetic
 structure of organisms has been well studied in China with a particular
 focus on the Tibetan Plateau. However, China has a complex topography and
 diversity of local climates, and how glacial cycles may have shaped the
 subtropical and tropical biota of the region remains mostly unaddressed.
 To investigate the factors that affected the phylogeography and population
 history of a widely distributed and nondeciduous forest species, we
 analysed morphological characters, mitochondrial DNA sequences and nuclear
 microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a
 pattern generally consistent with phenotypic clusters, but not nominal
 subspecies, deeply divergent mitochondrial lineages restricted to
 different geographic regions were detected. Coalescent simulations
 indicated that the time of main divergence events corresponded to major
 glacial periods in the Pleistocene and gene flow was only partially
 lowered by drainage barriers between some populations. Intraspecific
 cytonuclear discordance was revealed in mitochondrial lineages from Hainan
 Island and the Sichuan Basin with evidence of nuclear gene flow from
 neighbouring populations into the latter. Unexpectedly, hybridization was
 revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant
 (Lophura leucomelanos) with wide genetic introgression at both the mtDNA
 and nuclear levels. Our results highlight a novel phylogeographic pattern
 in a subtropical area generated from the combined effects of climate
 oscillation, partial drainage barriers and interspecific hybridization.
 Cytonuclear discordance combined with morphological differentiation
 implies that complex historical factors shaped the divergence process in
 this biodiversity hot spot area of southern China.
description: Morphological data of
 Silver pheasantSpecimen information for
 morphological analysis. Museum code: BNU: Beijing Normal University;
 GFIPI: Guangxi Forest Inventory and Planning Institute; GXAS: Guangxi
 Academic of Sciences; GXNU: Guangxi Normal University; GZM: Guizhou
 Museum; HNU: Hunan Normal University; KIZ: Kunming Institute of Zoology,
 CAS; MNHN: Muséum national d’Histoire Naturelle, Paris, France; NHM:
 Natural History Museum, London, UK; IOZ: Institute of Zoology, CAS; SCU:
 Sichuan University. WL: Wing chord length, TL: tail length, BL: bill
 length, TaL: tarsus length. Number of black stripes on feathers of the
 hind neck (Nhn), mantle (Nm), rump (Nr), and lesser coverts (Nc). The
 ratio of PWL (pure white length on tail) /TL was calculated as the pure
 white tail length proportion (WP)Morphological
 data.docSampling
 locationsSamples collected are
 listed as subspecies, sampling localities, geographic coordinates, sample
 type, and total sample size with corresponding Map references and
 population labels. 1 Numbers corresponding to localities shown in Fig. 1.
 2 Two types of sample were collected in the present study: b: blood; f:
 feather.Microsatellites
 genotypesMicrosatellites
 genotypes of 180 individuals (170 samples of silver pheasants and 10 kalij
 pheasants) for 11 STR loci. Pop code corresponding to "population
 label" in table "Smapling Locations".Genbank Accession
 Numbers of cyt b and CR for SIlver pheasant and Kalij pheasant in
 ChinaGenbank
 Accession Number.xlsx