Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers

Abstract

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.

Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq

“…Such studies are helpful in detecting more significant differences to study their phylogeny and biogeography though they tend to focus on a low number of genetic markers 1–3 . However, when species have relatively narrow distributions, the detection of population differences is more difficult through classical methods, owing to insufficient data.…”

Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range

“…) and the Silver Pheasant Lophura nycthemera (Dong et al . ). Although the genetic structure of the central and northern populations might be diminished by accelerated rate of dispersal and human‐mediated admixture, two geographical and genetic groups were identified, as featured in splitstree (Fig.…”

Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig‐pollinating wasp mutualism

“…Genetic differentiation between Hainan populations and adjacent populations in continental China has been reported for several other flying organisms such as the silver pheasant Lophura nycthemera (Dong et al . ), the horseshoe bat Rhinolophus sinicus (Mao et al . ) and the bee Apis cerana (Zhao et al .…”