Incomplete lineage sorting or secondary admixture: Disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)

Yanhua Qu, Ruiying Zhang, Qing Quan, Gang Song, Shou-Hsien Li, Fumin Lei

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Although Pleistocene glaciations had a major impact on the population genetic patterns of many species in North America and Europe, it remains unclear how these climatic fluctuations contributed to species diversification in East Asia. One reason for this is the difficulty of distinguishing genetic admixture following secondary contact from incomplete lineage sorting, both of which can generate similar patterns of genetic variation. Using a combination of multilocus analyses and coalescent simulation, we explore how these two processes occurred in the Pleistocene evolutionary history of a widespread East Asian bird, the Vinous-throated parrotbill, Paradoxornis webbianus. Maximum likelihood (ML) tree identified two major mitochondrial lineages, which are geographically separated in most parts of its range, but are sympatric at a few sampling sites. NJ tree and Structure analysis of microsatellite data set revealed an extensive level of admixture and little population structure, suggesting recent admixture between two formerly separated groups. Networks from nuclear DNA data sets, however, did not indicate any geographically isolated groups but rather a panmictic population, thus support incomplete lineage sorting. By using coalescent simulation approaches, we show that both processes did occur, although at different temporal scales. During the Pleistocene glaciations, probably around 0.1-0.5 Ma (the Marine Isotope Stage 6, MIS6), P. webbianus contracted into two separate refugia, and subsequently accumulated genetic divergence. During the interglacial MIS5, the species expanded into previously glaciated areas allowing the once separated groups to come into contact and become admixed. Taken together, our results indicate the current genetic variation within P. webbianus is a combination pattern of widespread distribution in pre-Pleistocene, then contraction and fragmentation into separated refugia during glacial advance, followed by recently postglacial expansion and admixture.

Original languageEnglish
Pages (from-to)6117-6133
Number of pages17
JournalMolecular Ecology
Volume21
Issue number24
DOIs
Publication statusPublished - 2012 Dec 1

Fingerprint

Gene Flow
Wine
sorting
gene flow
wines
divergence
Pleistocene
glaciation
refuge habitats
genetic variation
Far East
Population Genetics
refugium
North America
Isotopes
Microsatellite Repeats
Population
Birds
secondary contact
East Asia

Keywords

  • East Asia
  • Pleistocene glaciations
  • coalescent simulations
  • ecological niche model
  • multilocus analyses

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Incomplete lineage sorting or secondary admixture : Disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus). / Qu, Yanhua; Zhang, Ruiying; Quan, Qing; Song, Gang; Li, Shou-Hsien; Lei, Fumin.

In: Molecular Ecology, Vol. 21, No. 24, 01.12.2012, p. 6117-6133.

Research output: Contribution to journalArticle

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