University of Oulu

Zhou, Y; Duvaux, L; Ren, G; Zhang, L; Savolainen, O; Liu, J. Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity (2017) 118, 211–220; doi:10.1038/hdy.2016.72

Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions

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Author: Zhou, Yongfeng1,2,3; Duvaux, L4; Ren, G1;
Organizations: 1State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
2Plant Genetics Group, Department of Biology, University of Oulu, Oulu, Finland
3Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
4Animal and Plant Sciences, University of Sheffield, Sheffield, UK
5Biocenter Oulu, University of Oulu, Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.2 MB)
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Language: English
Published: Springer Nature, 2017
Publish Date: 2017-04-25


Genetic variation shared between closely related species may be due to retention of ancestral polymorphisms because of incomplete lineage sorting (ILS) and/or introgression following secondary contact. It is challenging to distinguish ILS and introgression because they generate similar patterns of shared genetic diversity, but this is nonetheless essential for inferring accurately the history of species with overlapping distributions. To address this issue, we sequenced 33 independent intron loci across the genome of two closely related pine species (Pinus massoniana Lamb. and Pinus hwangshanensis Hisa) from Southeast China. Population structure analyses revealed that the species showed slightly more admixture in parapatric populations than in allopatric populations. Levels of interspecific differentiation were lower in parapatry than in allopatry. Approximate Bayesian computation suggested that the most likely speciation scenario explaining this pattern was a long period of isolation followed by a secondary contact. Ecological niche modeling suggested that a gradual range expansion of P. hwangshanensis during the Pleistocene climatic oscillations could have been the cause of the overlap. Our study therefore suggests that secondary introgression, rather than ILS, explains most of the shared nuclear genomic variation between these two species and demonstrates the complementarity of population genetics and ecological niche modeling in understanding gene flow history. Finally, we discuss the importance of contrasting results from markers with different dynamics of migration, namely nuclear, chloroplast and mitochondrial DNA.

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Series: Heredity
ISSN: 0018-067X
ISSN-E: 1365-2540
ISSN-L: 0018-067X
Volume: 118
Issue: 3
Pages: 211 - 220
DOI: 10.1038/hdy.2016.72
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
Funding: This research was supported by grants from the National Key Project for Basic Research (2014CB954100 and 2012CB114504), the National Natural Science Foundation of China (30725004) and the ‘111’ collaboration Program. Data analyses were partly conducted on computer clusters in the Finnish IT Center for Science (CSC) and on the Iceberg cluster at the University of Sheffield. YZ was supported by the International Postdoctoral Exchange Fellowship Program 2015 by the Office of China Postdoctoral Council, the funding from the Center for International Mobility (CIMO, Finland) and Biocenter Oulu (to OS). LD was supported by the Natural Environment Research Council (Grant Number NE/J021660/1) and the Leverhulme trust (Grant Number RPG-2013-198).
Dataset Reference: The sequences of each locus reported in this study were deposited in GenBank under accession numbers: KJ921127–KJ921496.
Copyright information: © The Author(s) 2017. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission fromthe license holder to reproduce thematerial. To view a copy of this license, visit nd/4.0/