title: Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions.
abstract: 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.
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, People's Republic of China.|Plant Genetics Group, Department of Biology, University of Oulu, Oulu, Finland.|Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
authors.forename: L
authors.identifier: 0000-0003-0960-0312
authors.initials: L
authors.lastname: Duvaux
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
authors.forename: G
authors.initials: G
authors.lastname: Ren
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
authors.forename: L
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Plant Genetics Group, Department of Biology, University of Oulu, Oulu, Finland.|Biocenter Oulu, University of Oulu, Oulu, Finland.
authors.forename: O
authors.identifier: 0000-0001-9851-7945
authors.initials: O
authors.lastname: Savolainen
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
authors.forename: J
authors.initials: J
authors.lastname: Liu
mesh_terms: D001499:Bayes Theorem; D002681:China; D018744:DNA, Plant / Q000235:genetics; D051456:Gene Flow; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D007438:Introns; D008957:Models, Genetic; D028223:Pinus / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant