Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii

Zou, Jiabin; Sun, Yongshuai; Li, Long; Wang, Gaini; Yue, Wei; Lu, Zhiqiang; Wang, Qian; Liu, Jianquan

doi:10.1093/aob/mct241

Cited by 36 publications

(38 citation statements)

References 76 publications

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“…Fresh, mature leaf needles were collected from first‐year branches of 34, 40 and 40 individuals of P. wilsonii , P. purpurea and P. likiangensis, respectively, sampled allopatrically from spatially separated forest stands across the core distributions of each species (Figure ; Table ). Because of incomplete reproductive isolation in areas of overlap, hybridization occurs between P. purpurea and P. likiangensis (Du et al., ), and between P. wilsonii and other spruce species (Zou et al., ). However, our sampling excluded all forest stands where two or more spruce species co‐occurred and where there might be a legacy, therefore, of recent hybridization and introgression.…”

Section: Methodsmentioning

confidence: 99%

“…An alternative scenario is that P. purpurea diverged from P. wilsonii through bifurcation divergence and subsequently was subjected to a high level of nuclear gene flow (introgression) from P. likiangensis , while retaining the organelle genomes of P. wilsonii . Introgression occurs commonly between many conifer species (e.g., Bodare, Stocks, Yang, & Lascoux, ; Du et al., ; Li, Abbott et al., ; Li et al., ; Petit & Excoffier, ; Ru et al., ; Suarez‐Gonzalez, Hefer, Lexer, Douglas, & Cronk, ; Suarez‐Gonzalez et al., ; Sun et al., ; Zou et al., ) , lending support to this hypothesis. Coalescent ancestry analysis and modelling of whole‐genome sequence diversity can help distinguish between the alternative scenarios of hybrid speciation and introgressive admixture after bifurcating divergence (Nice et al., ).…”

Section: Introductionmentioning

confidence: 96%

“…A population genetic analysis utilizing 11 nuclear loci (Li et al., ; Sun et al., ) later indicated that P. purpurea originated through diploid hybridization between P. wilsonii and P. likiangensis with approximately 70% of its nuclear genome coming from P. likiangensis and the remainder from P. wilsonii . Surprisingly, however, both its mtDNA (maternally inherited via seed) and cpDNA (paternally inherited through pollen) were shown to be derived from P. wilsonii (Sun et al., ; Lookwood et al., ), though in areas of sympatry P. purpurea shares some mt‐ and cpDNA haplotypes with P. likiangensis (Du et al., ; Zou et al., ). These findings indicated that P. purpurea is a diploid hybrid species of P. wilsonii and P. likiangensis , but that backcrossing of an initial hybrid lineage to P. wilsonii may have occurred resulting in P. purpurea containing both the cpDNA and mtDNA of P. wilsonii .…”

Section: Introductionmentioning

confidence: 99%

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Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

Sun

Wang

et al. 2018

Molecular Ecology

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An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai–Tibet Plateau (QTP), originated through HHS from P. likiangensis and P. wilsonii. To investigate this origin in more detail, we analysed transcriptome data for 114 individuals collected from 34 populations of the three Picea species from their core distributions in the QTP. Phylogenetic, principal component and admixture analyses of nuclear SNPs showed the species to be delimited genetically and that P. purpurea was admixed with approximately 60% of its ancestry derived from P. wilsonii and 40% from P. likiangensis. Coalescent simulations revealed the best‐fitting model of origin involved formation of an intermediate hybrid lineage between P. likiangensis and P. wilsonii approximately 6 million years ago (mya), which backcrossed to P. wilsonii to form P. purpurea approximately one mya. The intermediate hybrid lineage no longer exists and is referred to as a “ghost” lineage. Our study emphasizes the power of population genomic analysis combined with coalescent analysis for reconstructing the stages involved in the origin of a homoploid hybrid species over an extended period. In contrast to other studies, we show that these stages can in some instances span a relatively long period of evolutionary time.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

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Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

Sun

Wang

et al. 2018

Molecular Ecology

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“…Another major difference between R. kunmingensis and R. tibetica is the relative timing of leafing and flowering, being flowering first in the former and leafing first in the latter. (Zou et al, 2013). Finally, phylogenetically, R. kunmingensis has a longer branch than R. tibetica (Fig.…”

Section: Speciesmentioning

confidence: 96%

A preliminary species‐level phylogeny of the alpine ginger Roscoea: Implications for speciation

Zhao

Zhong

Fan

et al. 2017

J of Sytematics Evolution

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Speciation, the evolutionary process forming new species, is a key mode generating biodiversity on the Earth. In this study, we produced a species‐level phylogeny of Roscoea using one nuclear ribosomal and two chloroplast DNA fragments based on Bayesian inference and maximum likelihood. We then explored the possible speciation processes using the species‐level phylogeny and the heterozygous sites in the nuclear DNA. The incongruence between nuclear and chloroplast phylogenies, and several heterozygous sites in the nuclear DNA, suggested that R. auriculata might have a hybrid origin with R. purpurea and R. alpina being two possible parental progenitors; however, one alternative possibility through incomplete lineage sorting cannot be ruled out. In addition, R. kunmingensis likely originated from R. tibetica Batalin through the process of “budding speciation”. These results provided a valuable framework to draw testable hypotheses for future in‐depth comparative studies to further our understanding of the underpinning speciation and adaptation mechanisms that contribute to ultrahigh biodiversity in the Himalayas and the Hengduan Mountains.

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“…cyathophorum , as in the scenarios proposed for Picea morrisonicola (Zou et al. 2013). But this hypothesis is rejected by the results of ABC analysis, which gave a low Bayes factor value.…”

Section: Discussionmentioning

confidence: 99%

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

Wang

Liang

et al. 2015

Ecology and Evolution

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It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD-psaI and the rpl16 intron) of 150 individuals, and the nuclear (ITS) region of 114 individuals, from 19 populations throughout the distributional ranges of these species. The divergence between the two species was dated at 779 - 714 thousand years before the present and was likely initiated by the most major glaciation in the QTP. Analysis of chlorotype diversity showed that A. spicata, the species occurring in the western QTP, contains much lower genetic diversity (0.25) than A. cyathophorum (0.93), which is distributed in the eastern QTP. Moreover, multiple independent tests suggested that the A. spicata population had expanded recently, while no such expansion was detected in A. cyathophorum, indicating a contrasting pattern of responses to Pleistocene climate changes. These findings highlight the importance of geographical topography in determining how species responded to the climate changes that took place in the QTP during the Pleistocene.

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Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii

Abstract: The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species.

Cited by 36 publications

References 76 publications

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

A preliminary species‐level phylogeny of the alpine ginger Roscoea: Implications for speciation

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

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