Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai–Tibet Plateau: homoploid hybrid origin and Pleistocene expansion
Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai–Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and...
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| Published in | Molecular ecology Vol. 23; no. 2; pp. 343 - 359 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Publishing Ltd
01.02.2014
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| Subjects | |
| Online Access | Get full text |
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| Summary: | Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai–Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and P. wilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and P. purpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well‐established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between P. purpurea and P. wilsonii, while variation at the nuclear se1364 gene suggested P. purpurea was more closely related to P. likiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that P. purpurea originated by homoploid hybrid speciation from P. wilsonii and P. likiangensis. The ABC analysis dated the origin of P. purpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by P. likiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from P. wilsonii such that it came to possess both mtDNA and cpDNA of P. wilsonii. The estimated parameters indicated that following its origin, P. purpurea underwent an expansion during/after the largest Pleistocene glaciation recorded for the QTP. |
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| Bibliography: | http://dx.doi.org/10.1111/mec.12599 Royal Society-NSF China Joint International Project ark:/67375/WNG-J74HT680-R istex:773C147DF5E0E0212E1C0B55A66DF2CA9072F40C National Natural Science Foundation - No. 30930072; No. 31300559 Ministry of Science and Technology - No. 2010DFB63500 ArticleID:MEC12599 National Key Project - No. 2014CB954100 Method S1 Supplementary methods and results of testing the instantaneous expansion model of Picea purpurea and estimating the parameters of a second contact model between P. likiangensis and P. wilsonii. Fig. S1 Diagrams showing the optimal number of groups (K) obtained by structure across Picea schrenkiana, P. purpurea, P. likiangensis and P. wilsonii. Fig. S2 Results of a neutrality test using MFDM. Fig. S3 Networks of haplotypes or alleles at nuclear loci of Picea purpurea. Fig. S4 Diagram for inferring the optimal K obtained by structure across Picea purpurea, P. likiangensis and P. wilsonii using ΔK statistic of Evanno et al. (). Fig. S5 Posterior distributions (red lines) estimated using ABCtoolbox based on the nuclear multilocus sequence data and prior (black lines) for all parameters in the hybrid speciation model. Fig. S6 The second contact model of P. likiangensis and P. wilsonii. Table S7 Fixation index ФST (Below diagonal) and Da (Above diagonal) between each species pair. S = P. schrenkiana,P = P. purpurea,L = P. likiangensis, W = P. wilsonii. Table S8 Prior distributions about model parameters used in the second contact model (Fig. S6, Supporting information). Table S9 Posterior mode and 95% HPDI of all parameters in the second contact model (Fig. S6, Supporting information). Nm0_1 and Nm1_0 is the population migration rate from Picea likiangensis to P. wilsonii and the opposite direction.Table S1 Geographical locations, sample sizes of Picea schrenkiana, P. purpurea, P. likiangensis and P. wilsonii.Table S2 Geographical origins, sample sizes (Num), and cpDNA/mtDNA haplotypes identified in the 29 populations of Picea purpurea, P. wilsonii and P. likiangensis. Table S3 Sequences used as outgroups. Table S4 Prior distributions about model parameters used in model comparisons. Table S5 Statistics derived from nrDNA data set of Picea purpurea, P. wilsonii and P. likiangensis.Table S6 Presence data used in niche modelling.Appendix S1 Data used in this study. SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 0962-1083 1365-294X 1365-294X |
| DOI: | 10.1111/mec.12599 |