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Determining the extent and direction of introgression between three spruce species based on molecular markers from three genomes with different rates of gene flow

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Abstract

Introgression frequently occurs between closely related plant species when there is incomplete reproductive isolation. However, few studies have been designed to examine the extent and direction of introgression from all three genomes, especially when they have different rates of gene flow. Conifers, in which chloroplast (cp), mitochondrial (mt) and nuclear (nr) genomes show contrasting rates of gene flow, provide a good model in which to carry out such a case study. Here we use data on sequence variation in 18 DNAs from three genomes for 311 individuals of 31 populations to investigate the extent and direction of introgressions between three spruce species in areas where they are sympatrically distributed. We found that one species seem to have introgressions derived from the other two species in areas of sympatric distribution; there were more introgressions from the maternally inherited mtDNA, which has the lowest rate of gene flow, and fewer introgressions from the bi-parentally inherited nrDNA. Further coalescent analysis of nrDNA population genetic data suggested that the species containing introgressions had experienced range expansion in the recent past while there was no such indication for the other two species. Our results support the hypotheses that introgressions occurred more frequently at genetic markers with lower rates of gene flow and that they usually took place from local species towards invading species that had undergone recent demographic expansion.

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Acknowledgments

We thank Lili Li for her help with experimental work. This research was supported by Grants from National Natural Science Foundation of China (30930072) and the Fundamental Research Funds for the Central Universities (lzujbky-2009-k05) and the International Collaboration 111 Projects of China.

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  1. State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, People’s Republic of China

    Xi Wang, Jing Lu, Wei Yue, Long Li, Jiabin Zou, Xiaowei Li, Xiaodong He, Bingbing Duan & Jianquan Liu

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  1. Xi Wang
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  2. Jing Lu
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  3. Wei Yue
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Online Resource 1. The distribution of sampling localities for Picea meyeri, P. wilsonii and P. neoveitchii.

Online Resource 2. Sampling sites. The location and number of samples for P. wilsonii, P. neoveitchii and P. meyeri

Online Resource 3. Alignments used to produce phylogenetic relationships (4 cl)

Online Resource 4. Alignments used to produce phylogenetic relationships (EBS)

Online Resource 5. Alignments used to produce phylogenetic relationships (FT3)

Online Resource 6. Alignments used to produce phylogenetic relationships (GI)

Online Resource 7. Alignments used to produce phylogenetic relationships (M002)

Online Resource 8. Alignments used to produce phylogenetic relationships (M007D1)

Online Resource 9. Alignments used to produce phylogenetic relationships (PCH)

Online Resource 10. Alignments used to produce phylogenetic relationships (Sb16)

Online Resource 11. Alignments used to produce phylogenetic relationships (Sb29)

Online Resource 12. Alignments used to produce phylogenetic relationships (Sb62)

Online Resource 13. Alignments used to produce phylogenetic relationships (Se1364 )

Online Resource 14. Alignments used to produce phylogenetic relationships (Se1390)

Online Resource 15. Alignments used to produce phylogenetic relationships (xy1420)

Online Resource 16. Alignments used to produce phylogenetic relationships (cpDNA)

Online Resource 17. Alignments used to produce phylogenetic relationships (mtDNA)

Online Resource 18. Descriptions of prior settings for all parameters used in DIYABC

Online Resource 19. Variable sites of aligned sequences of three cpDNA fragments from which eleven chlorotypes were identified

Online Resource 20. Estimates of average gene diversity within populations (H S), total gene diversity (H T), interpopulation differentiation (G ST) and number of substitution types (N ST)

Online Resource 21. Variable sites of aligned sequences of two mtDNA fragments from which ten mitotypes were identified

Online Resource 22. Analysis of molecular variance (AMOVA) of cpDNA and mtDNA for three species

Online Resource 23. Nucleotide variation, haplotype diversity and neutrality tests for P. wilsonii across all loci

Online Resource 24. Nucleotide variation, haplotype diversity and neutrality tests for P. neoveitchii across all loci

Online Resource 25. Nucleotide variation, haplotype diversity and neutrality tests for P. meyeri across all loci

Online Resource 26. r 2 values at each nuclear locus as measured by DnaSP to analyze the linkage disequilibrium

Online Resource 27. Genetic divergence at thirteen nuclear loci among species based on pairwise comparisons: (a) P. wilsonii (b) P. neoveitchii and (c) P. meyeri

Online Resource 28. Estimated the most likely number of clusters (K) obtained with Structure using the distribution of DeltaK (ΔK), the posterior probability of the data given each K, for K 1–6. Each K is represented by 10 separate runs. Variation among runs was limited

Online Resource 29. Posterior probabilities of five competing scenarios for each species

Online Resource 30. Histories for two species pairs (for sampled and ancestral populations) represented as boxes

Online Resource 31. Genetic divergence based on analysis of molecular variance (AMOVA) of cpDNA and mtDNA between three species

Online Resource 32. Genetic divergence at three genomes between species based on pairwise comparisons: (a) P. wilsonii (b) P. neoveitchii and (c) P. meyeri

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Wang, X., Lu, J., Yue, W. et al. Determining the extent and direction of introgression between three spruce species based on molecular markers from three genomes with different rates of gene flow. Plant Syst Evol 302, 691–701 (2016). https://doi.org/10.1007/s00606-016-1289-3

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