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RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

Citation

Linan, Alexander et al. (2020), RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees, Dryad, Dataset, https://doi.org/10.5061/dryad.18931zcrq

Abstract

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

Methods

Fresh leaf material was collected in field and immediately stored in silica gel to be later extracted using CTAB method.

Extracted DNA was then used to create 2bRAD libraries according to Mikhail Matz lab 2015 protocol.

2b-RAD: Wang S., Meyer E., McKay JK., Matz MV. (2012) 2b-RAD: a simple and flexible method for genome-wide genotyping. Nat Methods 9:808-10

Exact protocol used can be found at:

https://github.com/Kenizzer/2bRAD-Edwards-Lab

Usage Notes

dryad-data-upload_pt1n-5n.tar.gz - raw demultiplxed fastq files

ipyrad-parameter-files.zip - contains ipyrad parameters used for each dataset specified in table 3

ipyrad-summary-files.zip - contains summary files of assembled loci generated by ipyrad

phylip-files.zip - contains various phylip files for dataset min10 62 taxa (see table 3) used in RaxML, tetrad, and D-statistic analyses

vcf-files.zip - contains vcf files representing datasets summarized in table 3

Funding

Garden Club of America

National Geographic Society

Franklinia Foundation