DOI: 10.5061/dryad.d2547d84c
title: Interspecific hybridization and island colonization history, not rarity, most strongly affect the genetic diversity in a clade of Mascarene-endemic trees

description: Many factors shape the genetic diversity of island-endemic trees, with
 important implications for conservation. Oceanic island-endemic lineages
 undergo an initial founding bottleneck during the colonization process and
 subsequently accumulate diversity following colonization. Moreover, many
 island endemics occur in small populations and are further threatened by
 anthropogenic factors that cause population declines, making them
 susceptible to losses in genetic diversity through genetic drift,
 inbreeding, and bottlenecks. However, life-history traits
 commonly found in trees, such as outcrossing mechanisms, long lifespans,
 and a propensity for interspecific hybridization, may help buffer against
 losses of genetic variation. To assess the relative importance of
 colonization history, rarity, and distribution in shaping genetic
 diversity of island-endemic trees, we conducted a comparative
 population genomic analysis of 13 species
 of Diospyros (Ebenaceae) endemic to the Mascarene
 Islands that differ in island colonization history, distribution,
 population size, and IUCN threat status. We genotyped 328 individuals
 across the islands using 2b-RADseq, compared genetic diversity both among
 and within species, and assessed patterns of genetic
 structure. Genetic diversity did not vary significantly by IUCN
 status, but we found that species that co-occur with others on the same
 intermediate-aged island (Mauritius) had much greater genetic diversity
 than those that occur solitarily on an island (Réunion and Rodrigues),
 likely because of greater interspecific hybridization among species with
 overlapping distributions and processes related to time since island
 colonization. Results presented here were used to determine
 priority localities for in situ and ex
 situ conservation efforts to maximize the genetic diversity of
 each Mascarene Diospyros species.
description: leaf tissue was collected and stored in silica for DNA
 extraction. A voucher collection was made for each species at each
 sampling location; duplicates were deposited in the MO, CBMN, and/or MAU
 herbaria (Supplementary Table S1 in the manuscript).  DNA was extracted
 used a modified CTAB method (Doyle and Doyle 1987). 2bRAD libraries were
 prepared following Wang et al. 2012 using dual index barcoded adapters to
 multiplex 96 samples per library.  Samples were sequenced on an Illumina
 Hiseq 2000 using 1 × 50 bp reads. reads were assembled
 using STACKS v. 2.2.
description: What is provided is: 1.
 "dryad_reads.tar.gz" --&gt; post-processed reads in which
 samples were demultiplexed and adapters trimed (using custom script found
 at https://github.com/z0on/2bRAD_denovo; trim2bRAD_2barcodes_noAdap.pl)
 and quality filtered (using fastxtools) such that they are ready for use
 in locus assembly pipelines.<br>2.  
  "VCF_files_min50.tar.gz" --&gt; VCF files output from
 STACKS that were used for diversity metrics. note: loci were filtered in
 these datasets requiring loci to be present in 50% of samples. 
 individuals with &gt;50% missing data were also removed. each  species
 have a list of samples removed associated with it. 3.
 "popmap-spp-328indivs-ch3GeneticDiversity.txt" --&gt; the
 popmap file organizing individuals by species. notes on
 organization scheme:  species names are abbreviated with the first 4
 letters (i.e. D. nodosa ="nodo"). sample numbers (i.e. 022_18)
 can be associated with specific sample info (locality,voucher specimen
 etc.) in supplemental material table S1. voucher specimen information for
 these samples are stored in Tropicos database (www.tropicos.org)