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.

What is provided is: 1. "dryad_reads.tar.gz" --> 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.2. "VCF_files_min50.tar.gz" --> 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 >50% missing data were also removed. each species have a list of samples removed associated with it. 3. "popmap-spp-328indivs-ch3GeneticDiversity.txt" --> 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)

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.