DOI: 10.5061/dryad.37pvmcvm3
title: SNP matrices and vcf files for phylogenetic, genetic structure and historical demographic analyses of Podocarpus from Hispaniola

description: Aim: Hispaniola is the second largest island in the Caribbean and a
 hotspot of biodiversity. The island was formed by the fusion of a northern
 and southern palaeo-islands during the mid-Miocene (15 Ma). The historical
 split of Hispaniola together with repeated marine incursions during the
 Pleistocene are known to have influenced lineage divergence and genetic
 structure in a few birds and mammals, but the effect on vascular plants is
 less understood. The conifer genus Podocarpus has two species, P.
 hispaniolensis and P. buchii, that are endemic to the mountains of
 Hispaniola and are IUCN endangered. The former occurs in the mountains of
 the north, and the latter in the south, with a region of sympatry in the
 Central Cordillera. Here we evaluate the historical split of the two
 palaeo-islands, and repeated marine incursions as dispersal barriers to
 the geographical distribution of genetic diversity, genetic structure,
 divergence patterns, and the historical demography of the two species.
 Location: Hispaniola island, Caribbean. Methods: Using Genotyping by
 Sequencing in 47 Podocarpus samples we identified two sets of single
 nucleotide polymorphisms for our analyses (74,260 and 22,657 SNPs).
 Results: The results show a population genetic structure that corresponds
 to the geographic distribution of the species in mountainous areas.
 Podocarpus in Hispaniola followed a stepping-stone colonization pattern
 with bottlenecks at each mountain colonization event. Main conclusions:
 The historical events in question did not seem to have influenced the
 genetic structure, diversity, or demography of Podocarpus, instead the
 current geographic barriers imposed by lowland xeric valleys did. The
 clear divergence between species together with the elevated
 within-population genetic diversity and significant genetic structure call
 for a multi-population in situ conservation of each species.
description: We conducted SNPs discovery with <i>Stacks </i>1.47
 (Catchen et al. 2013). We demultiplexed and filtered sequencing reads
 using the <i>process_radtags </i>function. We trimmed reads to
 64 bp length, and eliminated uncalled reads and reads with low quality
 scores (phred score of 10). Since we did not have a reference genome, we
 conducted a ‘<i>de novo</i>’ assembly of loci with the module
 ‘<i>ustacks</i>’. In this step, reads were aligned into
 matching blocks, or stacks per sample. Then the stacks were compared, a
 set of putative loci produced and SNPs detected at each locus. We followed
 the recommendations of Paris et al. (2017) on the selection of parameter
 values through the pipeline, keeping those that rendered the highest
 number of loci. We used -m (minimum depth coverage to create a stack) = 5;
 -M (maximum distance allowed to create a stack) = 3; -p (parallel
 execution of several threads) = 15; and the –gapped option which allowed
 gapped alignments between stacks. Subsequently the module
 ‘<i>cstacks</i>’ built a catalog from the loci produced in
 ‘<i>ustacks</i>’ by merging stacks with at most 3 (-n = 3)
 mismatches between loci, and allowed parallel execution of several threads
 (-p = 15). The module ‘<i>sstacks</i>’ matches the loci
 produced by ‘<i>ustacks</i>’ with the catalog produced by
 ‘<i>cstacks</i>’, and again parallel execution of several
 threads (-p = 15) was allowed. We used the ‘<i>populations’
 </i>module of <i>Stacks </i>to obtain population level
 summary statistics, genetic diversity indexes (i.e. observed and expected
 heterozygosity, nucleotide polymorphism diversity),
 <i>F</i><i><sub>ST</sub> </i>values,
 and a SNP dataset. We chose the following parameters: -p (minimum number
 of populations containing each locus) = 1; -r (minimum percentage of
 individuals present in a population to process a locus for that
 population) = 0.4; and –min_maf (minimum allele frequency) = 0.1. We ran
 the ‘<i>populations’ </i>module of <i>Stacks</i>
 twice. In the first run we assigned samples to the 11 collection sites
 plus the outgroup, and in the second we assigned samples to five
 populations. The first SNP dataset was used to run a phylogenetic
 reconstruction, while the second to run the genetic structure, and
 demographic history analyses.