DOI: 10.5061/dryad.jsxksn0dv
title: Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

description: Aim: The biodiversity of the Malay Archipelago is the product of the
 region’s rich biogeographical history with periods of island connectivity
 and isolation during the Pleistocene glacial cycles. Here, the case of two
 endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi)
 warty pigs, was used to illustrate how biogeographic processes and recent
 anthropogenic pressures can shape demographic histories with significant
 implications for species conservation. Location: Malay Archipelago, with
 focus on Bawean and Java. Methods: We employed genome-wide single
 nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess
 interspecific genetic differentiation, to estimate divergence times, and
 to perform demographic model selection. Results: In contrast to the
 hypothesis of recent divergence during the last glacial maximum, S.
 blouchi was found to have diverged from S. verrucosus at least 166k years
 ago following a founder event. The contemporary S. blouchi population was
 characterised by a recent bottleneck that reduced the effective population
 size to less than 20. The genomic assessment supports the single species
 status of S. blouchi, as was previously proposed based on morphometrics.
 The demographic history of S. verrucosus showed evidence of secondary
 contact with the sympatric banded pig (S. scrofa vittatus) that colonised
 Java 70k years ago. Main conclusions: While the Javan and Bawean warty
 pigs have persisted throughout the Pleistocene climatic oscillations,
 contemporary pressures from human activities threaten their survival and
 immediate action should be taken to grant legal protection to both S.
 verrucosus and S. blouchi. This study highlighted the use of demographic
 history modelling using genomic data to identify evolutionary significant
 units and inform conservation.
description: Between 2006 and 2019, tissue, blood and hair samples were
 collected from suids from <em>ex</em>
 <em>situ</em> and <em>in</em>
 <em>situ</em> populations on Java and Bawean. Ten
 <em>Sus</em> <em>scrofa</em>
 <em>vittatus</em>, 14 <em>S</em>.
 <em>blouchi</em>, and 20 <em>S</em>.
 <em>verrucosus</em> were genotyped using the Porcine SNP60 v2
 BeadChip (Illumina Inc.) following manufacturer’s instructions.
 GenomeStudio 2.0 software (Illumina Inc.) was employed to call genotypes
 with the standard cluster file. Only autosomal SNPs, mapping to
 chromosomes 1 to 18 on the reference genome Sscrofa build 11.1, were
 retained for analysis. The resulting 50K genotypes were merged with
 publicly available data of five <em>S. verrucosus</em>, six
 <em>S. celebensis</em>, nine <em>S. barbatus</em>,
 and four common warthogs (<em>Phacochoerus</em>
 <em>africanus</em>; Yang et al., 2017) using PLINK 1.9
 (Purcell et al. 2007). Only loci present in both libraries were retained
 for analysis to reduce a potential batch effect. The presence of a batch
 effect was investigated by comparing clustering of <em>S.
 verrucosus</em> samples with respect to their library attribution.
 Subsequent filtering and infile preparations were carried out in PLINK
 1.9.