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.

Between 2006 and 2019, tissue, blood and hair samples were collected from suids from ex situ and in situ populations on Java and Bawean. Ten Sus scrofa vittatus, 14 S. blouchi, and 20 S. verrucosus 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 S. verrucosus, six S. celebensis, nine S. barbatus, and four common warthogs (Phacochoerus africanus; 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 S. verrucosus samples with respect to their library attribution. Subsequent filtering and infile preparations were carried out in PLINK 1.9.