Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

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.