Phylogeny and evolutionary history of the genus Nectogale (Soricidae) inferred from whole-genome analyses, with description of a new species endemic to the Himalayas.

Abstract

The genus Nectogale, endemic to the Himalayas, Hengduan Mountains, and adjacent ranges, comprises highly specialized semi-aquatic shrews adapted to high-elevation streams. Its diversity has likely been underestimated because of limited sampling and morphological conservatism, leaving species limits and evolutionary relationships unresolved. Here, we combined whole-genome data with morphological evidence to delimit species, infer phylogenetic history, and test for introgression and demographic change. Our results support three species: Nectogale elegans, Nectogale sikhimensis, and a newly identified species, Nectogale jilongensis sp. nov. Divergence-time analyses indicated that the Nectogale lineage diverged from its sister genus in the Middle Miocene (∼14 Ma), followed by diversification between the Late Miocene (∼7 Ma) and Early Pliocene (∼4.5 Ma), broadly coinciding with Himalayan uplift and regional climatic transitions. Admixture analyses and D-statistics (ABBA-BABA tests) indicated significant introgression near species range boundaries, while pairwise sequentially Markovian coalescent (PSMC) analyses revealed contrasting population histories among the three lineages. These results highlight the role of contact zones in facilitating lineage divergence through gene flow, and suggest that regional environmental heterogeneity contributes to distinct evolutionary trajectories across the Himalayas. Our study revises Nectogale taxonomy and clarifies its evolutionary history, offering new insights into diversification in the Himalayan biodiversity hotspot.