Unravelling the phylogeography of the H.azurea (Hypothymis azurea, Aves: Monarchidae) across Southeast Asian rainforests

Abstract

Biological diversification entails a dance between phenotypic divergence – as populations evolve morphological and behavioural differences from each other – and the underlying genetic differentiation. The two are seldom in perfect sync, as morphologically conservative lineages can be deeply diverged, whereas distinct populations may only exhibit shallow genetic divergence. To shed light on the interplay between phenotypic and genetic differentiation, we investigated the Black-naped Monarch (Hypothymis azurea) complex, distributed across mainland and insular tropical Asia, using whole-genome data sampled from populations across its distribution range. We found genetic cohesion in populations from across mainland Asia and shelf islands with a long history of continental connection, while some large island populations, especially from the Andamans and Taiwan, emerged as more deeply diverged. Phenotypically distinct populations from the Barusan island chain consistently formed a distinct clade embedded among the big continental-shelf clade, attesting to rapid morphological differentiation likely driven by founder effects and bottlenecks. Analyses of secondary gene flow revealed a recent full isolation of these Barusan populations, while other monarchs throughout the range, including those from distant islands like the Philippines, showed signs of recent admixture. Our results suggest peripatric founder effects can expedite phenotypic differentiation in short periods, insulating populations from secondary gene flow and driving differentiation that may result in speciation. This study demonstrates that geographic barriers and opportunities for gene flow play a central role in shaping the phylogeography within the H.azurea complex, emphasising the importance of using whole-genome approaches to understand evolutionary relationships and processes in widespread populations.