Phylogeography of the Common Butterfly Lizard, Leiolepis belliana, Reveals Multiple Instances of Mitochondrial Introgression Driven by Historical Changes in River Systems

Abstract

Aim

To test the hypothesis that historical changes in Indochinese river systems shaped phylogeographic structure, diversification and hybridization events in butterfly lizards of the genus Leiolepis.

Location

Mainland Southeast Asia (Thailand, Cambodia, Vietnam and Peninsular Malaysia).

Taxon

Common butterfly lizard (Leiolepis belliana).

Methods

We analysed a multi-locus dataset comprising one mitochondrial, NADH dehydrogenase subunit 2 (ND2), and two nuclear genes, Exophilin 5 (EXPH5) and Upstream transcription factor family member 3 (USF3; KIAA2018), from samples spanning the distribution of Leiolepis belliana and other congeneric species within the genus Leiolepis. Phylogenetic relationships using both mitochondrial and nuclear genes were inferred using Maximum Likelihood and Bayesian Inference analyses. Divergence times were estimated, and ancestral range reconstructions were conducted using Statistical Dispersal-Variance Analysis (S-DIVA). Mitochondrial and nuclear DNA datasets were analysed separately to distinguish historical biogeographic patterns from signals of hybridization. Population genetic structure and demographic history were assessed using genetic diversity indices, a haplotype network, AMOVA and neutrality tests.

Results

The nuclear phylogenies suggested that Leiolepis belliana originated on the Thai–Malay Peninsula during the late Oligocene–early Miocene, followed by diversification across Central and Northern Thailand consistent with major reorganizations of the Mekong River system. In contrast, the mitochondrial phylogeny revealed contrasting relationships with the nuDNA dataset, indicating three independent instances of mitochondrial introgression involving other species within the genus Leiolepis. Divergence time estimations and ancestral area reconstructions collectively suggested that repeated shifts in river courses and sea-level fluctuations transformed environmental barriers into areas of secondary contact and hybridization. Population genetic analyses further supported strong geographic structuring with different demographic signatures among populations.

Main Conclusions

The evolutionary history of L. belliana reflects a dynamic interplay between river system reorganizations and secondary contact. Indochinese river systems have not only promoted lineage divergence but also facilitated repeated hybridization in three different geographic areas subsequent to altering their courses and landscape connectivity. Integrating nuclear and mitochondrial evidence demonstrated how shifting river courses simultaneously drove diversification and introgression via hybridization, providing a framework for understanding the complex biogeographic patterns of Southeast Asian terrestrial biota.