# Diversification in the steppe rat snake Elaphe dione (Pallas, 1773) coincides with the Mid-Pleistocene climatic transition of Eurasia

## TL;DR

The steppe rat snake's diversification history is linked to climate changes in Eurasia during the Mid-Pleistocene era.

## Contribution

This is the most comprehensive phylogeographic analysis of Elaphe dione to date, revealing its diversification timeline and geographic patterns.

## Key findings

- Eleven phylogeographic lineages were identified, grouped into three clades diverging during the Late Miocene-Pliocene.
- A west-east split in one clade occurred around 1.7 million years ago, coinciding with the Mid-Pleistocene climatic transition.
- Central China is likely the ancestral area of Elaphe dione, with diversification later than other Palearctic species.

## Abstract

The steppe rat snake, Elaphe dione, has one of the broadest terrestrial distributions among snakes. Its distribution spans from the Azov Sea and the Caucasus to the Pacific coast of Far East Asia. The steppe rat snake is one of the few reptile species with an extensive distribution in both the Western and Eastern Palearctic, making its evolutionary history of particular interest in understanding biogeographical patterns and connections between these regions. However, knowledge of its genetic variability and phylogeography remains limited. In this study, we examined the phylogeographic structure of E. dione to shed light on its genetic diversity and diversification history in the Western and Eastern Palearctic.

We reconstructed phylogenies and analyzed the genetic structure of E. dione populations originating from most of its geographic range using three mitochondrial DNA gene fragments (12S rRNA, COI, ND4+tRNAs). In total, we analyzed sequences from 130 E. dione specimens from 100 locations. We used maximum likelihood and Bayesian inference methods to reconstruct phylogenetic trees, supplemented by an analysis of haplotype networks, molecular clocks, and a neutrality test for historical demography.

We identified 11 phylogeographic lineages grouped into three broader clades that diverged during the Late Miocene-Pliocene. The average uncorrected genetic distance between these 11 lineages ranged from 0.7% to 6.7% based on sequences of the COI fragment. Most of the contemporary range of E. dione is occupied by a single clade, with lineages distributed west and east of the Central Asian mountains. This west-east split in the clade occurred approximately 1.7 million years ago (Mya), followed by vicariant radiation in the Western and Eastern Palearctic during the Mid-Pleistocene era. Spatial patterns of mtDNA variation identified areas of post-last glacial maximum (LGM) dispersal and secondary contact zones of several lineages in the Altai and the Changbai Mountains.

Our study is the most comprehensive phylogeographic analysis of E. dione to date. The territory of central China most probably served as an ancestral area of this species, where E. dione diverged from its most recent common ancestor with E. bimaculata during the Late Miocene. The most active period of diversification in E. dione was estimated to have occurred later (∼1.3 Mya) than other widespread Palearctic species. Furthermore, this period is correlated across the species’ range and coincides with the beginning of the Mid-Pleistocene climatic transition. Climatic and environmental transitions during this period may have triggered the allopatric divergence of E. dione in multiple glacial refugia. Notably, diversification in the Western Palearctic resulted in a greater number of phylogeographic lineages, which could be linked to a greater number of suitable refugia. However, further evidence is needed to confirm these scenarios.