Comparative Phylogeography and Molecular Evolution of Australian Eugongylinae Skinks

Abstract

Temperature variation over time and space has shaped the population structure and diversity, as well as molecular evolution of species. In order to assess this idea, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks as examples of temperature-sensitive ectotherms. The effect of temperature in the late Quaternary is assessed based on nDNA data of southern Morethia skinks (a member of Eugongylinae subfamily) using custom bioinformatics pipelines (sequence assembly), IQTree (phylogenetic tree), PopGenome (population diversity), Structure, conStruct (population structure), and BEAST2 (population size). On the other hand, the association between temperature (and other factors) on long-term substitution rates was assessed based on a large exonic sequence of 44 species pairs from Eugongylinae subfamily using Poisson regression analysis. The results show that species with narrower realized climate niche (M. obscura, M. adelaidensis) have very weak phylogeographic structure with evidence of rapid population growth post-LGM, while other species persisted in multiple refugia during LGM. The aridification histories of northern and southern Australia also affected the timing of population expansion, with southern M. obscura experienced more recent radiation (~0.3Mya) than northern monsoonal M. ruficauda (~2Mya). At macroevolutionary scale, temperature is also the strongest, positively-correlated predictor of variation in synonymous and non-synonymous substitution rates across the Australian Eugongylinae. It explains 35% and 40% of variation in dN and dS, respectively, and about 20% of variation in both after controlling for other factors. Overall, this studies points to temperature as a strong driver of both micro- and macro-evolutionary processes in these lizards.