Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China

Abstract

The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.

Cryptic phylogeographic history sheds light on the generation of species diversity in sky‐island mountains

“…The ENM analyses also indicate the existence of more stable climatic conditions in the southern portion of the current distribution of S. fusicaudus (i.e., south of 29° N, Figure f; see Zhang, Boufford, Ree, & Sun, ). Although we acknowledge that our ecological niche model was not projected onto climatic scenarios older than ~120,000–140,000 years BP, much shorter than the evolutionary timeframe estimated for the origin of S. fusicaudus (projections onto older climatic scenarios require special considerations, assumptions and perhaps a more robust dataset of occurrences), the patterns shown by our ENM analyses coincide with the unevenly distributed genetic diversity in this taxon (Figure ), indicating that the higher diversity in the southern region of the sky islands is associated with a larger number of interglacial refugia (He et al, ).…”

“…To calculate the Bayes factor, the marginal likelihood of each analysis was estimated with 1,000,000 steps. The two fossil-based calibrations were used as "checkpoints", constraining the times of diversification (He, Hu, Chen, Li, & Jiang, 2016;Mercer & Roth, 2003). We considered Bayes Factor ≥10 as strong evidence against the alternative hypothesis (Kass & Raftery, 1995).…”

Climate niche conservatism and complex topography illuminate the cryptic diversification of Asian shrew‐like moles

“…These ecophysically varied zones result in a complex of sky islands (He & Jiang, 2014;McCormack, Huang, Knowles, Gillespie, & Clague, 2009). Many studies have revealed coarse genetic structure and substantial population changes among ecological generalists and/or widespread species in the MSC (He, Hu, Chen, Li, & Jiang, 2016;Liu, Chen, et al, 2012;Qu et al, 2015;Wang et al, 2013), while some ecological specialists and/or sedentary species appear to have finer genetic structure and stable population sizes over time (Chen et al, 2015;Lu et al, 2012;Yan et al, 2013;Zhang et al, 2010). The contrasting patterns may be due to intrinsic traits among species, such as physiology and behaviour.…”

Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys

“…For example, it has been suggested that the LIG (Last Interglacial Maximum) was an 8 unfavorable period for mole shrews (Anourosorex squamipes) because of increased seasonality in temperature extremes. During this period, mole shrews survived in 10 isolated interglacial refugia mainly located in the southern subregion and then rapidly expanded during the LGM (He et al 2016). The amount and distribution of suitable 12 habitat for snub-nosed monkeys also is likely to have been affected by these climatic events.…”