Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity

Abstract

Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species’ extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10–12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.

Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

“…The large historical effective population sizes are far greater than most PSMC reconstructions of mammal species thus far (e.g. Bunnefeld, Frantz, & Lohse, 2015;Ekblom et al, 2018;Liu et al, 2018;Mays et al, 2018;Miller et al, 2012;Tsuchiya, Dikow, & Cassin-Sackett, 2020;Westbury et al, 2018;Westbury, Petersen, Garde, Heide-Jørgensen, & Lorenzen, 2019;Yim et al, 2013;Yuan et al, 2018), with the potential exception of some bat species, depending on the generation time used (Chattopadhyay et al, 2019).…”

“…Determining how populations have responded to large fluctuations in climate and varying environments throughout the Quaternary may help us to understand how they could respond under future climate change (Chattopadhyay et al, 2019;Kozma et al, 2016;Kozma et al, 2018;Louis et al, 2020;Yannic et al, 2013). Particularly at northern latitudes, there were large changes in available habitat and levels of glaciation (Chattopadhyay et al, 2019) which would have influenced caribou distributions and abundance. Comparing the key dates of caribou population expansion, decline, and introgression events to temperature and ice coverage at the same time periods (Figure 8; maps reconstructed from data from Batchelor et al, 2019) could lead to some insights.…”

“…; Heintzman et al, 2016), and subspecies and genetic diversity of tree species in western North America (Roberts & Hamann, 2015) all provided valuable information on how the LGM and more recent times shaped phylogeography but did not investigate the impact of events prior to the LGM. However, population sizes have been shown to fluctuate considerably throughout the Quaternary, such as in a demographic reconstruction of avian species (Nadachowska-Brzyska, Smeds, Zhang, & Ellegren, 2015), and of 11 bat species (Chattopadhyay, Garg, Ray, & Rheindt, 2019), among others (e.g. Kozma, Melsted, Magnússon, & Höglund, 2016;Louis et al, 2020;Miller et al, 2012).…”

Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae)

“…The severity of LGM‐driven extinction risk is regarded as having had much more influence on local endemic species than on widespread and common species (Rosenblad et al., 2019). Populations influenced by Pleistocene glaciations in local endemic species are particularly vulnerable to long‐term population decline and fail to recover to their previous population size (Nadachowska‐Brzyska et al., 2015; Zhao et al., 2013), as shown by recent phylogeographical studies using genomic coalescent analyses and palaeoclimate niche modelling (e.g., Chattopadhyay et al., 2019; Fedorov et al., 2020; Mays et al., 2018; Nadachowska‐Brzyska et al., 2015; Zhao et al., 2013).…”

“…With the accelerating development and accessibility of high‐throughput sequencing (HTS), a number of new methods have become available that make use of reduced representation (e.g., RAD sequencing) or whole‐genome sequencing data for tracking detailed demographic history since the LGM (e.g., Li & Durbin, 2011; Liu & Hansen, 2017; Liu & Fu, 2015), which have indicated that different species, or even different lineages within species, might have had varying sensitivities to the temperature decline during the LGM. Many threatened species or lineages became extinct or failed to recover to pre‐LGM population sizes (e.g., Mays et al., 2018; Yang et al., 2018), but others were able to recover at the end of the LGM and rapidly expanded with Holocene climate warming (e.g., Chattopadhyay et al., 2019; Ye et al., 2018). In addition, some species or lineages unaffected by the LGM maintained relatively stable population sizes or even expanded moderately during the LGM (Lu et al., 2020; Wang et al., 2018).…”