Integrating phylogeography and species distribution models: cryptic distributional responses to past climate change in an endemic rodent from the central Chile hotspot

Abstract

Aim Biodiversity losses under the species level may have been severely underestimated in future global climate change scenarios. Therefore, it is important to characterize the diversity units at this level, as well as to understand their ecological responses to climatic forcings. We have chosen an endemic rodent from a highly endangered ecogeographic area as a model to look for distributional responses below the species level: Phyllotis darwini. Location The central Chile biodiversity hotspot: This area harbours a high number of endemic species, and it is known to have experienced vegetational displacements between two mountain systems during and after the Last Glacial Maximum. Methods We have characterized cryptic lineages inside P. darwini in a classic phylogeographic approach; those intraspecific lineages were considered as relevant units to construct distribution models at Last Glacial Maximum and at present, as border climatic conditions. Differences in distribution between border conditions for each lineage were interpreted as distributional responses to post-glacial climate change. Results The species is composed of two major phylogroups: one of them has a broad distribution mainly across the valley but also in mountain ranges, whereas the other displays a disjunct distribution across both mountain ranges and always above 1500 m. The lineage distribution model under LGM climatic conditions suggests that both lineages were co-distributed in the southern portion of P. darwini’s current geographic range, mainly at the valley and at the coast. Main conclusions Present distribution of lineages in P. darwini is the consequence of a cryptic distributional response to climate change after LGM: postglacial northward colonization, with strict altitudinal segregation of both phylogroups.

Mountaintops phylogeography: A case study using small mammals from the Andes and the coast of central Chile

“…darwini’s lineage A is distributed in both mountain ranges, it is noteworthy that this lineage is distributed exclusively in localities above 1,500 m altitude. This pattern has been previously reported for the species, with a completely different sample set using only D-LOOP mitochondrial sequences [42]. The Neighbor-Net analysis, on the other hand, showed similar patterns of divergence to that recovered through the intraspecific phylogenies for the Coastal cordillera (blue), the lowlands (green) and the Andean (red) haplogroups for A .…”

Evaluating presence‐only species distribution models with discrimination accuracy is uninformative for many applications

“…These methods have been used since the 1920s (Cook, 1925;Sutherst, 2014), but recent years have seen rapid growth in the number of studies employing SDM in fields including ecology, conservation biology, evolutionary biology and epidemiology (Allen & Lendemer, 2016;Coro, Pagano, & Ellenbroek, 2013;Guisan, Thuiller, & Zimmermann, 2017;Gutierrez-Tapia & Palma, 2016;Lezama-Ochoa et al, 2016;Peterson et al, 2011;Raghavan et al, 2016). These methods have been used since the 1920s (Cook, 1925;Sutherst, 2014), but recent years have seen rapid growth in the number of studies employing SDM in fields including ecology, conservation biology, evolutionary biology and epidemiology (Allen & Lendemer, 2016;Coro, Pagano, & Ellenbroek, 2013;Guisan, Thuiller, & Zimmermann, 2017;Gutierrez-Tapia & Palma, 2016;Lezama-Ochoa et al, 2016;Peterson et al, 2011;Raghavan et al, 2016).…”

“…Species distribution models (SDM, alternatively environmental niche models or ENM) use data on species occurrences in conjunction with environmental data to generate statistical models of species' ecological tolerances, environmental limits and potential to occupy different geographic areas. These methods have been used since the 1920s (Cook, 1925;Sutherst, 2014), but recent years have seen rapid growth in the number of studies employing SDM in fields including ecology, conservation biology, evolutionary biology and epidemiology (Allen & Lendemer, 2016;Coro, Pagano, & Ellenbroek, 2013;Guisan, Thuiller, & Zimmermann, 2017;Gutierrez-Tapia & Palma, 2016;Lezama-Ochoa et al, 2016;Peterson et al, 2011;Raghavan et al, 2016). The primary appeal of SDMs is their tractability; estimating environmental tolerances experimentally is expensive and timeconsuming at best and impractical for many species.…”

Climate change, extinction, and Sky Island biogeography in a montane lizard

“…Some previous studies (mostly in other regions) have also combined phylogeography with niche modelling to address the impacts of past climate change (e.g., Carstens & Richards, ; Carnaval, Hickerson, Haddad, Rodrigues, & Moritz, ), including some that focused on montane species (Bryson, Murphy, Graham, Lathrop, & Lazcano, ; Gutierrez‐Tapia & Palma, ; Mastretta‐Yanes et al, ) and some that discussed implications for future climate change (Cordellier & Pfenninger, ). Here, we integrate these two approaches (niche modelling, phylogeography) with analyses of distributional, climatic, and physiological data to address the causes of Sky Island distributions and their implications for future climate change.…”