Interglacial refugia on tropical mountains: novel insights from the summit rat (Rattus baluensis), a Borneo mountain endemic

[Aim] The genetics of organisms currently isolated in refugia has received little attention compared to post-glacial expansions. We study the population history and connectivity of a rat endemic to montane habitat in Borneo to better understand the history and potential of populations in interglacial mountain refugia.
[Location] Sabah, Borneo, Malaysia.
[Methods] We performed a field survey of the summit rat (Rattus baluensis) on two mountains, Mt. Kinabalu and Mt. Tambuyukon, its entire known distribution. We sequenced mitogenomes and 27 introns (19 of which were polymorphic) in 49 individuals from both populations. We analysed their current genetic structure and diversity, and inferred their demographic history with approximate Bayesian computation.
[Results] Summit rats were tightly associated with mountain mossy forest and scrubland above 2,000 m, facilitating the prediction of their past and future distributions. The genetic analysis supports a Holocene fragmentation of a larger population into smaller ones that are now isolated in interglacial refugia on mountaintops. These findings are consistent with climatic reconstructions and the retreat of upland forest to higher elevations after the Last Glacial Maximum (LGM), ~21 kya.
[Main conclusions] The two isolated populations of summit rats formed through the upland shift of their habitat after the LGM. The current trend of global warming will likely lead to diminishing suitable upland habitat and result in the extinction of the population on Mt. Tambuyukon. The population on Mt. Kinabalu, the higher peak, could persist at higher elevations, highlighting the singular value of high tropical mountains as reservoirs of biodiversity during past and ongoing climate change.
Logistical support was provided by Laboratorio de Ecología Molecular, Estación Biológica de Doñana, CSIC (LEM‐EBD). Digital elevation models for maps was obtained from the U.S. The Spanish Ministry of Science and Innovation grants CGL2010‐21524 and CGL2014‐58793‐P supported this work. MCS is supported by the Spanish Ministry of Science and Innovation Predoctoral Fellowship BES‐2011‐049186, and part of his fieldwork was also funded by EEBB‐I‐12‐05317.