Historical connections among river basins and climatic changes explain the biogeographic history of a water rat

Jeronymo Dalapicolla,Yuri Luiz Reis Leite

doi:10.7717/peerj.5333

Jeronymo Dalapicolla, Yuri Luiz Reis Leite

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https://doi.org/10.7717/peerj.5333

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Abstract

BackgroundThe water rat Nectomys squamipes (Cricetidae: Sigmodontinae) is a semiaquatic rodent from eastern South America that shows shallow genetic structure across space, according to some studies. We tested the influence of hydrography and climatic changes on the genetic and phylogeographic structure of this semiaquatic small mammal.MethodsDNA sequences of two mitochondrial genetic markers (Cyt b and D-loop) and six microsatellite loci from water rats were collected at 50 localities in five river basins in the Atlantic Forest along the eastern coast of South America. We evaluated the genetic structure within and among river basins, and we estimated divergence dates. Species distribution models for the present and past were built to identify possible gene flow paths.ResultsMitochondrial data and species distribution models showed coherent results. Microsatellite loci showed a more complex pattern of genetic differentiation. The diversification of N. squamipes haplotypes occurred during the Pleistocene and the river basin cannot explain most of the genetic structure. We found evidence of population expansion during the last glacial maximum, and gene flow paths indicate historical connections among rivers in the Atlantic Forest.DiscussionHistorical connections among rivers in the Atlantic Forest may have allowed N. squamipes to disperse farther across and within basins, leading to shallow genetic structure. Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, thus challenging the forest refuge hypothesis.

Highlights

In recent years, many phylogeographic studies have tested different hypotheses to explain the diversity and genetic structuring patterns found in vertebrates in the Atlantic Forest, eastern South America (Thomé et al, 2014)
Two DNA sequence was obtained from GenBank, five were donated by researchers, and 154 liver and muscle samples preserved in ethanol were supplied by three mammal collections: CTA-UFES (Colecão de Tecidos Animais da Universidade Federal do Espírito Santo, Vitória, Brazil), MBML (Museu de Biologia Professor Mello Leitão, Santa Teresa, Brazil), and Museu de Ciências Naturais da PUC-Minas (MCN-M) (Museu de Ciências Naturais PUC Minas, Belo Horizonte, Brazil)
Of the 161 initial samples, 83 cytochrome b (Cyt b) sequences and 149 D-loop sequences of Nectomys squamipes were obtained (77 and 148 sequences with no ambiguities, respectively); sequences for both markers were obtained from 70 samples (Table S2.3)

Summary

Introduction

Many phylogeographic studies have tested different hypotheses to explain the diversity and genetic structuring patterns found in vertebrates in the Atlantic Forest, eastern South America (Thomé et al, 2014). Originally formulated to account for species diversity in the Amazon, it was later adapted to explain high contemporary diversity and endemism at historically stable Atlantic Forest areas, or refuges (Carnaval & Moritz, 2008; Valdez & D’Elía, 2013). In this model, population size reductions are expected in unstable areas due to habitat loss during glacial periods and population stability or expansion during interglacials (Leite & Rogers, 2013). Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, challenging the forest refuge hypothesis

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