Reticulate Pleistocene evolution of Ethiopian rodent genus along remarkable altitudinal gradient

[Display omitted] •Most comprehensive phylogenetic analysis of the endemic Ethiopian rodent genus.•Complex reticulate evolution affected by Pleistocene climate changes.•Secondary contacts resulted in mito-nuclear discordance.•Great Rift Valley is not absolute barrier to gene flow for Afroalpine spec...

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Published in:Molecular phylogenetics and evolution 2018-01, Vol.118, p.75-87
Main Authors: Bryja, Josef, Kostin, Danila, Meheretu, Yonas, Šumbera, Radim, Bryjová, Anna, Kasso, Mohammed, Mikula, Ondřej, Lavrenchenko, Leonid A.
Format: Article
Language:English
Subjects:
Animals
Cytochromes b - chemistry
Cytochromes b - classification
Cytochromes b - genetics
DNA, Mitochondrial - chemistry
DNA, Mitochondrial - isolation & purification
DNA, Mitochondrial - metabolism
Ecological speciation
Ecosystem
Ethiopia
Ethiopian highlands
Evolution, Molecular
Great Rift Valley
Haplotypes
Hybridization, Genetic
Karyotype
Mitochondrial introgression
Murinae - anatomy & histology
Murinae - classification
Murinae - genetics
Phylogeny
Rodentia
Stenocephalemys
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Summary:[Display omitted] •Most comprehensive phylogenetic analysis of the endemic Ethiopian rodent genus.•Complex reticulate evolution affected by Pleistocene climate changes.•Secondary contacts resulted in mito-nuclear discordance.•Great Rift Valley is not absolute barrier to gene flow for Afroalpine species.•Repeated ecological speciation at elevation gradient is supposed. The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved asa consequence of the interplay between geomorphology and past climatic changes. In this study, we used the largest available multi-locus genetic dataset of the murid genus Stenocephalemys (347 specimens from ca 40 localities across the known distributional area of all taxa) to investigate the relative importance of disruptive selection, temporary geographic isolation and introgression in their adaptive radiations in the Pleistocene. We confirmed the four main highly supported mitochondrial (mtDNA) clades that were proposed as four species in a previous pilot study: S. albipes is a sister species of S. griseicauda (both lineages are present on both sides of the GRV), while the second clade is formed by two Afro-alpine species, S. albocaudata (east of GRV) and the undescribed Stenocephalemys sp. A (west of GRV). There is a clear elevational gradient in the distribution of the Stenocephalemys taxa with two to three species present at different elevations of the same mountain range. Surprisingly, the nuclear species tree corresponded only a little to the mtDNA tree. Multispecies coalescent models based on six nuclear markers revealed the presence of six separate gene pools (i.e. candidate species), with different topology. Phylogenetic analysis, together with the geographic distribution of the genetic groups, suggests a complex reticulate evolution. We propose a scenario that involves (besides classical allopatric speciation) two cases of disruptive selection along the elevational ecological gradient, multiple crosses of GRV in dry and cold periods of the Pleistocene, followed by hybridization and mtDNA introgression on imperfect reproductive barrier
ISSN:1055-7903
1095-9513
DOI:10.1016/j.ympev.2017.09.020