Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data

Jacobo Reyes-Velasco, Joseph D. Manthey, Yann Bourgeois, Xenia Freilich, Stephane Boissinot

Research output: Contribution to journalArticle

Abstract

Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon’s range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot. We used thousands of genome-wide SNPs obtained from double digest restriction site associated DNA sequencing (ddRAD-seq) in populations of the Ptychadena neumanni species complex from the Ethiopian highlands in order to infer their phylogenetic relationships and genetic structure, as well as to study their demographic history. Our genome-wide phylogenetic study supports the existence of approximately 13 lineages clustered into 3 species groups. Our phylogenetic and phylogeographic reconstructions suggest that those endemic lineages diversified in allopatry, and subsequently specialized to different habitats and elevations. Demographic analyses point to a continuous decrease in the population size across the majority of lineages and populations during the Pleistocene, which is consistent with a continuous period of aridification that East Africa experienced since the Pliocene. We discuss the taxonomic implications of our analyses and, in particular, we warn against the recent practice to solely use Bayesian species delimitation methods when proposing taxonomic changes.

Original languageEnglish (US)
Article numbere0190440
JournalPLoS One
Volume13
Issue number2
DOIs
StatePublished - Feb 1 2018

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Phylogeography
Taxonomies
phylogeography
demography
Anura
Single Nucleotide Polymorphism
frogs
highlands
Genes
Demography
Genome
taxonomy
Eastern Africa
genome
Genetic Structures
Biodiversity
phylogeny
demographic statistics
Population Density
Poaceae

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. / Reyes-Velasco, Jacobo; Manthey, Joseph D.; Bourgeois, Yann; Freilich, Xenia; Boissinot, Stephane.

In: PLoS One, Vol. 13, No. 2, e0190440, 01.02.2018.

Research output: Contribution to journalArticle

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