Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands.

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Publisher: Elsevier B.V.
Document Type: Report
Length: 594 words

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Keywords Afrotropics; Anchored phylogenomics; Natatanura; Phylogeography; Reticulate evolution; Taxonomy Highlights * Genomic phylogeography of western Central African montane puddle frogs. * Hybrids form a ladder-like pattern between parental species in phylogenetic trees. * A deep mtDNA divergence is not reflected in genome-wide data. * Hybrids are morphologically intermediate in these largely cryptic frogs. * Biogeographic history of montane forests of the Cameroon Volcanic Line. Abstract Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level -- southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late. Author Affiliation: (a) Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic (b) Masaryk University, Department of Botany and Zoology, Brno, Czech Republic (c) Museum of Comparative Zoology, Harvard University, Cambridge, USA (d) Natural History Museum of Geneva, Geneva, Switzerland (e) University of Buea, Department of Zoology and Animal Physiology, Buea, Cameroon (f) Florida State University, Department of Biological Sciences, Tallahassee, USA (g) Florida State University, Department of Scientific Computing, Dirac Science Library, Tallahassee, USA (h) National Museum, Department of Zoology, Prague, Czech Republic * Corresponding author at: Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Studenec 122, 675 02, Czech Republic. Article History: Received 8 October 2020; Revised 28 June 2021; Accepted 7 July 2021 Byline: Matej Dolinay (a,b), Tadeás Necas (a,b), Breda M. Zimkus (c), Andreas Schmitz (d), Eric B. Fokam (e), Emily Moriarty Lemmon (f), Alan R. Lemmon (g), Václav Gvozdík [] (a,h,*)

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Gale Document Number: GALE|A670338127