title: Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River.
abstract: The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.
authors.affiliation: Department of Biology, York College/The City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11451, USA.|The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.|The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.
authors.forename: S Elizabeth
authors.identifier: http://orcid.org/0000-0003-0597-9206
authors.initials: SE
authors.lastname: Alter
authors.affiliation: Louis Calder Center-Biological Field Station, Fordham University, Armonk, NY, 10504, USA.
authors.forename: Jason
authors.identifier: http://orcid.org/0000-0002-8067-4341
authors.initials: J
authors.lastname: Munshi-South
authors.affiliation: The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.|Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.
authors.forename: Melanie L J
authors.initials: ML
authors.lastname: Stiassny
mesh_terms: D000818:Animals; D023681:Cichlids / Q000145:classification*; D003223:Congo; D004272:DNA, Mitochondrial; D019143:Evolution, Molecular; D005260:Female; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D045483:Rivers; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: African biogeography; RAD-Seq; diversification; fish; phylogeography