@article{Hulsey2017-09Phylo-40060,
  year={2017},
  doi={10.1016/j.ympev.2017.05.027},
  title={Phylogenomic analysis of Lake Malawi cichlid fishes : Further evidence that the three-stage model of diversification does not fit},
  volume={114},
  issn={1055-7903},
  journal={Molecular Phylogenetics and Evolution},
  pages={40--48},
  author={Hulsey, Christopher Darrin and Zheng, Jimmy and Faircloth, Brant C. and Meyer, Axel and Alfaro, Michael E.}
}

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    <dc:contributor>Alfaro, Michael E.</dc:contributor>
    <dc:creator>Hulsey, Christopher Darrin</dc:creator>
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    <dc:contributor>Zheng, Jimmy</dc:contributor>
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    <dcterms:title>Phylogenomic analysis of Lake Malawi cichlid fishes : Further evidence that the three-stage model of diversification does not fit</dcterms:title>
    <dc:language>eng</dc:language>
    <dc:creator>Meyer, Axel</dc:creator>
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    <dc:creator>Faircloth, Brant C.</dc:creator>
    <dc:creator>Alfaro, Michael E.</dc:creator>
    <dcterms:abstract xml:lang="eng">Adaptive radiations could often occur in discrete stages. For instance, the species flock of ∼1000 species of Lake Malawi cichlid fishes might have only diverged once between rocky and sandy environments during the initial stage of their diversification. All further diversification within the rock-dwelling (mbuna) or sand-dwelling (utaka) cichlids would have occurred during a subsequent second stage of extensive trophic evolution that was followed by a third stage of sexual trait divergence. We provide an improved phylogenetic framework for Malawi cichlids to test this three-stage hypothesis based on newly reconstructed phylogenetic relationships among 32 taxonomically disparate Malawi cichlids species. Using several reconstruction methods and 1037 ultra-conserved element (UCE) markers, we recovered a molecular phylogeny that confidently resolved relationships among most of the Malawi lineages sampled when a bifurcating framework was enforced. These bifurcating reconstructions also indicated that the sand-dwelling species Cyathochromis obliquidens was well-nested within the primarily rock-dwelling radiation known as the mbuna. In contrast to predictions from the three-stage model of vertebrate diversification, the recovered phylogeny reveals an initial colonization of rocky reefs, followed by substantial diversification of rock-dwelling lineages, and then at least one instance of subsequent evolution back into sandy habitats. This repeated evolution into major habitat types provides further evidence that the three-stage model of Malawi cichlid diversification has numerous exceptions.</dcterms:abstract>
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