The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura,Microhylidae) |
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| Authors: | Pedro L.V. Peloso Darrel R. Frost Stephen J. Richards Miguel T. Rodrigues Stephen Donnellan Masafumi Matsui Cristopher J. Raxworthy S.D. Biju Emily Moriarty Lemmon Alan R. Lemmon Ward C. Wheeler |
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| Affiliation: | 1. Division of Vertebrate Zoology (Herpetology), American Museum of Natural History, New York, NY, USA;2. Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA;3. Herpetology Department, South Australian Museum, Adelaide, SA, Australia;4. Departamento de Zoologia, Instituto de Biociências, Universidade de S?o Paulo, Rua do Mat?o, S?o Paulo, S?o Paulo, Brazil;5. Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA, Australia;6. Graduate School of Human and Environmental Studies, Kyoto University, Sakyo‐ku, Kyoto, Japan;7. Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India;8. Department of Biological Science, Florida State University, Tallahassee, FL, USA;9. Department of Scientific Computing, Florida State University, Tallahassee, FL, USA;10. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA |
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| Abstract: | Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum‐likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree‐alignment framework are generally better resolved and better supported than those inferred within a similarity‐alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model‐based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic. |
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