title: Evaluating topological conflict in centipede phylogeny using transcriptomic data sets.
abstract: Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.
authors.affiliation: Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.
authors.forename: Rosa
authors.initials: R
authors.lastname: Fernández
authors.affiliation: Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Laumer
authors.affiliation: Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MAZoological Museum, Department of Biology, University of Turku, Turku, Finland.
authors.forename: Varpu
authors.initials: V
authors.lastname: Vahtera
authors.affiliation: Marine Science Center, Northeastern University, Nahant, MA.
authors.forename: Silvia
authors.initials: S
authors.lastname: Libro
authors.affiliation: Marine Science Center, Northeastern University, Nahant, MA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Kaluziak
authors.affiliation: Division of Invertebrate Zoology, American Museum of Natural History, New York, NY.
authors.forename: Prashant P
authors.initials: PP
authors.lastname: Sharma
authors.affiliation: Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MACentre d'Estudis Avançats de Blanes (CEAB-CSIC), Catalonia, Spain.
authors.forename: Alicia R
authors.initials: AR
authors.lastname: Pérez-Porro
authors.affiliation: Department of Earth Sciences, The Natural History Museum, London, United Kingdom.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Edgecombe
authors.affiliation: Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA ggiribet@g.harvard.edu.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Giribet
mesh_terms: D000818:Animals; D001181:Arthropods / Q000145:classification* / Q000235:genetics*; D001499:Bayes Theorem; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D016013:Likelihood Functions; D010802:Phylogeny; D059467:Transcriptome
keywords: Chilopoda; Illumina; Myriapoda; incongruence; molecular dating; next-generation sequencing; phylogenomics