Sponsor
This work was supported by grant DEB-0643840 from the National Science Foundation to T.H.O. and by the Center for Scientific Computing at the CNSI and MRL: an NSF MRSEC (DMR-1121053) and NSF CNS-0960316.
Published In
Molecular Biology and Evolution
Document Type
Post-Print
Publication Date
9-12-2012
Subjects
Genomics, Genetic transcription, Fossil ostracoda -- Genetics, Crustacea -- Phylogeny
Abstract
An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, and Pentastomida); Multicrustacea (Copepoda, Malacostraca, and Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, and Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda + Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. However, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a “total evidence” philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylo- genetic insights into long-standing questions, especially when carefully analyzed in combination with other data.
DOI
10.1093/molbev/mss216
Persistent Identifier
http://archives.pdx.edu/ds/psu/10640
Citation Details
Oakley, Todd H., et al. "Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Accepted for publication in: Molecular biology and evolution 30.1 (2013): 215-233.
Included in
Biology Commons, Ecology and Evolutionary Biology Commons, Other Genetics and Genomics Commons
Description
The definitive publisher-authenticated version is available online at: http://mbe.oxfordjournals.org/content/30/1/215
Copyright The Author 2012.
Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.