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A Phylogenomic Framework, Evolutionary Timeline, and Genomic Resources for Comparative Studies of Decapod Crustaceans

View ORCID ProfileJoanna M. Wolfe, Jesse W. Breinholt, View ORCID ProfileKeith A. Crandall, Alan R. Lemmon, Emily Moriarty Lemmon, View ORCID ProfileLaura E. Timm, Mark E. Siddall, Heather D. Bracken-Grissom
doi: https://doi.org/10.1101/466540
Joanna M. Wolfe
1Division of Invertebrate Zoology & Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
2Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3Museum of Comparative Zoology & Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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  • For correspondence: jowolfe@mit.edu hbracken@fiu.edu
Jesse W. Breinholt
4Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
5RAPiD Genomics, Gainesville, FL 32601, USA
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Keith A. Crandall
6Computational Biology Institute, The George Washington University, Ashburn, VA 20147, USA
7Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20012, USA
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Alan R. Lemmon
8Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306, USA
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Emily Moriarty Lemmon
9Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Laura E. Timm
10Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
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Mark E. Siddall
1Division of Invertebrate Zoology & Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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Heather D. Bracken-Grissom
10Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
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  • For correspondence: jowolfe@mit.edu hbracken@fiu.edu
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Abstract

Comprising over 15,000 living species, decapods (crabs, shrimp, and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (>86,000 bp) conserved across all lineages of Decapoda, eight times more molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, ‘lobster’, and ‘crab’ groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Paleozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behavior, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

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Posted November 09, 2018.
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A Phylogenomic Framework, Evolutionary Timeline, and Genomic Resources for Comparative Studies of Decapod Crustaceans
Joanna M. Wolfe, Jesse W. Breinholt, Keith A. Crandall, Alan R. Lemmon, Emily Moriarty Lemmon, Laura E. Timm, Mark E. Siddall, Heather D. Bracken-Grissom
bioRxiv 466540; doi: https://doi.org/10.1101/466540
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A Phylogenomic Framework, Evolutionary Timeline, and Genomic Resources for Comparative Studies of Decapod Crustaceans
Joanna M. Wolfe, Jesse W. Breinholt, Keith A. Crandall, Alan R. Lemmon, Emily Moriarty Lemmon, Laura E. Timm, Mark E. Siddall, Heather D. Bracken-Grissom
bioRxiv 466540; doi: https://doi.org/10.1101/466540

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