DOI: 10.5061/dryad.4v875
title: Data from: The emergence of the lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida)

description: Lobsters are a ubiquitous and economically important group of decapod
 crustaceans that includes the infraorders Polychelida, Glypheidea,
 Astacidea and Achelata. They include familiar forms such as the spiny,
 slipper, clawed lobsters and crayfish and unfamiliar forms such as the
 deep-sea and “living fossil” species. The high degree of morphological
 diversity among these infraorders has led to a dynamic classification and
 conflicting hypotheses of evolutionary relationships. In this study, we
 estimated phylogenetic relationships amongst the major groups of all
 lobster families and 94% of the genera using 6 genes (mitochondrial and
 nuclear) and 195 morphological characters across 173 species of lobsters
 for the most comprehensive sampling to date. Lobsters were recovered as a
 non-monophyletic assemblage in the combined (molecular + morphology)
 analysis. All families were monophyletic, with the exception of
 Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A
 rich fossil history coupled with dense taxon coverage allowed us to
 estimate and compare divergence times and origins of major lineages using
 two drastically different approaches. Age priors were constructed and/or
 included based on fossil age information or fossil discovery, age, and
 extant species count data. Results from the two approaches were largely
 congruent across deep to shallow taxonomic divergences across major
 lineages. The origin of the first lobster-like decapod (Polychelida) was
 estimated in the Devonian (~409-372 million years ago (Ma)) with all
 infraorders present in the Carboniferous (~353-318 Ma). Fossil calibration
 subsampling studies examined the influence of sampling density (number of
 fossils) and placement (deep, middle, shallow) on divergence time
 estimates. Results from our study suggest including at least 1 fossil per
 10 operational taxonomic units (OTUs) in divergence dating analyses.
description: NEWAppendix
 1_Jan_2014Taxonomy, voucher
 catalog numbers, and GenBank accession numbers for gene sequences used in
 study. An “N/A” (not available) indicates missing sequence
 data.Appendix 1_Final_Table ALL
 EDITS.xlsAppendix 2_ATOL Lobsters
 morpho listMorphological characters
 and states used in combined Bayesian analysis.Appendix
 3_morphomatrixMorphomatrix used in
 combined Bayesian analysisNEWAppendix
 4_morpho_FINALPhylogenetic tree based
 on 156 morphological charactersAppendix
 4_morpho_FINAL.pdfNEWAppendix
 5mito_FINAL2Mitochondrial (12S, 16S,
 COI) gene tree for species included in combined
 analysis.Appendix
 5mito_FINAL2.pdfNEWAppendix
 6_18S-FINAL3Maximum likelihood tree
 based on 18S dataAppendix
 6_18S-FINAL3.pdfNEWAppendix
 7_28S_FINAL2Maximum likelihood tree
 based on 28S dataAppendix
 7_28S_FINAL2.pdfNewAppendix_8_H3_FINAL2Maximum Likelihood tree based on H3 dataAppendix_8_H3_FINAL2.pdfNEWAppendix_9_IGTP_FINAL2IGTP Species Tree Analysis for all taxa in this studyAppendix_9_IGTP_FINAL2.pdfNewAppendix 10 Molecular_FINALMaximum likelihood tree based on molecular data (6 genes)Appendix 10 Molecular_FINAL.pdfNEWAppendix 11_PhyloBayes_species_FINALPhylobayes analysis of all taxa in this studyAppendix 11_PhyloBayes_species_FINAL.pdfNewAppendix 12_fossil justificationJustification for each fossil included in the 28 fossil divergence time analysis.Appendix 12_fossil justification.docxAppendix 13Posterior distributions and parameters of τ1, τ2, and τ 3 (BPBP model) used in BEAST.