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BYU BIO 465 - Pancrustacean phylogeny

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Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyleticIntroductionMaterial and methodsTaxon sampling and data generationPhylogenetic analysesDivergence time estimatesResults and discussionAssessing node supportMonophyly of Pancrustacea, Myriapoda and Chelicerata, but uncertain interrelationshipsMajor splits within PancrustaceaAbsolute divergence timesREFERENCESProc. R. Soc. B (2005) 272, 395–401doi:10.1098/rspb.2004.2917Published online 21 February 2005Pancrustacean phylogeny: hexapods are terrestrialcrustaceans and maxillopods are not monophyleticJerome C. Regier1, Jeffrey W. Shultz2and Robert E. Kambic21Center for Biosystems Research, University of Maryland Biotechnology Institute, and2Department of Entomology, Universityof Maryland, College Park, MD 20742, USARecent molecular analyses indicate that crustaceans and hexapods form a clade (Pancrustacea or Tetra-conata), but relationships among its constituent lineages, including monophyly of crustaceans, are contro-versial. Our phylogenetic analysis of three protein-coding nuclear genes from 62 arthropods and lobopods(Onychophora and Tardigrada) demonstrates that Hexapoda is most closely related to the crustaceansBranchiopoda (fairy shrimp, water fleas, etc.) and Cephalocarida þ Remipedia, thereby making hexapodsterrestrial crustaceans and the traditionally defined Crustacea paraphyletic. Additional findings are thatMalacostraca (crabs, isopods, etc.) unites with Cirripedia (barnacles, etc.) and they, in turn, with Cope-poda, making the traditional crustacean class Maxillopoda paraphyletic. Ostracoda (seed shrimp)—either allor a subgroup—is associated with Branchiura (fish lice) and likely to be basal to all other pancrustaceans. ABayesian statistical (non-clock) estimate of divergence times suggests a Precambrian origin for Pancrustacea(600 Myr ago or more), which precedes the first unambiguous arthropod fossils by over 60 Myr.Keywords: arthropod phylogeny; Cambrian explosion; Crustacea; Hexapoda; molecular systematics;Pancrustacea1. INTRODUCTIONEstablishing phylogenetic relationships among the majorarthropod groups, especially the hyper-speciose Hexapodaand the morphologically diverse Crustacea, would be amajor advance toward resolving the tree of life. Recentmolecular analyses indicate that hexapods and crustaceansform a clade (Pancrustacea or Tetraconata) (Friedrich &Tautz 1995; Boore et al. 1998; Giribet et al. 2001; Regier &Shultz 2001; Mallatt et al. 2004), but relationships amongits constituent lineages are controversial (Spears & Abele1998; Giribet et al. 2001; Martin & Davis 2001; Regier &Shultz 2001; Lavrov et al. 2004; Mallatt et al. 2004).Resolving these lineages would provide an improved phylo-genetic context for documenting the many complexmorphological transformations that have occurred duringarthropod evolution. Clarifying the role of homoplasy (i.e.parallelisms due to constraints and convergences due tonatural selection) would be another benefit of a robust phy-logeny. Unfortunately, identifying sufficient characters torobustly resolve closely spaced Palaeozoic (or earlier)divergences has been a challenge. Sequence data from mul-tiple, appropriately evolving, protein-coding nuclear geneshave been successfully used to resolve other lineages (see,for example, Murphy et al. 2001) and also hold promise forarthropods. We address relationships within Pancrustaceaby analysing sequence data from three such genes andstrongly resolve relationships of several major groups.2. MATERIAL AND METHODS(a) Taxon sampling and data generationSixty-two species of Arthropoda, Tardigrada and Onychophorawere sampled (see table S1 in electronic Appendix A). SpecificRNA sequences were amplified by reverse transcription followedby polymerase chain reaction (PCR); gel-isolated PCR fragmentswere then reamplified using nested PCR, re-gel-isolated andsequenced; sequences were assembled and datasets for phylogen-etic analyses constructed (see references in Regier & Shultz(2001)). Sequence data were derived from three genes: elongationfactor-1a (1131 nucleotides), the largest subunit of RNA poly-merase II (2025 nucleotides) and elongation factor-2 (2178nucleotides). GenBank numbers (see table S1 in electronicAppendix A) and the aligned nucleotide dataset (see dataset in theelectronic Appendices or go to www.umbi.umd.edu/users/jcrlab/Arthropoda3gn2004.doc) are available.(b) Phylogenetic analysesNucleotides with third codon positions removed from the3-gene concatenated sequence were analysed by maximum parsi-mony under equal weights and by maximum likelihood (Swofford2002). The latter incorporated a general time reversible modelwith among-site-rate-variation modelled by a gamma distributionplus a separate parameter for invariable sites. Concatenatedamino acids (conceptually translated in MACCLADE; Maddison &Maddison 2002) were analysed by maximum parsimony underequal weights (Swofford 2002), a Bayesian statistical approach(Huelsenbeck & Ronquist 2001) using the Jones, Taylor andThornton model (Jones et al. 1992), and a modified-likelihoodapproach (Adachi & Hasegawa 1994), in which the favouredprotml tree was selected from the 91 673 most-parsimonious trees(tree lengths ¼ 68536861). Non-parametric bootstrap analyses(Felsenstein 1985) were performed for all approaches exceptprotml. To calculate bootstrap values for the Bayesian analysis, wewrote a computer program in C (called BP_link, freely down-loadable from http://www.umbi.umd.edu/users/jcrlab) that semi-automates this process by linking already available softwarepackages. This allowed a direct comparison of bootstrap percent-ages and posterior probabilities.Author for correspondence ([email protected]).Received 17 May 2004Accepted 26 August 2004395#2005 The Royal Society(c) Divergence time estimatesDivergence time estimates at 12 nodes were performed using aMarkov chain Monte Carlo procedure for Bayesian analysis ofamino acid sequences (Thorne & Kishino 2002) from 17 diversearthropods, one onychophoran and one tardigrade. Evolutionaryrates at adjoining nodes were assumed to be autocorrelated ratherthan following a strict molecular clock, and individual genes wereassigned separate autocorrelation parameters. Fossil-basedboundary conditions were also incorporated (Benton 1993).More details can be found in the legend to figure S1 (seeelectronic Appendices).3. RESULTS AND DISCUSSION(a) Assessing node supportIn the current study, 40 new


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BYU BIO 465 - Pancrustacean phylogeny

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