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      Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase I

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      Molecular Phylogenetics and Evolution

      Elsevier BV

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          Most cited references 25

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          The Limits of Amino Acid Sequence Data in Angiosperm Phylogenetic Reconstruction

           Kare Bremer (1988)
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            Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.

            Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.
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              Higher level relationships of leeches (Annelida: Clitellata: Euhirudinea) based on morphology and gene sequences.

              The evolutionary patterns of divergence of seven euhirudinean families were investigated by cladistic analysis of 33 euhirudinean species. Oligochaetes, Acanthobdella peledina, and branchiobdellidans were included as outgroup taxa. Cladistic analysis employed 1.8 kb of nuclear 18S ribosomal DNA and 651 bp of mitochondrial cytochrome c oxidase subunit I in addition to morphological data. The use of two molecular data sets, one nuclear gene and one mitochondrial gene, as well as morphological data combined historical information evolving under a variety of different constraints and therefore was less susceptible to the biases that could confound the use of only one type of data. Results suggest that the nuclear 18S rDNA gene yields a meaningful historical signal for determining higher level relationships. The more rapidly evolving CO-I gene was informative for recent or local areas of the evolutionary hypothesis, such as within-family relationships. Analyses combining all data from the three character sets yielded one most-parsimonious tree. Most of the higher taxa in recent leech systematics were well corroborated in the resulting topology. However, these results suggested paraphyly of the order Rhynchobdellida, which contradicts the presence of a proboscis as a synapomorphy. The medicinal leech family Hirudinidae was polyphyletic because Haemadipsidae and Haemopidae each have a hirudinid ancestor. In addition, all but one of the genera within the family Erpobdellidae must be either abandoned or renamed. Unusual findings included compelling evidence of historical plasticity in bloodfeeding behavior, having been lost at least four times in the course of euhirudinean evolution. Biogeographic patterns supported a New World origin for Arhynchobdellida. Copyright 1999 Academic Press.
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                Author and article information

                Journal
                Molecular Phylogenetics and Evolution
                Molecular Phylogenetics and Evolution
                Elsevier BV
                10557903
                January 2004
                January 2004
                : 30
                : 1
                : 50-63
                Article
                10.1016/S1055-7903(03)00180-5
                © 2004

                http://www.elsevier.com/tdm/userlicense/1.0/

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