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      Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

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          Abstract

          Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

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          Most cited references 93

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          Gene Trees in Species Trees

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            The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

             Kevin Nixon (1999)
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              Is a new and general theory of molecular systematics emerging?

              The advent and maturation of algorithms for estimating species trees-phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes-represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a "local optimum" for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term "phylogeny" for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.
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                Author and article information

                Journal
                Biology (Basel)
                Biology (Basel)
                biology
                Biology
                MDPI
                2079-7737
                13 March 2013
                March 2013
                : 2
                : 1
                : 419-444
                Affiliations
                [1 ]Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: tyuri@ 123456ou.edu (T.Y.); rkimball@ 123456ufl.edu (R.T.K.); kixs4@ 123456uga.edu (J.L.C.); hankin@ 123456ufl.edu (K.-L.H.)
                [2 ]Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
                [3 ]4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail: jharshman@ 123456pacbell.net
                [4 ]Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail: bowie@ 123456berkeley.edu
                [5 ]Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: braunm@ 123456si.edu (M.J.B.); huddlestonc@ 123456si.edu (C.J.H.)
                [6 ]Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
                [7 ]Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail: shackett@ 123456fieldmuseum.org
                [8 ]Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail: wmoore1415@ 123456gmail.com
                [9 ]Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail: sreddy6@ 123456luc.edu
                [10 ]Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail: fsheld@ 123456lsu.edu
                [11 ]Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail: dws@ 123456flmnh.ufl.edu
                [12 ]Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail: cwitt@ 123456unm.edu
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: ebraun68@ 123456ufl.edu ; Tel.: +1-352-846-1124; Fax: +1-352-392-3704.
                Article
                biology-02-00419
                10.3390/biology2010419
                4009869
                88dd72d7-4a2f-4383-904d-39f6c42a5092
                © 2013 by the authors; licensee MDPI, Basel, Switzerland.

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).

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