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      Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

      research-article
      Author(s): ,
      Publication date (Electronic):
      Journal: Ecology and Evolution
      Publisher: Blackwell Publishing Ltd
      Keywords: Ebola virus, filovirus, lineage identity, Marburg virus

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          Abstract

          Filoviruses have to date been considered as consisting of one diverse genus (Ebola viruses) and one undifferentiated genus (Marburg virus). We reconsider this idea by means of detailed phylogenetic analyses of sequence data available for the Filoviridae: using coalescent simulations, we ascertain that two Marburg isolates (termed the “RAVN” strain) represent a quite-distinct lineage that should be considered in studies of biogeography and host associations, and may merit recognition at the level of species. In contrast, filovirus isolates recently obtained from bat tissues are not distinct from previously known strains, and should be considered as drawn from the same population. Implications for understanding the transmission geography and host associations of these viruses are discussed.

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          Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

          Bruce Rannala, Ziheng Yang (2003)
          The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be approximately 20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.
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            Emerging patterns in the comparative analysis of phylogenetic community structure.

            S M Vamosi, S B Heard, J C Vamosi … (2009)
            The analysis of the phylogenetic structure of communities can help reveal contemporary ecological interactions, as well as link community ecology with biogeography and the study of character evolution. The number of studies employing this broad approach has increased to the point where comparison of their results can now be used to highlight successes and deficiencies in the approach, and to detect emerging patterns in community organization. We review studies of the phylogenetic structure of communities of different major taxa and trophic levels, across different spatial and phylogenetic scales, and using different metrics and null models. Twenty-three of 39 studies (59%) find evidence for phylogenetic clustering in contemporary communities, but terrestrial and/or plant systems are heavily over-represented among published studies. Experimental investigations, although uncommon at present, hold promise for unravelling mechanisms underlying the phylogenetic community structure patterns observed in community surveys. We discuss the relationship between metrics of phylogenetic clustering and tree balance and explore the various emerging biases in taxonomy and pitfalls of scale. Finally, we look beyond one-dimensional metrics of phylogenetic structure towards multivariate descriptors that better capture the variety of ecological behaviours likely to be exhibited in communities of species with hundreds of millions of years of independent evolution.
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              On the Genealogy of Large Populations

              J. Kingman (1982)
              Article 0 comments Cited 209 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Ecol Evol
                Journal ID (iso-abbrev): Ecol Evol
                Journal ID (publisher-id): ece3
                Title: Ecology and Evolution
                Publisher: Blackwell Publishing Ltd (Oxford, UK )
                ISSN (Print): 2045-7758
                ISSN (Electronic): 2045-7758
                Publication date (Print): August 2012
                Publication date (Electronic): 01 July 2012
                Volume: 2
                Issue: 8
                Pages: 1826-1833
                Affiliations
                simpleDepartment of Ecology and Evolutionary Biology, The University of Kansas Lawrence, Kansas, 66045
                Author notes
                A. Townsend Peterson, Biodiversity Institute, The University of Kansas, Lawrence, KS 66045. Tel: +1-785-864-3926; Fax: +1-785-864-5335; E-mail: town@ 123456ku.edu

                Funding Information Funded in part by a grant from the National Institutes of Health (R01 TW 8859-3).

                Article
                DOI: 10.1002/ece3.297
                PMC ID: 3433987
                PubMed ID: 22957185
                SO-VID: e75f5e35-efde-4c0d-86ae-c840f855e8c3
                Copyright © © 2012 Published by Blackwell Publishing Ltd.
                License:

                Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

                History
                Date received : 02 March 2012
                Date revision received : 07 May 2012
                Date accepted : 08 May 2012
                Categories
                Subject: Original Research

                ScienceOpen disciplines: Evolutionary Biology
                Keywords: ebola virus,lineage identity,filovirus,marburg virus
                Data availability:
                ScienceOpen disciplines: Evolutionary Biology
                Keywords: ebola virus, lineage identity, filovirus, marburg virus

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