12
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Previous estimates of a generic level phylogeny for the ubiquitous parasitoid wasp subfamily Microgastrinae (Hymenoptera) have been problematic due to short internal branches deep in the phylogeny. These short branches might be attributed to a rapid radiation among the taxa, the use of genes that are unsuitable for the levels of divergence being examined, or insufficient quantity of data. We added over 1200 nucleotides from four nuclear genes to a dataset derived from three genes to produce a dataset of over 3000 nucleotides per taxon. While the number of well-supported short branches in the phylogeny increased, we still did not obtain strong bootstrap support for every node. Parametric and nonparametric bootstrap simulations projected that an enormous, and likely unobtainable, amount of data would be required to get bootstrap support greater than 50% for every node. However, a marked increase in the number of well-supported nodes was seen when we conducted a Bayesian analysis of a combined dataset generated from morphological characters added to the seven gene dataset. Our results suggest that, in some cases, combining morphological and genetic characters may be the most practical way to increase support for short branches deep in a phylogeny.

          Related collections

          Most cited references68

          • Record: found
          • Abstract: found
          • Article: not found

          Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China.

          Y Guan (2003)
          A novel coronavirus (SCoV) is the etiological agent of severe acute respiratory syndrome (SARS). SCoV-like viruses were isolated from Himalayan palm civets found in a live-animal market in Guangdong, China. Evidence of virus infection was also detected in other animals (including a raccoon dog, Nyctereutes procyonoides) and in humans working at the same market. All the animal isolates retain a 29-nucleotide sequence that is not found in most human isolates. The detection of SCoV-like viruses in small, live wild mammals in a retail market indicates a route of interspecies transmission, although the natural reservoir is not known.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            The general stochastic model of nucleotide substitution.

            DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.

              Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap. Seq-Gen can be obtained by WWW from http:/(/)evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html++ + or by FTP from ftp:/(/)evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites.
                Bookmark

                Author and article information

                Contributors
                Journal
                Mol Phylogenet Evol
                Mol. Phylogenet. Evol
                Molecular Phylogenetics and Evolution
                Elsevier Inc.
                1055-7903
                1095-9513
                7 June 2006
                December 2006
                7 June 2006
                : 41
                : 3
                : 690-703
                Affiliations
                Department of Entomology, University of Illinois, Urbana Champaign, 505 S Goodwin Ave., Urbana, IL 61801, USA
                Author notes
                [* ]Corresponding author. Present address: Department of Biological Sciences, The University of Waikato, Private Bag 3105, Hamilton, New Zealand. Fax: +64 7 838 4123. j.banks@ 123456waikato.ac.nz
                Article
                S1055-7903(06)00231-4
                10.1016/j.ympev.2006.06.001
                7129091
                16854601
                7e2913b5-5259-4e55-a001-d2da11dcf7b7
                Copyright © 2006 Elsevier Inc. All rights reserved.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 24 February 2006
                : 30 May 2006
                : 1 June 2006
                Categories
                Article

                Evolutionary Biology
                bayesian,braconidae,hymenoptera,morphology,support
                Evolutionary Biology
                bayesian, braconidae, hymenoptera, morphology, support

                Comments

                Comment on this article