Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species
Emese Meglécz1,2*, Gabriel Nève1,2, Ed Biffin3, Michael G. Gardner2,3,4
1 IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France, 2 School of Biological Sciences, Flinders University, Adelaide, Australia, 3 Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, Adelaide, Australia, 4 Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
Abstract
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
Citation: Meglécz E, Nève G, Biffin E, Gardner MG (2012) Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species. PLoS ONE 7(7): e40861. doi:10.1371/journal.pone.0040861
Editor: Richard Cordaux, University of Poitiers, France
Received: March 19, 2012; Accepted: June 14, 2012; Published: July 16, 2012
Copyright: © 2012 Meglécz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Development of this work was funded by institutional support from the Flinders University and the Department of Environment and Natural Resources South Australia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: emese.meglecz@imbe.fr
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NOTA DESTE BLOGGER:
A Árvore da Vida de Darwin deveria ser mostrada pelo DNA, mas não mostra. Por que??? Os autores não tiveram a coragem de dizer que a teoria da evolução de Darwin está errada, mas é o que a pesquisa deles revela! Os dados não revelam um padrão filogenético, mas design comum com alguma variação!!!
A Árvore da Vida de Darwin deveria ser mostrada pelo DNA, mas não mostra. Por que??? Os autores não tiveram a coragem de dizer que a teoria da evolução de Darwin está errada, mas é o que a pesquisa deles revela! Os dados não revelam um padrão filogenético, mas design comum com alguma variação!!!
