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      Independently Evolving Species in Asexual Bdelloid Rotifers

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          Abstract

          Asexuals are an important test case for theories of why species exist. If asexual clades displayed the same pattern of discrete variation as sexual clades, this would challenge the traditional view that sex is necessary for diversification into species. However, critical evidence has been lacking: all putative examples have involved organisms with recent or ongoing histories of recombination and have relied on visual interpretation of patterns of genetic and phenotypic variation rather than on formal tests of alternative evolutionary scenarios. Here we show that a classic asexual clade, the bdelloid rotifers, has diversified into distinct evolutionary species. Intensive sampling of the genus Rotaria reveals the presence of well-separated genetic clusters indicative of independent evolution. Moreover, combined genetic and morphological analyses reveal divergent selection in feeding morphology, indicative of niche divergence. Some of the morphologically coherent groups experiencing divergent selection contain several genetic clusters, in common with findings of cryptic species in sexual organisms. Our results show that the main causes of speciation in sexual organisms, population isolation and divergent selection, have the same qualitative effects in an asexual clade. The study also demonstrates how combined molecular and morphological analyses can shed new light on the evolutionary nature of species.

          Author Summary

          The evolution of distinct species has often been considered a property solely of sexually reproducing organisms. In fact, however, there is little evidence as to whether asexual groups do or do not diversify into species. We show that a famous group of asexual animals, the bdelloid rotifers, has diversified into distinct species broadly equivalent to those found in sexual groups. We surveyed diversity within a single clade, the genus Rotaria, from a range of habitats worldwide, using DNA sequences and measurements of jaw morphology from scanning electron microscopy. New statistical methods for the combined analysis of morphology and DNA sequence data confirmed two fundamental properties of species, namely, independent evolution and ecological divergence by natural selection. The two properties did not always coincide to define unambiguous species groups, but this finding is common in sexual groups as well. The results show that sex is not a necessary condition for speciation. The methods offer the potential for increasing our understanding of the nature of species boundaries across a wide range of organisms.

          Abstract

          New analyses of genetic and morphological data reveal that the bdelloid rotifers, a famous asexual group, have diversified into distinct species and that sex is not a necessary condition for speciation.

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          R: A Language and Environment for Statistical Computing.

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            Molecular signatures of natural selection.

            There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. The interest stems from a basic desire to learn more about evolutionary processes in humans and other organisms, and from the realization that inferences regarding selection may provide important functional information. This review provides a nonmathematical description of the issues involved in detecting selection from DNA sequences and SNP data and is intended for readers who are not familiar with population genetic theory. Particular attention is placed on issues relating to the analysis of large-scale genomic data sets.
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              Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

              Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS Biol
                pbio
                PLoS Biology
                Public Library of Science (San Francisco, USA )
                1544-9173
                1545-7885
                April 2007
                20 March 2007
                : 5
                : 4
                : e87
                Affiliations
                [1 ] Dipartimento di Biologia, Università di Milano, Milan, Italy
                [2 ] Division of Biology, Imperial College London, Ascot, United Kingdom
                [3 ] Natural Environment Research Council Centre for Population Biology, Imperial College London, Ascot, United Kingdom
                [4 ] Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom
                [5 ] Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
                Duke University, United States of America
                Author notes
                * To whom correspondence should be addressed. E-mail: t.barraclough@ 123456imperial.ac.uk
                Article
                06-PLBI-RA-1689R3 plbi-05-04-12
                10.1371/journal.pbio.0050087
                1828144
                17373857
                ad584272-e89a-46a9-b7bd-094cce363400
                Copyright: © 2007 Fontaneto e 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.
                History
                : 11 September 2006
                : 26 January 2007
                Page count
                Pages: 8
                Categories
                Research Article
                Computational Biology
                Ecology
                Ecology
                Ecology
                Ecology
                Evolutionary Biology
                Evolutionary Biology
                Evolutionary Biology
                Genetics and Genomics
                Animals
                Custom metadata
                Fontaneto D, Herniou EA, Boschetti C, Caprioli M, Melone G, et al. (2007) Independently evolving species in asexual bdelloid rotifers. PLoS Biol 5(4): e87. doi: 10.1371/journal.pbio.0050087

                Life sciences
                Life sciences

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