Blog
About

43
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

      Read this article at

      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

          The onset of prezygotic and postzygotic barriers to gene flow between populations is a hallmark of speciation. One of the earliest postzygotic isolating barriers to arise between incipient species is the sterility of the heterogametic sex in interspecies' hybrids. Four genes that underlie hybrid sterility have been identified in animals: Odysseus, JYalpha, and Overdrive in Drosophila and Prdm9 ( Meisetz) in mice. Mouse Prdm9 encodes a protein with a KRAB motif, a histone methyltransferase domain and several zinc fingers. The difference of a single zinc finger distinguishes Prdm9 alleles that cause hybrid sterility from those that do not. We find that concerted evolution and positive selection have rapidly altered the number and sequence of Prdm9 zinc fingers across 13 rodent genomes. The patterns of positive selection in Prdm9 zinc fingers imply that rapid evolution has acted on the interface between the Prdm9 protein and the DNA sequences to which it binds. Similar patterns are apparent for Prdm9 zinc fingers for diverse metazoans, including primates. Indeed, allelic variation at the DNA–binding positions of human PRDM9 zinc fingers show significant association with decreased risk of infertility. Prdm9 thus plays a role in determining male sterility both between species (mouse) and within species (human). The recurrent episodes of positive selection acting on Prdm9 suggest that the DNA sequences to which it binds must also be evolving rapidly. Our findings do not identify the nature of the underlying DNA sequences, but argue against the proposed role of Prdm9 as an essential transcription factor in mouse meiosis. We propose a hypothetical model in which incompatibilities between Prdm9-binding specificity and satellite DNAs provide the molecular basis for Prdm9-mediated hybrid sterility. We suggest that Prdm9 should be investigated as a candidate gene in other instances of hybrid sterility in metazoans.

          Author Summary

          Speciation, the process by which one species splits into two, involves reproductive barriers between previously interbreeding populations. The question of how speciation occurs has rightly occupied the attention of biologists since before Darwin's “On the Origin of Species.” Studies of recently diverged species have revealed the presence of hybrid sterility genes (colloquially referred to as “speciation genes”), alleles of which are associated with sterility of interspecies hybrids. Mouse Prdm9 is the only known such gene in vertebrate animals. Here we report that the Prdm9 protein has evolved extremely rapidly in its DNA-binding domain, comprising an array of “zinc fingers.” This suggests that hybrid sterility may arise from a mismatch between the DNA-binding specificity of Prdm9 and rapidly evolving DNA. We propose that Prdm9 binds to satellite-DNA repeats evolving rapidly within and between different species. Prdm9 evolution is unusual because other hybrid sterility genes appear only to evolve rapidly in isolated bursts, whereas Prdm9 has evolved rapidly over 700 million years, in many rodent species, diverse primates and other metazoans. This leads to the tantalizing possibility that Prdm9 may have served as a “speciation gene” on other occasions in metazoan evolution, a possibility that will now need to be investigated.

          Related collections

          Most cited references 70

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

          A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

          The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            PAML 4: phylogenetic analysis by maximum likelihood.

             Ziheng Yang (2007)
            PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

               F Tajima (1989)
              The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
                Bookmark

                Author and article information

                Affiliations
                [1 ]Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
                [2 ]Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
                [3 ]Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
                [4 ]Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
                [5 ]School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
                [6 ]Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
                University of Arizona, United States of America
                Author notes

                Conceived and designed the experiments: PLO LG JJB GL HSM CPP. Performed the experiments: PLO LG ZB KCR GL HSM. Analyzed the data: LG. Contributed reagents/materials/analysis tools: SAB. Wrote the paper: PLO LG JJB KCR NP GL HSM CPP.

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, USA )
                1553-7390
                1553-7404
                December 2009
                December 2009
                4 December 2009
                : 5
                : 12
                2779102
                19997497
                09-PLGE-RA-0852R3
                10.1371/journal.pgen.1000753
                (Editor)
                Oliver 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.
                Counts
                Pages: 14
                Categories
                Research Article
                Evolutionary Biology
                Evolutionary Biology/Evolutionary and Comparative Genetics
                Evolutionary Biology/Human Evolution
                Genetics and Genomics/Bioinformatics
                Genetics and Genomics/Gene Function
                Molecular Biology/Bioinformatics
                Molecular Biology/Molecular Evolution

                Genetics

                Comments

                Comment on this article