Article

Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes.

Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.
Genome Research (Impact Factor: 13.85). 01/2008; 17(12):1837-49. DOI: 10.1101/gr.6249707
Source: PubMed

ABSTRACT The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding genes were predicted using established Drosophila melanogaster genes as templates, with recovery rates ranging from 81%-97% depending on species divergence and on genome assembly quality. Orthology and paralogy assignments were shown to be self-consistent among the different Drosophila species and to be consistent with regions of conserved gene order (synteny blocks). Next, we investigated the rates of diversification among these species' gene repertoires with respect to amino acid substitutions and to gene duplications. Constraints on amino acid sequences appear to have been most pronounced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages. Codons predicted to have been subject to positive selection were found to be significantly over-represented among genes with roles in immune response and RNA metabolism, with the latter category including each subunit of the Dicer-2/r2d2 heterodimer. The vast majority of gene duplications (96.5%) and synteny rearrangements were found to occur, as expected, within single Müller elements. We show that the rate of ancient gene duplications was relatively uniform. However, gene duplications in terminal lineages are strongly skewed toward very recent events, consistent with either a rapid-birth and rapid-death model or the presence of large proportions of copy number variable genes in these Drosophila populations. Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins.

0 Bookmarks
 · 
85 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes – a marker of the effective population size – in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.
    Journal of Evolutionary Biology 02/2014; · 3.48 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The evolutionary impact of gene duplication events has been a theme of Drosophila genetics dating back to the Morgan School. While considerable attention has been placed on the genetic novelties that duplicates are capable of introducing, and the role that positive selection plays in their early stages of duplicate evolution, much less attention has been given to the potential consequences of ectopic (non-allelic) gene conversion on these evolutionary processes. In this paper we consider the historical origins of ectopic gene conversion models and present a synthesis of the current Drosophila data in light of several primary questions in the field.
    Genes. 12/2011; 2(1):131-51.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Graphical Abstract Highlights d Genome and two transcriptomes of the bowhead whale, the longest-lived mammal d Bowhead-specific mutations in genes associated with cancer and aging (e.g., ERCC1) d Duplications in genes associated with DNA repair, cell cycle, and aging (e.g., PCNA) d Changes in genes related to thermoregulation (UCP1) and other bowhead traits Correspondence jp@senescence.info In Brief The bowhead whale is the longest-lived mammal, possibly living over 200 years. Keane et al. sequence the bowhead genome and transcriptome and perform a comparative analysis with other cetaceans and mammals. Changes in bowhead genes related to cell cycle, DNA repair, cancer, and aging suggest alterations that may be biologically relevant.
    Cell Reports 01/2015; 10(1):112-122. · 7.21 Impact Factor

Preview

Download
0 Downloads
Available from