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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Parasites constitute a strong selective force in nature, and organisms evolve defence mechanisms to cope with them. The central questions of this thesis are how these mechanisms evolve and are encoded in the genome, and how they can be lost during evolution. My research focused on an immune response called melanotic encapsulation, which is used by Drosophila fruitflies to survive attacks by parasitoid wasps that lay their eggs in the fruitfly larvae. Drosophila species and populations vary largely in how successful they are in surviving parasitoid attack, with some species completely lacking the ability to resist. My research indicates that this defence mechanism evolved recently in a subgroup of Drosophila species that contains D. melanogaster. Its evolution is associated with the acquisition of new genes and a new type of blood cells. Comparisons among Drosophila species and populations of D. melanogaster revealed considerable variation in the expression of some of these genes. Inside the group of species able to resist, the encapsulation ability was lost in the endemic island species D. sechellia that specialized on a fruit that can be toxic to other insects. My experiments and field study showed a reduced risk of parasitoid attack in these fruits. In conclusion, by combining evolutionary genomics with ecological information, I characterized the components that enable some Drosophila species to mount a successful immune response to a lethal parasitoid infection, how this response is modulated among populations of one species and how it was lost in a particular ecological setting
    12/2014, Degree: PhD, Supervisor: Bregje Wertheim, Leo Beukeboom
  • [Show abstract] [Hide abstract]
    ABSTRACT: Ethanol-induced locomotor stimulation has been variously described as reflective of the disinhibitory, euphoric, or reinforcing effects of ethanol and is commonly used as an index of acute ethanol sensitivity in rodents. The fruit fly Drosophila melanogaster also shows a locomotor stimulant response to ethanol that is believed to occur via conserved, ethanol-sensitive neurobiological mechanisms, but it is currently unknown whether this response is conserved among arthropod species or is idiosyncratic to D. melanogaster. The current experiments surveyed locomotor responses to ethanol in a phylogenetically diverse panel of insects and other arthropod species. A clear ethanol-induced locomotor stimulant response was seen in 9 of 13 Drosophilidae species tested, in 8 of 10 other species of insects, and in an arachnid (wolf spider) and a myriapod (millipede) species. Given the diverse phylogenies of the species that showed the response, these experiments support the hypothesis that locomotor stimulation is a conserved behavioral response to ethanol among arthropod species. Further comparative studies are needed to determine whether the specific neurobiological mechanisms known to underlie the stimulant response in D. melanogaster are conserved among arthropod and vertebrate species. © 2015 S. Karger AG, Basel.
    Brain Behavior and Evolution 02/2015; DOI:10.1159/000370099 · 4.29 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Dicer, an ribonuclease type III type endonuclease, is the key enzyme involved in biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs), and thus plays a critical role in RNA interference through post transcriptional regulation of gene expression. This enzyme has not been well studied in the Indian water buffalo, an important species known for disease resistance and high milk production. In this study, the primary coding sequence (5,778 bp) of bubaline dicer (GenBank: AB969677.1) was determined and the bubaline Dicer1 biocomputationally characterized to determine the phylogenetic signature among higher eukaryotes. The evolutionary tree revealed that all the transcript variants of Dicer1 belonging to a specific species were within the same node and the sequences belonging to primates, rodents and lagomorphs, avians and reptiles formed independent clusters. The bubaline dicer1 is closely related to that of cattle and other ruminants and significantly divergent from dicer of lower species such as tapeworm, sea urchin and fruit fly. Evolutionary divergence analysis conducted using MEGA6 software indicated that dicer has undergone purifying selection over the time. Seventeen divergent sequences, representing each of the families/taxa were selected to study the specific regions of positive vis-à-vis negative selection using different models like single likelihood ancestor counting, fixed effects likelihood, and random effects likelihood of Datamonkey server. Comparative analysis of the domain structure revealed that Dicer1 is conserved across mammalian species while variation both in terms of length of Dicer enzyme and presence or absence of domain is evident in the lower organisms.
    Asian Australasian Journal of Animal Sciences 02/2015; 28(6). DOI:10.5713/ajas.14.0767 · 0.56 Impact Factor


Available from