Dataset Information

Dynamics of Dark-Fly Genome Under Environmental Selections.

ABSTRACT: Environmental adaptation is one of the most fundamental features of organisms. Modern genome science has identified some genes associated with adaptive traits of organisms, and has provided insights into environmental adaptation and evolution. However, how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution remain mostly unclear. To approach these issues, we utilize "Dark-fly", a Drosophila melanogaster line maintained in constant dark conditions for more than 60 years. Our previous analysis identified 220,000 single nucleotide polymorphisms (SNPs) in the Dark-fly genome, but did not clarify which SNPs of Dark-fly are truly adaptive for living in the dark. We found here that Dark-fly dominated over the wild-type fly in a mixed population under dark conditions, and based on this domination we designed an experiment for genome reselection to identify adaptive genes of Dark-fly. For this experiment, large mixed populations of Dark-fly and the wild-type fly were maintained in light conditions or in dark conditions, and the frequencies of Dark-fly SNPs were compared between these populations across the whole genome. We thereby detected condition-dependent selections toward approximately 6% of the genome. In addition, we observed the time-course trajectory of SNP frequency in the mixed populations through generations 0, 22, and 49, which resulted in notable categorization of the selected SNPs into three types with different combinations of positive and negative selections. Our data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly.

SUBMITTER: Izutsu M

PROVIDER: S-EPMC4751556 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Dynamics of Dark-Fly Genome Under Environmental Selections.

Izutsu Minako M Toyoda Atsushi A Fujiyama Asao A Agata Kiyokazu K Fuse Naoyuki N

G3 (Bethesda, Md.) 20151204 2

Environmental adaptation is one of the most fundamental features of organisms. Modern genome science has identified some genes associated with adaptive traits of organisms, and has provided insights into environmental adaptation and evolution. However, how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution remain mostly unclear. To approach these issues, we utilize "Dark-fly", a Drosophila melanogaster line maintained in constant dark ...[more]

PMID: 26637434

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Project description:Selecting appropriate environmental variables is a key step in ecology. Terrain attributes (e.g. slope, rugosity) are routinely used as abiotic surrogates of species distribution and to produce habitat maps that can be used in decision-making for conservation or management. Selecting appropriate terrain attributes for ecological studies may be a challenging process that can lead users to select a subjective, potentially sub-optimal combination of attributes for their applications. The objective of this paper is to assess the impacts of subjectively selecting terrain attributes for ecological applications by comparing the performance of different combinations of terrain attributes in the production of habitat maps and species distribution models. Seven different selections of terrain attributes, alone or in combination with other environmental variables, were used to map benthic habitats of German Bank (off Nova Scotia, Canada). 29 maps of potential habitats based on unsupervised classifications of biophysical characteristics of German Bank were produced, and 29 species distribution models of sea scallops were generated using MaxEnt. The performances of the 58 maps were quantified and compared to evaluate the effectiveness of the various combinations of environmental variables. One of the combinations of terrain attributes-recommended in a related study and that includes a measure of relative position, slope, two measures of orientation, topographic mean and a measure of rugosity-yielded better results than the other selections for both methodologies, confirming that they together best describe terrain properties. Important differences in performance (up to 47% in accuracy measurement) and spatial outputs (up to 58% in spatial distribution of habitats) highlighted the importance of carefully selecting variables for ecological applications. This paper demonstrates that making a subjective choice of variables may reduce map accuracy and produce maps that do not adequately represent habitats and species distributions, thus having important implications when these maps are used for decision-making.

Dataset Information

Dynamics of Dark-Fly Genome Under Environmental Selections.

Publications

Dynamics of Dark-Fly Genome Under Environmental Selections.

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