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Pseudoobscura

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https://www.readbyqxmd.com/read/27897175/accelerated-pseudogenization-on-the-neo-x-chromosome-in-drosophila-miranda
#1
Masafumi Nozawa, Kanako Onizuka, Mai Fujimi, Kazuho Ikeo, Takashi Gojobori
Y chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. By contrast, little is known about X-chromosome degeneration. Here we compare the pseudogenization process between genes on the neo-sex chromosomes in Drosophila miranda and their autosomal orthologues in closely related species. The pseudogenization rate on the neo-X is much lower than the rate on the neo-Y, but appears to be higher than the rate on the orthologous autosome in D. pseudoobscura. Genes under less functional constraint and/or genes with male-biased expression tend to become pseudogenes on the neo-X, indicating the accumulation of slightly deleterious mutations and the feminization of the neo-X...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27760228/mistaken-identity-another-bias-in-the-use-of-relative-genetic-divergence-measures-for-detecting-interspecies-introgression
#2
Kathryn R Ritz, Mohamed A F Noor
Measures of genetic divergence have long been used to identify evolutionary processes operating within and between species. However, recent reviews have described a bias in the use of relative divergence measures towards incorrectly identifying genomic regions that are seemingly immune to introgression. Here, we present a novel and opposite bias of relative divergence measures: misidentifying regions of introgression between sister species. We examine two distinct haplotypes of intermediate frequency within Drosophila pseudoobscura at the DPSX009 locus...
2016: PloS One
https://www.readbyqxmd.com/read/27535930/repeated-duplication-of-argonaute2-is-associated-with-strong-selection-and-testis-specialization-in-drosophila
#3
Samuel H Lewis, Claire L Webster, Heli Salmela, Darren J Obbard
Argonaute2 (Ago2) is a rapidly evolving nuclease in the Drosophila melanogaster RNA interference (RNAi) pathway that targets viruses and transposable elements in somatic tissues. Here we reconstruct the history of Ago2 duplications across the D. obscura group and use patterns of gene expression to infer new functional specialization. We show that some duplications are old, shared by the entire species group, and that losses may be common, including previously undetected losses in the lineage leading to D. pseudoobscura We find that while the original (syntenic) gene copy has generally retained the ancestral ubiquitous expression pattern, most of the novel Ago2 paralogs have independently specialized to testis-specific expression...
October 2016: Genetics
https://www.readbyqxmd.com/read/27527791/potential-direct-regulators-of-the-drosophila-yellow-gene-identified-by-yeast-one-hybrid-and-rnai-screens
#4
Gizem Kalay, Richard Lusk, Mackenzie Dome, Korneel Hens, Bart Deplancke, Patricia J Wittkopp
The regulation of gene expression controls development, and changes in this regulation often contribute to phenotypic evolution. Drosophila pigmentation is a model system for studying evolutionary changes in gene regulation, with differences in expression of pigmentation genes such as yellow that correlate with divergent pigment patterns among species shown to be caused by changes in cis- and trans-regulation. Currently, much more is known about the cis-regulatory component of divergent yellow expression than the trans-regulatory component, in part because very few trans-acting regulators of yellow expression have been identified...
October 13, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27516612/hubby-and-lewontin-on-protein-variation-in-natural-populations-when-molecular-genetics-came-to-the-rescue-of-population-genetics
#5
Brian Charlesworth, Deborah Charlesworth, Jerry A Coyne, Charles H Langley
The 1966 GENETICS papers by John Hubby and Richard Lewontin were a landmark in the study of genome-wide levels of variability. They used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of Drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. Together with the independent study of human populations by Harry Harris, this seminal study provided the first relatively unbiased picture of the extent of genetic variability in protein sequences within populations, revealing that many genes had surprisingly high levels of diversity...
August 2016: Genetics
https://www.readbyqxmd.com/read/27513559/comparative-genomic-analyses-provide-new-insights-into-the-evolutionary-dynamics-of-heterochromatin-in-drosophila
#6
Ruggiero Caizzi, Roberta Moschetti, Lucia Piacentini, Laura Fanti, Renè Massimiliano Marsano, Patrizio Dimitri
The term heterochromatin has been long considered synonymous with gene silencing, but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes. Several studies have addressed the epigenetic changes that enable the expression of genes in pericentric heterochromatin, yet little is known about the evolutionary processes through which this has occurred. By combining genome annotation analysis and high-resolution cytology, we have identified and mapped 53 orthologs of D...
August 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27512614/genomic-and-expression-analysis-of-transition-proteins-in-drosophila
#7
Zain A Alvi, Tin-Chun Chu, Valerie Schawaroch, Angela V Klaus
The current study was aimed at analyzing putative protein sequences of the transition protein-like proteins in 12 Drosophila species based on the reference sequences of transition protein-like protein (Tpl (94D) ) expressed in Drosophila melanogaster sperm nuclei. Transition proteins aid in transforming chromatin from a histone-based nucleosome structure to a protamine-based structure during spermiogenesis - the post-meiotic stage of spermatogenesis. Sequences were obtained from NCBI Ref-Seq database using NCBI ORF-Finder (PSI-BLAST)...
September 2015: Spermatogenesis
https://www.readbyqxmd.com/read/27432989/union-of-phylogeography-and-landscape-genetics
#8
Leslie J Rissler
Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the "microgeographic races" of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y...
July 19, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27401754/genomics-of-natural-populations-how-differentially-expressed-genes-shape-the-evolution-of-chromosomal-inversions-in-drosophila-pseudoobscura
#9
Zachary L Fuller, Gwilym D Haynes, Stephen Richards, Stephen W Schaeffer
Chromosomal rearrangements can shape the structure of genetic variation in the genome directly through alteration of genes at breakpoints or indirectly by holding combinations of genetic variants together due to reduced recombination. The third chromosome of Drosophila pseudoobscura is a model system to test hypotheses about how rearrangements are established in populations because its third chromosome is polymorphic for >30 gene arrangements that were generated by a series of overlapping inversion mutations...
September 2016: Genetics
https://www.readbyqxmd.com/read/27189981/comparative-expression-dynamics-of-intergenic-long-noncoding-rnas-in-the-genus-drosophila
#10
Kevin G Nyberg, Carlos A Machado
Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, we identified and characterized lncRNAs in a second Drosophilid-the evolutionary model Drosophila pseudoobscura Using RNA-Seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncRNA loci in D. pseudoobscura We surveyed multiple sex-specific developmental stages and found, like in Drosophila melanogaster, increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes...
2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27021916/evolution-of-gc-content-in-the-histone-gene-repeating-units-from-drosophila-lutescens-d-takahashii-and-d-pseudoobscura
#11
Yuko Nakashima, Asako Higashiyama, Ayana Ushimaru, Nozomi Nagoda, Yoshinori Matsuo
A subset of histone genes (H1, H2A, H2B and H4), which are encoded along with H3 within repeating units, were analyzed in Drosophila lutescens, D. takahashii and D. pseudoobscura to investigate the evolutionary mechanisms influencing this multigene family and its GC content. Nucleotide divergence among species was more marked in the less functional regions. A strong inverse relationship was observed between the extent of evolutionary divergence and GC content within the repeating units; this finding indicated that the functional constraint on a region must be associated with both divergence and GC content...
July 20, 2016: Genes & Genetic Systems
https://www.readbyqxmd.com/read/27004012/temperature-can-shape-a-cline-in-polyandry-but-only-genetic-variation-can-sustain-it-over-time
#12
Michelle L Taylor, Tom A R Price, Alison Skeats, Nina Wedell
Multiple mating by females (polyandry) is a widespread behavior occurring in diverse taxa, species, and populations. Polyandry can also vary widely within species, and individual populations, so that both monandrous and polyandrous females occur together. Genetic differences can explain some of this intraspecific variation in polyandry, but environmental factors are also likely to play a role. One environmental factor that influences many fundamental biological processes is temperature. Higher temperatures have been shown to directly increase remating in laboratory studies of insects...
March 2016: Behavioral Ecology: Official Journal of the International Society for Behavioral Ecology
https://www.readbyqxmd.com/read/26970522/sexual-selection-and-assortative-mating-an-experimental-test
#13
A Debelle, M G Ritchie, R R Snook
Mate choice and mate competition can both influence the evolution of sexual isolation between populations. Assortative mating may arise if traits and preferences diverge in step, and, alternatively, mate competition may counteract mating preferences and decrease assortative mating. Here, we examine potential assortative mating between populations of Drosophila pseudoobscura that have experimentally evolved under either increased ('polyandry') or decreased ('monogamy') sexual selection intensity for 100 generations...
July 2016: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/26344774/kr%C3%A3-ppel-expression-levels-are-maintained-through-compensatory-evolution-of-shadow-enhancers
#14
Zeba Wunderlich, Meghan D J Bragdon, Ben J Vincent, Jonathan A White, Javier Estrada, Angela H DePace
Many developmental genes are controlled by shadow enhancers—pairs of enhancers that drive overlapping expression patterns. We hypothesized that compensatory evolution can maintain the total expression of a gene, while individual shadow enhancers diverge between species. To test this hypothesis, we analyzed expression driven by orthologous pairs of shadow enhancers from Drosophila melanogaster, Drosophila yakuba, and Drosophila pseudoobscura that control expression of Krüppel, a transcription factor that patterns the anterior-posterior axis of blastoderm embryos...
September 22, 2015: Cell Reports
https://www.readbyqxmd.com/read/26146165/hybrid-male-sterility-and-genome-wide-misexpression-of-male-reproductive-proteases
#15
Suzanne Gomes, Alberto Civetta
Hybrid male sterility is a common barrier to gene flow between species. Previous studies have posited a link between misregulation of spermatogenesis genes in interspecies hybrids and sterility. However, in the absence of fully fertile control hybrids, it is impossible to differentiate between misregulation associated with sterility vs. fast male gene regulatory evolution. Here, we differentiate between these two possibilities using a D. pseudoobscura species pair that experiences unidirectional hybrid sterility...
2015: Scientific Reports
https://www.readbyqxmd.com/read/26129990/natural-variation-of-the-expression-pattern-of-the-segmentation-gene-even-skipped-in-melanogaster
#16
Pengyao Jiang, Michael Z Ludwig, Martin Kreitman, John Reinitz
The evolution of canalized traits is a central question in evolutionary biology. Natural variation in highly conserved traits can provide clues about their evolutionary potential. Here we investigate natural variation in a conserved trait-even-skipped (eve) expression at the cellular blastoderm stage of embryonic development in Drosophila melanogaster. Expression of the pair-rule gene eve was quantitatively measured in three inbred lines derived from a natural population of D. melanogaster. One line showed marked differences in the spacing, amplitude and timing of formation of the characteristic seven-striped pattern over a 50-min period prior to the onset of gastrulation...
September 1, 2015: Developmental Biology
https://www.readbyqxmd.com/read/26098542/conservation-of-olfactory-avoidance-in-drosophila-species-and-identification-of-repellents-for-drosophila-suzukii
#17
Christine Krause Pham, Anandasankar Ray
Flying insects use olfaction to navigate towards fruits in complex odor environments with remarkable accuracy. Some fruits change odor profiles substantially during ripening and related species can prefer different stages. In Drosophila species attractive odorants have been studied extensively, but little is understood about the role of avoidance pathways. In order to examine the role of the avoidance cue CO2 emitted from fruit on behavior of two species with different ripening stage preferences, we investigated the CO2-detection pathway in Drosophila melanogaster and Drosophila suzukii, a harmful pest of fruits...
2015: Scientific Reports
https://www.readbyqxmd.com/read/25969560/temporal-stability-of-molecular-diversity-measures-in-natural-populations-of-drosophila-pseudoobscura-and-drosophila-persimilis
#18
Jennifer N Gredler, Alexander J Hish, Mohamed A F Noor
Many molecular ecological and evolutionary studies sample wild populations at a single point in time, but that data represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and Drosophila pseudoobscura collected 16 years apart at the same time of year and same site at 4 X-linked and 2 mitochondrial loci to assess genetic stability...
July 2015: Journal of Heredity
https://www.readbyqxmd.com/read/25938821/dyeing-insects-for-behavioral-assays-the-mating-behavior-of-anesthetized-drosophila
#19
Rudi L Verspoor, Chloe Heys, Thomas A R Price
Mating experiments using Drosophila have contributed greatly to the understanding of sexual selection and behavior. Experiments often require simple, easy and cheap methods to distinguish between individuals in a trial. A standard technique for this is CO2 anaesthesia and then labelling or wing clipping each fly. However, this is invasive and has been shown to affect behavior. Other techniques have used coloration to identify flies. This article presents a simple and non-invasive method for labelling Drosophila that allows them to be individually identified within experiments, using food coloring...
2015: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/25887658/opposite-environmental-and-genetic-influences-on-body-size-in-north-american-drosophila-pseudoobscura
#20
Michelle L Taylor, Alison Skeats, Alastair J Wilson, Tom A R Price, Nina Wedell
BACKGROUND: Populations of a species often differ in key traits. However, it is rarely known whether these differences are associated with genetic variation and evolved differences between populations, or are instead simply a plastic response to environmental differences experienced by the populations. Here we examine the interplay of plasticity and direct genetic control by investigating temperature-size relationships in populations of Drosophila pseudoobscura from North America. We used 27 isolines from three populations and exposed them to four temperature regimes (16°C, 20°C, 23°C, 26°C) to examine environmental, genetic and genotype-by-environment sources of variance in wing size...
2015: BMC Evolutionary Biology
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