Project description:Characterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype. However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein-Uhlenbeck (OU) process. This stochastic process models expression trajectories across time as Gaussian distributions whose variance is parameterized by the rate of genetic drift and strength of stabilizing selection. We use these mathematical properties to identify expression pathways under neutral, stabilizing, and directional selection, quantify the extent of selective pressure on a gene’s expression, and detect deleterious expression levels outside expected evolutionary distributions in single patients. Our work provides a statistical framework for interpreting expression data across species and in disease.

2018-10-21 | GSE106077 | GEO

Tibetan Population History and High Altitude Adaptation Study

Project description:Due to a unique adaptation to high altitude, the Tibetan Plateau population has been the subject of much research interest. In this study, we conducted whole genome sequencing of 27 Tibetan individuals. Through our analysis, we inferred a detailed history of demography and revealed the natural selection of Tibetan population. We provided evidence of genetic separation between the two subpopulations of Han and Tibetans as early as 44 to 58 thousand years ago, replicated previously reported high altitude adaptation genes, including EPAS1 and EGLN1, and reported three new candidate genes, including PTGIS, VDR, and KCTD12.

| phs001338 | dbGaP

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

Project description: Not available

| S-EPMC4943195 | biostudies-literature

Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes.

Project description: Not available

| S-EPMC9298040 | biostudies-literature

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data.

Project description: Not available

| S-EPMC3820794 | biostudies-other

Evolutionary history of host, rather than plant phylogeny, determines gene expression in a generalist butterfly

Project description:Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were fed six different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Science for Life Laboratory (SciLifeLab, Sweden) conducted the sequencing of RNA samples. The cDNA libraries (Illumina TruSeq RNA) were sequenced using the Illumina HiSeq 2000 platform using 100-bp paired-end sequencing. We obtained more than 9 million read-pairs from seventy one cDNA libraries sequenced and the transcriptome assembly (TA) of these sequences resulted in 213, 237 transcripts (162,189 components) with a contig N50 of 2,193 bp. Thus, we covered approximately 300x the transcriptome of caterpillars of the species V. cardui.

2015-11-18 | E-MTAB-3861 | biostudies-arrayexpress

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