Transcriptome changes after genome wide admixture in invasive sculpins
Ontology highlight
ABSTRACT:
ORGANISM(S): Cottus rhenanus Cottus Cottus perifretum
PROVIDER: GSE36755 | GEO | 2012/03/27
SECONDARY ACCESSION(S): PRJNA156889
REPOSITORIES: GEO
Similar Datasets
Project description:European sculpins (Cottus) harbor an example of a recent hybrid speciation event, which entails the invasion of a new habitat by the hybrid species. We compare the transcriptomes of both parental species and the hybrid species to understand how they differ. F2 crosses between the parent species are compared to the hybrid species and its parent species to identify unique patterns of the hybrid species due to the initial hybridization process or respectively to other processes. See the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology no doi yet) for more information. The transcriptome was compared between an invasive hybrid species of Cottus (Sieg population n = 8) and its parent species C.rhenanus and C.perifretum. Expression profiles of both parental populations were assessed by two independent replicate population (C.rhenanus: Broel and Naaf; C.perifretum Laarse Beek and Witte Nete; each population n = 8). The transcriptomes of F2 crosses between the populations of C.rhenanus and C.perifretum were assessed with for independent crosses with 4 biological replicates for each cross (n = 4 x 4 = 16). We used a custom design microarray with probes designed based on transcriptome sequencing. We used a newly developed calibration method to account for differences in individual probe binding behavior and to detect and remove probes unfit for analysis. Data stored as “normalized data” are normalized and quality filtered based on this new calibration method and normalized for interarray comparability by division by the 75%tile signal intensity for each array. Please refer to the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology; no doi yet) for more information.
2012-03-26 | E-GEOD-36755 | biostudies-arrayexpress
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2011-05-12 | E-GEOD-29243 | biostudies-arrayexpress
Project description:We designed a custom expression 8x15 k microarray for Cottus fishes based on transcriptome sequencing. It is a known fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet) for more information. Labeled cRNA was prepared from 3 Cottus fish. These 3 fish were representative of species (C.rhenanus, C.perifretum, invasive hybrid species) used in another experiment. An calibration pool was prepared from equimolar amounts of this cRNA. Increasing amounts of labeled cRNA (75 ng, 150 ng, 300 ng, 600 ng, 1200 ng, 2400 ng, 4800 ng), corresponding to (1/8, 1/4, 1/2, 1, 2, 4 and 8 times the recommended amount of 600 ng) were hybridized to 7 microarrays (one microarray per dilution-step). The change in observed signal intensity in relation to the change in amount of labeled cRNA was used to infer the target-binding behavior of the individual probes. This information was extracted, to be used for a normalization procedure in another experiment with the same microarray (see Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet)
2012-03-26 | E-GEOD-36800 | biostudies-arrayexpress
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Project description:Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient human ancestors and have demonstrated that contemporary humans harbour genetic material from ancient close relatives, the Neanderthals and Denisovans, and that ancient human individuals are often genetically distinct from nearby extant populations whilst also showing affinities with populations from further afield. Across West Eurasia, there is growing genetic evidence of large-scale, dynamic population movements over the period between 10,000 to 2,000 years ago, such that the ancestry across present-day populations is likely to be a mixture of several ancient groups. Whilst these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled, or have been either too regional or global in their outlook. Here, using recently described haplotype-based techniques, we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1500 years are likely to have maintained differentiation amongst groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia. 20 individuals from Croatia included as part of an analysis of admixture in West Eurasia
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2014-02-14 | E-GEOD-53626 | biostudies-arrayexpress
Project description:Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient human ancestors and have demonstrated that contemporary humans harbour genetic material from ancient close relatives, the Neanderthals and Denisovans, and that ancient human individuals are often genetically distinct from nearby extant populations whilst also showing affinities with populations from further afield. Across West Eurasia, there is growing genetic evidence of large-scale, dynamic population movements over the period between 10,000 to 2,000 years ago, such that the ancestry across present-day populations is likely to be a mixture of several ancient groups. Whilst these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled, or have been either too regional or global in their outlook. Here, using recently described haplotype-based techniques, we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1500 years are likely to have maintained differentiation amongst groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.
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Project description:Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.
2014-02-14 | GSE53626 | GEO
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