Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1109731 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29018800_1.fastq.gz | Fastqsanger.gz | |||
| SRR29018800_2.fastq.gz | Fastqsanger.gz | |||
| SRR29018801_1.fastq.gz | Fastqsanger.gz | |||
| SRR29018801_2.fastq.gz | Fastqsanger.gz | |||
| SRR29018802_1.fastq.gz | Fastqsanger.gz |
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Project description:Understanding the conditions that promote the evolution of reproductive isolation, and thus speciation. Here we empirically test some of the key predictions of speciation theory (Coyne 2004; Kohn 2005) by experimentally evolving the initial stages of speciation in yeast. After allowing replicate populations to adapt to two divergent environments, we observed the consistent, de novo evolution of two forms of postzygotic isolation: reduced rate of mitotic reproduction and reduced efficiency of meiotic reproduction. In general, divergent selection resulted in greater reproductive isolation than parallel selection, as predicted by ecological speciation theory. Our experimental system allowed for the first controlled comparison of the relative importance of ecological and genetic mechanisms of isolation, and the novel ability to quantify the effects of antagonistic epistasis. For mitotic reproduction, hybrid inferiority was conditional upon the selective environments and was both ecological and genetic in basis. In contrast, isolation associated with meiotic reproduction was unconditional and was caused solely by genetic mechanisms. Overall, our results show that adaption to divergent environments promotes the evolution of isolation through antagonistic epistasis, providing evidence of a plausible common avenue to speciation and adaptive radiation in nature (Schluter 2000,2001: Funk 2006) Keywords: Speciation, antagonistic epistasis, divergent adaptation
2007-06-21 | GSE6870 | GEO
Project description:Genetic analyses of speciation have focused nearly exclusively on retrospective analyses of reproductive isolation between highly divergent species. Yet, a full understanding of the speciation process must encompass analysis of the consequences of genomic divergence in young lineages still capable of exchanging genes under natural conditions. The accumulation of conditionally neutral genetic variation may lead to the evolution of divergent gene networks. In a hybrid background, such mutations may no longer compensate one another, resulting in the appearance of selectively disadvantageous traits, including disruption of gene expression regulation. Here, we documented genome-wide patterns of gene expression divergence between young lineages of normal and dwarf lake whitefish and their backcross hybrids for which strong, yet incomplete post-zygotic isolation barriers exist. A significant proportion (33%) of backcross hybrids showed developmental abnormalities not seen in parental forms and eventually leading to death. While the transcriptome of parental forms was nearly identical during embryonic development, suggesting a role for stabilizing selection, all hybrids displayed strongly divergent patterns of gene expression. By comparing healthy, surviving hybrids against moribund ones, we observed that over 2000 genes were misregulated in these abnormal embryos. In particular, misregulation was significantly biased towards essential developmental genes which were strongly underexpressed. Furthermore, genes previously documented to be highly transgressive (exaggerated inter-individual variance) were almost invariably underexpressed in hybrids. Our results thus clearly showed a transcriptome-wide signature of hybrid breakdown in young, incipient species and demonstrated a persuasive link between misexpression of essential developmental genes and post zygotic isolation. Samples of dwarf, normal, backcross-healthy and backcross-moribund were hybridized in a loop design, involving eight biological replicates for the backcross-healthy and backcross-moribund comparison and six for the others. Dye swap was performed between each replicate. As a result, we obtained a final set of 32 microarray slides.
2010-07-31 | E-GEOD-23095 | biostudies-arrayexpress
Project description:The evolution of female choice mechanisms favouring males of their own kind is considered as crucial step during the early stages of speciation. However, although the genomics of mate choice may influence both the likelihood and speed of speciation, the identity and location of genes underlying assortative mating remain largely unknown. We used mate choice experiments and gene expression analysis of female D. melanogaster to examine three key components influencing speciation. We show that the 1,498 genes in Zimbabwean female Drosophila melanogaster whose expression levels differ when mating with more (Zimbabwean) versus less (Cosmopolitan strain) preferred males include many with high expression in the central nervous system and ovaries, are disproportionately X-linked and form a number of clusters with low recombination distance. Significant involvement of the brain and ovaries is consistent with the action of a combination of pre- and post-copulatory female choice mechanisms, while sex linkage and clustering of genes lead to high potential evolutionary rate and sheltering against the homogenizing effects of gene exchange between populations. Taken together our results imply favourable genomic conditions for the evolution of reproductive isolation through mate choice in Zimbabwean D. melanogaster and suggest that mate choice may, in general, act as an even more important engine of speciation than previously realized. We measured gene expression of adult female Drosophila melanogaster from a composite Zimbabwe (Z) strain population named SZ, produced by mixing the genomes of six Z strain isofemale lines, shortly after mating them with either SZ strain or cosmopolitan (M strain) males. Data from four replicates of each of the two treatments (SZ mated with SZ; SZ mated with M) are presented, giving a total of eight arrays.
2011-02-05 | E-GEOD-27076 | biostudies-arrayexpress
Project description:To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning. Illumina sequencing of mono-nucleosome fragments isolated by MNase digestion. Samples include pooled DNA fragments of S. cerevisiae and S. paradoxus or DNA fragments of the interspecific hybrid. Experiments were performed for WT strains as well as strains deleted of 5 chromatin regulators.
2010-03-01 | E-GEOD-18939 | biostudies-arrayexpress
Project description:Background The evolution of female choice mechanisms favouring males of their own kind is considered as crucial step during the early stages of speciation. However, although the genomics of mate choice may influence both the likelihood and speed of speciation, the identity and location of genes underlying assortative mating remain largely unknown. Methods and Findings We used mate choice experiments and gene expression analysis of female D. melanogaster to examine three key components influencing speciation. We show that the 1,498 genes in Zimbabwean female Drosophila melanogaster whose expression levels differ when mating with more (Zimbabwean) versus less (Cosmopolitan strain) preferred males include many with high expression in the central nervous system and ovaries, are disproportionately X-linked and form a number of clusters with low recombination distance. Significant involvement of the brain and ovaries is consistent with the action of a combination of pre- and postcopulatory female choice mechanisms, while sex linkage and clustering of genes lead to high potential evolutionary rate and sheltering against the homogenizing effects of gene exchange between populations. Conclusion Taken together our results imply favourable genomic conditions for the evolution of reproductive isolation through mate choice in Zimbabwean D. melanogaster and suggest that mate choice may, in general, act as an even more important engine of speciation than previously realized.
2011-02-05 | GSE27076 | GEO
Project description:Genetic analyses of speciation have focused nearly exclusively on retrospective analyses of reproductive isolation between highly divergent species. Yet, a full understanding of the speciation process must encompass analysis of the consequences of genomic divergence in young lineages still capable of exchanging genes under natural conditions. The accumulation of conditionally neutral genetic variation may lead to the evolution of divergent gene networks. In a hybrid background, such mutations may no longer compensate one another, resulting in the appearance of selectively disadvantageous traits, including disruption of gene expression regulation. Here, we documented genome-wide patterns of gene expression divergence between young lineages of normal and dwarf lake whitefish and their backcross hybrids for which strong, yet incomplete post-zygotic isolation barriers exist. A significant proportion (33%) of backcross hybrids showed developmental abnormalities not seen in parental forms and eventually leading to death. While the transcriptome of parental forms was nearly identical during embryonic development, suggesting a role for stabilizing selection, all hybrids displayed strongly divergent patterns of gene expression. By comparing healthy, surviving hybrids against moribund ones, we observed that over 2000 genes were misregulated in these abnormal embryos. In particular, misregulation was significantly biased towards essential developmental genes which were strongly underexpressed. Furthermore, genes previously documented to be highly transgressive (exaggerated inter-individual variance) were almost invariably underexpressed in hybrids. Our results thus clearly showed a transcriptome-wide signature of hybrid breakdown in young, incipient species and demonstrated a persuasive link between misexpression of essential developmental genes and post zygotic isolation.
2010-08-01 | GSE23095 | GEO
Project description:Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses Examination of small RNA of diploid Parent, Tetraploid parent, F1 hybrid and hexaploid amhiploid. Four pools of plants for each sample
2011-05-12 | E-GEOD-29243 | biostudies-arrayexpress