Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1116128 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29190900.fastq.gz | Fastqsanger.gz | |||
| SRR29190900_1.fastq.gz | Fastqsanger.gz | |||
| SRR29190900_2.fastq.gz | Fastqsanger.gz | |||
| SRR29190901.fastq.gz | Fastqsanger.gz | |||
| SRR29190901_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
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Project description:Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression (DGE) technology and the paired-end RNA sequencing (RNA-Seq) method, we obtained 21,415 expressed genes across three reproduction-related tissues at two critical developmental stages. Of them, ~8% (1717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5’flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and highlight the dominant role of regulatory evolution in ecological divergence and adaptation.
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Project description:Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression (DGE) technology and the paired-end RNA sequencing (RNA-Seq) method, we obtained 21,415 expressed genes across three reproduction-related tissues at two critical developmental stages. Of them, ~8% (1717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5â??flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and highlight the dominant role of regulatory evolution in ecological divergence and adaptation. We selected accessions representing typical Oryza rufipogon and O. nivara, which were sampled exclusively from South and Southeast Asia where the two species overlap. We chose to collect three types of tissues, i.e., flag leaves at the heading stage (2â??7 cm above the primary branch) (L), panicles at the heading stage (H) and panicles at the flowering stage (10â??15 cm above the primary branch) (F). Sample collection was repeated twice in two consecutive years (2009 and 2010) under the same controlled conditions. A total of 36 samples were sequenced by Illuminaâ??s digital gene expression (DGE) system, with each type of tissues collected from six individuals of each species as biological replicates. To access the quality of DGE technology, we also selected six samples representing three tissues from each of two individuals (one individual per species) for paired-end RNA-Seq sequencing.
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Project description:Gigantopithecus blacki was a giant hominid that inhabited Southeast Asia during the Pleistocene. Its evolutionary relationship to other great ape species, and their divergence during the Middle and Late Miocene (16-5.3 Mya), remains disputed. In part, this is due to the absence of cranial and postcranial remains and size-induced allometry. Proposed hypothesis on the phylogenetic positions of Gigantopithecus have therefore been wide-ranging among hominoids, but none has received independent validation based on molecular evidence. To clarify the phylogenetic placement of Gigantopithecus blacki, we retrieved enamel proteome sequences from a 1.9 million years (Mya) old molar found in Chuifeng Cave, China. We demonstrate that Gigantopithecus is most closely related to orangutans (genus Pongo). We also estimate the Gigantopithecus-Pongo divergence to about 10-12 Mya, implying its speciation is part of the Miocene radiation of great apes. These sequences are approximately 6 times older, in a normalized thermal context, than any previously published mammalian proteome or genome. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographic areas and time periods previously considered incompatible with biomolecular preservation.
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