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ABSTRACT:
PROVIDER: PRJNA1078584 | ENA |
REPOSITORIES: ENA
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Project description:Background: The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts have small genomes, can be easily cultured, and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair has been found, between S. bayanus and S. cerevisiae, comprising the mitochondrially targeted product of a nuclear gene, AEP2, and a mitochondrially encoded locus, OLI1, the 5' region of whose transcript is bound by Aep2. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. Methods: We report here the first detailed genome-wide analysis of rare F2 progeny from an otherwise sterile hybrid, and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions may be responsible for their post-zygotic separation. These interactions most likely involve multiple loci having weak effects, as there were multiple significant pairwise combinations of loci, with no single combination being completely excluded from the viable F2s. Conclusions: The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions, suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that "death by a thousand cuts" leads to speciation, whereby an accumulation of polymorphisms can lead to an incompatibility between the species "transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. Genotypes for hybrids between S. cerevisiae and S. paradoxus. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
2010-06-08 | GSE19683 | GEO
Project description:Transcriptome sequencing of non-model organisms is valuable resource of the genetic basis of ecological-meaningful traits. The Royal Irises, Iris section Oncocyclus (Iris: Iridaceae, order Asparagales), are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises, which are a symbol of conservation in the Middle-east, serve as a model for evolutionary processes of speciation and plant ecology. However, there are not sufficient transcriptomic and genomic data for molecular characterization. Thus, it is necessary to generate massive transcript sequences for functional characterization and molecular marker development for the Royal Irises. The Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.
2021-08-18 | GSE121786 | GEO
Project description:Genomic differentiation across the speciation continuum in three hummingbird species pairs
| PRJNA640148 | ENA
Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)
2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress
Project description:To understand allopoyploid speciation into hydrologically fluctuating niches, we observed gene expressions of two parental species and their allotetraploid species under wet and dry conditions
2016-07-01 | GSE77673 | GEO
Project description:To understand allopoyploid speciation into hydrologically fluctuating niches, we observed gene expressions of two parental species and their allotetraploid species under wet and dry conditions Gene expression of leafs from control, dry and wet conditions over three Caramine species: C. amara, C. hirsuta and C. flexuosa
2016-07-01 | E-GEOD-77673 | biostudies-arrayexpress
Project description:Cichlids fishes exhibit extensive phenotypic diversification and speciation. In this study we integrate transcriptomic and proteomic signatures from two cichlids species, identify novel open reading frames (nORFs) and perform evolutionary analysis on these nORF regions. We embark comparative transrcriptomics and proteogenomic analysis of two metabolically active tissues, the testes and liver, of two cichlid species Oreochromis niloticus (Nile tilapia, ON) and Pundamilia nyererei (Makobe Island, PN). Our results suggest that the time scale of speciation of the two species can be better explained by the evolutionary divergence of these nORF genomic regions.
2021-05-17 | GSE150744 | GEO