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343 results for “genomic divergence”
Genome-wide Analysis Reveals Conserved and Divergent Features of Notch1/RBPJ Binding in Human and Murine T Lymphoblastic Leukemia Cells
GEO Series GSE29600. Homo sapiens; Mus musculus. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Widespread and adaptive alterations in genome-wide gene expression associated with ecological divergence of two Oryza species
GEO Series GSE71044. Oryza rufipogon; Oryza nivara. 42 samples. Type: Expression profiling by high throughput sequencing.
Data from: Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences
Beetles (Coleoptera) are the most diverse and species-rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of "traditional markers" (e.g., mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome-wide survey to search nuclear protein-coding (NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community for NPC marker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95 NPC markers which can be PCR amplified from standard genomic DNA extracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support > 95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the "traditional markers", and show great potential to expedite resolution of many parts in the Beetle Tree of Life.
Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (Mean FST = 0.016) than between ecotypes within sites (Mean FST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions support the presence of a continuum of divergence in Lake Trout.
Data from: Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation
[No abstract entered]
Data from: A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence
Understanding the genetics of speciation and the processes that drive it is a central goal of evolutionary biology. Grasshoppers of the Chorthippus species group differ strongly in calling song (and corresponding female preferences) but are exceedingly similar in other characteristics such as morphology. Here, we performed a population genomic scan on three Chorthippus species (Chorthippus biguttulus, C. mollis and C. brunneus) to gain insight into the genes and processes involved in divergence and speciation in this group. Using an RNA-seq approach, we examined functional variation between the species by calling SNPs for each of the three species pairs and using FST-based approaches to identify outliers. We found approximately 1% of SNPs in each comparison to be outliers. Between 37% and 40% of these outliers were nonsynonymous SNPs (as opposed to a global level of 17%) indicating that we recovered loci under selection. Among the outliers were several genes that may be involved in song production and hearing as well as genes involved in other traits such as food preferences and metabolism. Differences in food preferences between species were confirmed with a behavioural experiment. This indicates that multiple phenotypic differences implicating multiple evolutionary processes (sexual selection and natural selection) are present between the species.
Data from: Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences
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Data from: A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence
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Data from: Genomic divergence between Spanish Littorina saxatilis ecotypes unravels limited admixture and extensive parallelism associated with population history
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Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior
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Data from: Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation
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Divergent genome expression profiles during hepatic ischemia in young and adult mice
GEO Series GSE10652. Mus musculus. 24 samples. Type: Expression profiling by array.
Genome-Wide Analysis Reveals Divergent Patterns of Gene Expression During Zygotic and Somatic Embryo Maturation of Theobroma cacao L., The Chocolate Tree
GEO Series GSE55476. Theobroma cacao. 6 samples. Type: Expression profiling by array.
Architecture of the genome-wide transcriptional regulatory network reveals the dynamic biological functions and divergent evolutionary trajectory in Pseudomonas syringae
GEO Series GSE247395. Pseudomonas syringae pv. actinidiae str. Shaanxi_M228; Pseudomonas syringae pv. syringae B728a; Pseudomonas syringae pv. tomato str. DC3000; Pseudomonas savastanoi pv. phaseolicola 1448A. 396 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content
GEO Series GSE58551. Gallus gallus. 475 samples. Type: Genome variation profiling by SNP array.
Genome and transcriptome divergence in Bacillus subtilis after 6,000 generations of evolution
GEO Series GSE4469. Bacillus subtilis. 22 samples. Type: Expression profiling by array; Genome variation profiling by array.
Figure 3 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 3. Ancestral distribution ranges inferred by dispersal-vicariance analysis (DIVA) of 18 lineages at the subfamilial rank. Arrays of presence (1) or absence (0) state shown at each branch are in the order Africa, South Asia, East Asia, Europe, Siberia, western North America, and eastern North America (also see the inset). A number of arrays at some branches indicate equally optimal ancestral patterns. There were 1753 equally optimal combinations of these patterns given by DIVA.
Figure 4 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 4. Ancestral distribution ranges reconstructed parsimoniously using PAUP*. Two representative character state (see legend for Fig. 3) optimizations are shown on the upper (delayed transition) and lower (accelerated transition) rows. Minimum F optimization was the same as delayed transition. The parsimonious reconstruction of character states allows an unrealistic all zero state. It does not give the character state at the root. In such cases the character state was manually optimized (asterisks).
Regulatory divergence in Drosophila melanogaster and D. simulans: a genome-wide analysis of allele-specific expression
GEO Series GSE17453. Drosophila melanogaster; Drosophila sp. (in: flies); Drosophila simulans. 24 samples. Type: Expression profiling by genome tiling array.
How to Make an Elephant: Functional Genomic Divergence and the Evolution of Cancer Suppression
GEO Series GSE148098. Loxodonta africana. 4 samples. Type: Expression profiling by high throughput sequencing.
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