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77 results for “chromosomal differentiation”
Data from: Recent speciation and elevated Z-chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals
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Data from: Dmrt1 polymorphism and sex-chromosome differentiation in Rana temporaria
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Data from: Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage
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Data from: On the Coyne and Orr-igin of species: effects of intrinsic postzygotic isolation, ecological differentiation, X-chromosome size, and sympatry on Drosophila speciation
Coyne and Orr found that mating discrimination (premating isolation) evolves much faster between sympatric than allopatric Drosophila species pairs. Their meta-analyses established that this pattern, expected under reinforcement, is common and that Haldane's rule is ubiquitous in Drosophila species divergence. We examine three possible contributors to the reinforcement pattern: intrinsic postzygotic isolation, dichotomized as to whether hybrid males show complete inviability/sterility; host-plant divergence, as a surrogate for extrinsic postzygotic isolation; and X chromosome size, whether roughly 20% or 40% of the genome is X-linked. We focus on "young" species pairs with overlapping ranges, contrasted with allopatric pairs. Using alternative criteria for "sympatry" and tests that compare either level of prezygotic isolation in sympatry or frequency of sympatry, we find no statistically significant effects associated with X chromosome size or our coarse quantifications of intrinsic postzygotic isolation or ecological differentiation. Although sympatric speciation seems very rare in animals, the pervasiveness of the reinforcement pattern and the commonness of range overlap for close relatives indicate that speciation in Drosophila is often not purely allopatric. It remains to determine whether increased premating isolation with sympatry results from secondary contact versus parapatric speciation and what drives this pattern.
Data from: Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here we study an ecologically diversifying lineage of An. gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An. gambiae, and the sister species An. coluzzii to investigate evolutionary relationships and genome-wide patterns of nucleotide diversity and differentiation among lineages. Despite extensive shared polymorphism and limited differentiation from the other taxa, Bamako clusters apart from the other taxa, and forms a maximally supported clade in neighbor-joining trees based on whole genome data (including inversions) or solely on collinear regions. Nevertheless, FST outlier analysis reveals that the majority of differentiated regions between Bamako and typical An. gambiae are located inside chromosomal inversions, consistent with their role in the ecological isolation of Bamako. Exceptionally differentiated genomic regions were enriched for genes implicated in nervous system development and signaling. Candidate genes associated with a selective sweep unique to Bamako contain substitutions not observed in sympatric samples of the other taxa, and several insecticide resistance gene alleles shared between Bamako and other taxa segregate at sharply different frequencies in these samples. Bamako represents a useful window into the initial stages of ecological and genomic differentiation from sympatric populations in this important group of malaria vectors.
Data from: Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling
Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MATa cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type.
Non canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia
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Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci
<p><span>Repetitive DNA represents an important driver of sex chromosome differentiation. Yet repetitive sequences tend to be misrepresented or overlooked in genomic studies. We analysed repetitive landscape of sex chromosomes in several populations of a turquoise killifish <em>Nothobranchius</em> <em>furzeri</em> and its sister species <em>N</em>. <em>kadleci</em> (Teleostei: Nothobranchiidae), representatives of African annual killifishes with high rate of karyotype and sex chromosome evolution. We combined bioinformatic analyses of repeatome with molecular cytogenetic techniques such as comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, genes for ribosomal RNAs (rDNA) and bacterial artificial chromosomes (BACs) and immunostaining of </span><span>SYCP3 and MLH1 proteins, which marked lateral elements of synaptonemal complexes and recombination sites, respectively</span><span>. We revealed that <em>N</em>. <em>furzeri</em> and <em>N</em>. <em>kadleci</em> share the XY sex chromosome system, which is thus much older than previously assumed. Sex chromosomes are mostly heteromorphic as evidenced by distinct distribution of satellite DNAs and major rDNA. Yet, the heteromorphic X and Y sex chromosomes pair almost exclusively regularly in meiosis, which implies synaptic adjustment. Physical mapping of BACs identified inversions on Y chromosomes of the <em>N</em>. <em>kadleci</em> populations, similar to the pattern previously reported in <em>N</em>. <em>furzeri</em>. Yet, the repetitive DNA landscape of X and Y sex chromosomes either diverged in parallel in populations of both species, or it evolved in their common ancestor and thus predates the inversions. The observed differentiation via repeat repatterning thus cannot be explained by the classical sexual antagonistic model. Rather, we hypothesized that relaxed meiotic drive and recombination reduced by neutral processes could drive changes in repeatome and secondary inversions could be maintained </span><span>by sexually antagonistic regulatory effects resulting from evolution of dosage compensation. </span><span><br></span></p>
Figure 1 in New insights into the chromosomal differentiation patterns among cichlids from Africa and Madagascar
Figure 1. – Map of Africa showing the eleven collection sites of the cichlid specimens. A: West-central Africa. 1: Chromidotilapia guntheri guntheri; 2: Hemichromis fasciatus; 3: Steatocranus irvinei; 4: Stomatepia pindu; B: East central Africa. 1: Altolamprologus compressiceps, Gnathochromis permaxillaris; 2: Ctenochromis horei, Neolamprologus tetracanthus; 3: Eretmodus cyanostictus, Neolamprologus brevis; 4: Haplochromis paludinosus; 5: Astatoreochromis alluaudi, Pseudocrenilabrus multicolor victoriae; 6: Nimbochromis livingstonii, Nimbochromis polystigma; 7: Haplochromis callipterus. (Paugy et al., 2008).
Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci
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Data from: On the Coyne and Orr-igin of species: effects of intrinsic postzygotic isolation, ecological differentiation, X-chromosome size, and sympatry on Drosophila speciation
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Data from: Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing
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Data from: Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling
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Data from: Social chromosome variants differentially affect queen determination and the survival of workers in the fire ant Solenopsis invicta
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Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex: RNA-Seq Data
GEO Series GSE184098. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
Differentially expressed genes and chromosomal alterations in ovarian cancer cell lines sensitive or resistant to a Src-inihibitor, saracatinib
GEO Series GSE55628. Homo sapiens. 25 samples. Type: Expression profiling by array; Genome variation profiling by SNP array.
Differential regulation of telomere associated transcriptome homeostasis by Translin and Trax is linked to Argonaute-mediated chromosome stability control
GEO Series GSE71983. Schizosaccharomyces pombe. 24 samples. Type: Expression profiling by array.
Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation
GEO Series GSE162865. Streptomyces ambofaciens ATCC 23877. 31 samples. Type: Expression profiling by high throughput sequencing; Other.
Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex: Whole Genome OXBS-Seq Data
GEO Series GSE184013. Mus musculus. 12 samples. Type: Methylation profiling by high throughput sequencing.
Novel parent-of-origin specific differentially methylated loci on chromosome 16
GEO Series GSE125589. Homo sapiens. 10 samples. Type: Methylation profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.