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3,458 results for “chromosomes”
Data from: The evolutionary dynamics of sexually antagonistic mutations in pseudoautosomal regions of sex chromosomes
Sex chromosomes can evolve gene contents that differ from the rest of the genome, as well as larger sex differences in gene expression compared with autosomes. This probably occurs because fully sex-linked beneficial mutations substitute at different rates from autosomal ones, especially when fitness effects are sexually antagonistic (SA). The evolutionary properties of genes located in the recombining pseudo-autosomal region (PAR) of a sex chromosome have not previously been modelled in detail. Such PAR genes differ from classical sex-linked genes by having two alleles at a locus in both sexes; in contrast to autosomal genes, however, variants can become associated with gender. The evolutionary fates of PAR genes may therefore differ from those of either autosomal or fully sex-linked genes. Here, we model their evolutionary dynamics by deriving expressions for the selective advantages of PAR gene mutations under different conditions. We show that, unless selection is very strong, the probability of invasion of a population by an SA mutation is usually similar to that of an autosomal mutation, unless there is close linkage to the sex-determining region. Most PAR genes should thus evolve similarly to autosomal rather than sex-linked genes, unless recombination is very rare in the PAR.
Data from: X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression
Meiotic drivers are selfish genetic elements that promote their own transmission into the gametes, which results in intragenomic conflicts. In the Paris sex-ratio system of Drosophila simulans, drivers located on the X chromosome prevent the segregation of the heterochromatic Y chromosome during meiosis II, and hence the production of Y-bearing sperm. The resulting sex-ratio bias strongly impacts population dynamics and evolution. Natural selection, which tends to restore an equal sex ratio, favors the emergence of resistant Y chromosomes and autosomal suppressors. This is the case in the Paris sex-ratio system where the drivers became cryptic in most of the natural populations of D. simulans. Here, we used a Quantitative Trait Locus (QTL) mapping approach based on the analysis of 152 highly recombinant inbred lines (RILs) to investigate the genetic determinism of autosomal suppression. The RILs were derived from an advanced intercross between two parental lines, one showing complete autosomal suppression while the other one was sensitive to drive. The confrontation of RIL autosomes with a reference XSR chromosome allowed us to identify two QTLs on chromosome 2 and three on chromosome 3, with strong epistatic interactions. Our findings highlight the multiplicity of actors involved in this intragenomic battle over the sex ratio.
FIGURE 4. Chromosome II in Karyotype of Propsilocerus akamusi (Tokunaga) from China (Diptera: Chironomidae)
FIGURE 4. Chromosome II of P. akamusi; designations as in Figs1 and 2.
Data from: Tracking changes in chromosomal arrangements and their genetic content during adaptation
There is considerable evidence for an adaptive role of inversions, but how their genetic content evolves and affects the subsequent evolution of chromosomal polymorphism remains controversial. Here, we track how life-history traits, chromosomal arrangements and 22 microsatellites, within and outside inversions, change in three replicated populations of Drosophila subobscura for 30 generations of laboratory evolution since founding from the wild. The dynamics of fitness-related traits indicated adaptation to the new environment concomitant with directional evolution of chromosomal polymorphism. Evidence of selective changes in frequency of inversions was obtained for seven of 23 chromosomal arrangements, corroborating a role for inversions in adaptation. The evolution of linkage disequilibrium between some microsatellites and chromosomes suggested that adaptive changes in arrangements involved changes in their genetic content. Several microsatellite alleles increased in frequency more than expected by drift in targeted inversions in all replicate populations. In particular, there were signs of selection in the O3+4 arrangement favouring a combination of alleles in two loci linked to the inversion and changing along with it, although the lack of linkage disequilibrium between these loci precludes epistatic selection. Seven other alleles increased in frequency within inversions more than expected by drift, but were not in linkage disequilibrium with them. Possibly these alleles were hitchhiking along with alleles under selection that were not specific to those inversions. Overall, the selection detected on the genetic content of inversions, despite limited coverage of the genome, suggests that genetic changes within inversions play an important role in adaptation.
Data from: Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus
Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from non-model organisms. This manuscript details the application of restriction site associated DNA sequencing (RADseq) to generate a marker dense genetic map for Brook trout (Salvelinus fontinalis). The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic salmon for 38 linkage groups, with Rainbow trout for 37 linkage groups, Arctic char for 36 linkage groups, and with a previously published Brook trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of eight metacentric and 34 acrocentric chromosomes in Brook trout. Six metacentric chromosomes seem to be conserved with Arctic char suggesting there have been at least two species specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome) was mapped to Brook trout BC35, which is homologous with Atlantic salmon Ssa09qa, Rainbow trout Omy25, and Arctic char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.
Data from: Accounting for heteroscedasticity and censoring in chromosome partitioning analyses
A fundamental assumption in quantitative genetics is that traits are controlled by many loci of small effect. Using genomic data, this assumption can be tested using chromosome partitioning analyses, where the proportion of genetic variance for a trait explained by each chromosome (h2c), is regressed on its size. However, as h2c-estimates are necessarily positive (censoring) and the variance increases with chromosome size (heteroscedasticity), two fundamental assumptions of ordinary least squares (OLS) regression are violated. Using simulated and empirical data we demonstrate that these violations lead to incorrect inference of genetic architecture. The degree of bias depend mainly on the number of chromosomes and their size distribution and are therefore specific to the species; using published data across many different species we estimate that not accounting for this effect overall resulted in 28% false positives. We introduce a new and computationally efficient resampling method that corrects for inflation caused by heteroscedasticity and censoring and that works under a large range of data set sizes and genetic architectures in empirical data sets. Our new method substantially improves the robustness of inferences from chromosome partitioning analyses.
Data from: Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging
We report a method for the sensitive detection of rare chromosome breaks and translocations in interphase cells. HiBA-FISH (High-throughput break-apart FISH) combines high-throughput imaging with the measurement of the spatial separation of FISH probes flanking target genome regions of interest. As proof-of-principle, we apply hiBA-FISH to detect with high sensitivity and specificity rare chromosome breaks and translocations in the anaplastic large cell lymphoma breakpoint regions of NPM1 and ALK. This method complements existing approaches to detect translocations by overcoming the need for precise knowledge of translocation breakpoints and it extends traditional FISH by its quantitative nature.
FIGURE 1 in The Peruvian species of Cristaria (Malveae, Malvaceae): taxonomic revision, chromosome counts, and breeding system
FIGURE 1. Holotype (Ferreyra 14281) of Cristaria multifida subsp. moquipana.
Figure 6 from: Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L (2021) Chromosome numbers for the Italian flora: 11. Italian Botanist 11: 145-153. https://doi.org/10.3897/italianbotanist.11.70173
Figure 6 Hieracium australe Fr. subsp. australe from Sforza Castle (Milano), 2n = 27. Scale bar: 10 μm.
Figure 5 from: Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L (2021) Chromosome numbers for the Italian flora: 11. Italian Botanist 11: 145-153. https://doi.org/10.3897/italianbotanist.11.70173
Figure 5 Micromeria graeca (L.) Benth. ex Rchb. subsp. graeca from San Marco Argentano (Cosenza), Scalo Ferroviario, 2n = 60. Scale bar: 10 μm.
Figure 4 from: Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L (2021) Chromosome numbers for the Italian flora: 11. Italian Botanist 11: 145-153. https://doi.org/10.3897/italianbotanist.11.70173
Figure 4 Micromeria graeca (L.) Benth. ex Rchb. subsp. consentina (Ten.) Guinea from San Marco Argentano (Cosenza), Scalo Ferroviario, 2n = 30. Scale bar: 10 μm.
Figure 3 from: Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L (2021) Chromosome numbers for the Italian flora: 11. Italian Botanist 11: 145-153. https://doi.org/10.3897/italianbotanist.11.70173
Figure 3 Lysimachia arvensis (L.) U.Manns & Anderb. subsp. arvensis from Fossa Garofala (Palermo), 2n = 40. Scale bar: 10 μm.
Figure 1 from: Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L (2021) Chromosome numbers for the Italian flora: 11. Italian Botanist 11: 145-153. https://doi.org/10.3897/italianbotanist.11.70173
Figure 1 Centaurea aegusae Domina, Greuter & Raimondo from Isola di Favignana (Favignana, Trapani), 2n = 18. Scale bar: 10 μm.
Figure 2 from: Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L (2021) Chromosome numbers for the Italian flora: 11. Italian Botanist 11: 145-153. https://doi.org/10.3897/italianbotanist.11.70173
Figure 2 Hieracium racemosum subsp. lucanum Di Grist., Domina, Gottschl. & Scafidi from Timpa Rossa (Lauria, Potenza) 2n = 27. Scale bar: 10 μm.
Figure 5. Male C in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 5. Male C-banded karyotype of the Guenther's vole from Rodop Mountains.
Figure 4 in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 4. Female metaphase plate and its karyotype of the Guenther's vole from Rodop Mountains.
Figure 2 in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 2. Female metaphase plate and its karyotype of the Guenther's vole from Strandzha Mountain.
Figure 3. Male C in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 3. Male C-banded karyotype of the Guenther's vole from Strandzha Mountain.
Fig. 50 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 50. Degree of external uterine fusion (character 131) optimized onto the strict consensus tree from our character congruence analysis. The ''intermediate'' state of external uterine fusion (character 131: horns one quarter the length of uterine body) is derived from the simplex condition, suggesting that external uterine fusion is not progressive. The equivocal optimization within Phyllostominae is due to missing data in Lonchorhinini. To prevent an equivocal reconstruction for the base of the clade that includes all phyllostomids except desmodontines, we examined trees in which the position of Brachyphylla was resolved and fixed the node at the base of the clade that includes all phyllostomids except desmodontines with the state that occurred under the two alternative placements for this genus.
Fig. 18 in Phylogeny Of Phyllostomid Bats (Mammalia: Chiroptera): Data From Diverse Morphological Systems, Sex Chromosomes, And Restriction Sites
Fig. 18. Closeup view of the lateral column(s) of vibrissae and vibrissal papillae in A. Phyllostomus hastatus (AMNH 202308). B. Rhinophylla pumilio (AMNH 267163). C. Sphaeronycteris toxophyllum (AMNH 194213). D. Noctilio leporinus (AMNH 267408). Scale bar = 5 mm.
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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)
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DANDI Archive for NWB datasets
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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.
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