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151 results for “genome size”
Data from: Evolutionary patterns of ploidy and genome size variations show positive correlations with taxonomic diversity in tropical gingers (Zingiberaceae)
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Data from: Roads to isolation: similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes
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Data from: Heritability estimates from genome wide relatedness matrices in wild populations: application to a passerine, using a small sample size
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Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages
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Data from: Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish
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Data from: The battle of the sexes over seed size: support for both kinship genomic imprinting and interlocus contest evolution
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Data from: Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA
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Genomic prediction with non-additive effects in beef cattle: Stability of variance component and genetic effect estimates against population size
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Data from: Karyotype and genome size variation in genus Ajuga L. (Ajugoideae–Lamiaceae)
Chromosome number changes and karyotype evolution play an important role in plant genome diversification and eventually in speciation. The genus Ajuga L. (Lamiaceae) has approximately 50 species distributed in temperate to subtropical regions. Four of these species are currently recognized in Korea (A. decumbens Thunb., A. multiflora Bunge, A. nipponensis Makino and A. spectabilis Nakai). Understanding the karyotype evolution in Ajuga has been hampered by the small size of their chromosomes and symmetrical karyotypes. Here we used classic Feulgen staining to establish chromosome numbers and construct karyotypes of the four species of Ajuga recognized in Korea and flow cytometry was used to study their variation in genome. The chromosome number of all investigated plants was 2n = 32. Still, the 2C DNA content ranged from 2.18 pg (A. decumbens) to 4.53 pg (A. multiflora). While the chromosome numbers were the same for all investigated species, the genome size variation could potentially be used as a taxonomic marker.
Data from: Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution
Genomewide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so‐called "chromosome partitioning" where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has now been repeatedly used in other species, but there has been no evaluation of the suitability of this method in species that can differ in their genome characteristics such as number and size of chromosomes. Nor has the influence of sample size, heritability of the trait, effect size distribution of loci controlling the trait or the physical distribution of the causal loci in the genome been examined. Using simulated data, we show that these characteristics have major influence on the inferences of the genetic architecture of traits we can infer using chromosome partitioning analyses. In particular, small variation in chromosome size, small sample size, low heritability, a skewed effect size distribution and clustering of loci can lead to a loss of power and consequently altered inference from chromosome partitioning analyses. Future studies employing this approach need to consider and derive an appropriate null model for their study system, taking these parameters into consideration. Our simulation results can provide some guidelines on these matters, but further studies examining a broader parameter space are needed.
Data from: Chromosome number evolves independently of genome size in a clade with non-localized centromeres (Carex: Cyperaceae)
The effects of chromosome rearrangement on genome size are poorly understood. While chromosome duplications and deletions have predictable effects on genome size, chromosome fusion, fission, and translocation do not. In this study, we investigate genome size and chromosome number evolution in 87 species of Carex, one of the most species-rich genera of flowering plants and one that has undergone an exceptionally high rate of chromosome rearrangement. Using phylogenetic generalized least squares regression, we find that the correlation between chromosome number and genome size in the genus grades from flat or weakly positive at fine phylogenetic scales to weakly negative at deeper phylogenetic scales. The rate of chromosome evolution exhibits a significant increase near the crown of a species-rich clade that arose approximately 5 million years ago. Genome size evolution, however, demonstrates a nearly constant rate across the entire tree. We hypothesize that this decoupling of genome size from chromosome number helps explain the high lability of chromosome number in the genus, as it reduces indirect selection on chromosome number.
Data from: Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants
A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast, and nuclear genomes and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynonymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate that drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of divergence between populations, generating higher rates of diversification. These observations link mutation in individuals to population-level processes and to patterns of lineage divergence.
Data from: You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts
There exists remarkable interspecific variation in mitochondrial sequence evolution rates and in mitochondrial genome sizes. A number of hypotheses based on the forces of mutation and selection have been proposed to explain this variation. Among such hypotheses, we test three: 1) the 'longevity-dependent selection', 2) the 'functional constraints' and 3) the 'race for replication' hypotheses, using published mtDNA genomic sequences of 47 Nematoda species. We did not find any relationship between body size (used as a proxy for longevity) and genome size or the substitution rate of protein sequences, providing little evidence for the first hypothesis. Parasitic species from different thermal habitats, as determined by their definitive host type (ectothermal vs. endothermal), did not differ in their rates of protein evolution. Therefore, little support was obtained for the second hypothesis. However, we revealed that mitogenomes of parasites of endotherms were significantly smaller than those of parasites of ectotherms, supporting the race for replication hypothesis. As mitochondrial genomes of endothermal animals are usually more compact than those of ectothermal animals, intriguingly, nematode parasites of endotherms and ectotherms exhibit similar patterns of mtDNA length variation to their hosts.
Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species
Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum); patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated ddRAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning.
Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds
The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.
Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison
<p>Petal size determines the value of ornamental plants, and thus their economic worth. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes regulating petal size in rapeseed (<i>Brassica napus</i>), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 17 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with extreme differences in petal size identified 11 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, <i>BnaA05</i><i>.</i><i>RAP2.2</i> homologous to <i>RAP2.2</i> in rapeseed may be a critical gene negatively influencing petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two extreme accessions were determined mainly by cell number differences. Finally, we propose a preliminary model for the control of petal size in rapeseed. Our results provide insights into the genetic mechanisms regulating petal size, and also lay the foundation for a better understanding of petal development in plants.</p>
Figure 3 from: Mitrenina EY, Erst AS, Peruzzi L, Skaptsov MV, Ikeda H, Nikulin VY, Wang W (2021) Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae). PhytoKeys 187: 207-227. https://doi.org/10.3897/phytokeys.187.75715
Figure 3 Haploid idiograms of white-flowered Eranthis sect. Shibateranthis species. I–VIII – chromosome pairs; m – metacentric chromosome; sm – submetacentric chromosome; st – subtelocentric chromosome; t – acrocentric chromosome; T – telocentric chromosome; B – B chromosome.
Figure 2 from: Mitrenina EY, Erst AS, Peruzzi L, Skaptsov MV, Ikeda H, Nikulin VY, Wang W (2021) Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae). PhytoKeys 187: 207-227. https://doi.org/10.3897/phytokeys.187.75715
Figure 2 Mitotic metaphase plates of white-flowered Eranthis sect. ShibateranthisAE. lobulata, 2n = 16 BE. stellata (pop. 2), 2n = 16 CE. stellata (pop. 6), 2n = 16 DE. tanhoensis (pop. 12), 2n = 14 EE. tanhoensis (pop. 10), 2n = 14+0–8B (arrows point at B chromosomes) FE. sibirica (pop. 15), 2n = 42 GE. byunsanensis, 2n = 16 (arrows point at the heteromorphic chromosome pair) HE. pinnatifida (pop. 21), 2n = 16 IE. pinnatifida (pop. 20), 2n = 16 (arrows point at heteromorphic chromosome pair). Scale bars: 10 μm. Microphotographs by E.Yu. Mitrenina.
Figure 1 from: Mitrenina EY, Erst AS, Peruzzi L, Skaptsov MV, Ikeda H, Nikulin VY, Wang W (2021) Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae). PhytoKeys 187: 207-227. https://doi.org/10.3897/phytokeys.187.75715
Figure 1 The studied species of white-flowered Eranthis sect. ShibateranthisAE. stellata (photo by V.V. Yakubov) BE. sibirica (photo by A.S. Erst); CE. tanhoensis (photo by A.S. Erst) DE. lobulata (photo by K.-L. Xiang) EE. pinnatifida (photo by A.S. Erst) FE. byunsanensis (photo by H.J. Choi).
Figure 4 from: Mitrenina EY, Erst AS, Peruzzi L, Skaptsov MV, Ikeda H, Nikulin VY, Wang W (2021) Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae). PhytoKeys 187: 207-227. https://doi.org/10.3897/phytokeys.187.75715
Figure 4 PCoA (Coordinate 1, 65.31% of variance explained vs. Coordinate 2, 16% of variance explained) based on six karyological parameters of white-flowered Eranthis sect. Shibateranthis species.
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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)
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.