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197 results for “comparative genetics”
A comparative evaluation of ChatGPT 3.5 and ChatGPT 4 in responses to selected genetics questions - Full study data
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Data from: Does mating behaviour affect connectivity in marine fishes? Comparative population genetics of two protogynous groupers (Family Serranidae)
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Data from: Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes
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Data from: Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.
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Comparative analysis of genetic and morphological variation within the Platanthera hyperborea complex (Orchidaceae)
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Data for: The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey
<p>Coevolutionary theory predicts that differences in the genetic demography of interacting species can influence patterns of local adaptation <span>by </span>affecting the potential of local populations to respond to selection. <span>We conducted a comparative phylogeographic study of</span> venomous rattlesnakes and their venom-resistant ground squirrel prey across California<span>, and </span>assessed <span>how </span>effective population size (N<sub>e</sub>) estimates correspond with a previously documented pattern of rattlesnake local adaptation<span>. </span><span>Using</span> RAD-seq markers, we detected lineage relationships among both the rattlesnakes <span>(<i>Crotalus </i></span><i><span>oreganus </span>ssp.</i>) and ground squirrels (<i>Otospermophilus sp.</i>) that are incongruent with previous phylogenetic hypotheses. Both rattlesnakes and squirrels share a deep divergence at the Sacramento-San Joaquin River Delta. At this broad phylogeographic scale, <span>we </span>found that the locally adapted rattlesnakes had higher N<sub>e</sub> than squirrels. <span>A</span>t the population scale, snakes also had larger N<sub>e </sub>accompanied by larger values of several metrics of population genetic diversity. However, the specific magnitude of local adaptation of venom activity to ground squirrel venom resistance <span>was </span>not significantly correlated with local differences in N<sub>e</sub> or other diversity statistics between predator and prey populations, suggesting other factors in the geographic mosaic of coevolution contribute to the specific local-scale outcomes of this interaction. These results <span>suggest an evolutionary mechanism that may explain some (but clearly not all) of rattlesnake local adaptation</span> in this coevolutionary interaction – larger population sizes raise adaptive potential of rattlesnakes compared to ground squirrels.</p>
Using multiple seedlots in restoration planting enhances genetic diversity compared to natural regeneration in fragmented tropical forests
<p>Catastrophic degradation of forests is ongoing worldwide and leads to severe forest fragmentation. Restoration plantings are often necessary to restore fragmented forests, complementing the limited natural regeneration. High genetic diversity is critical for the long-term viability of restored forests. However, there is limited knowledge of whether planted populations capture a genetic variation comparable to natural populations. We measured the efficiency of two forest restoration strategies using the common tropical oak <em>Quercus bambusifolia</em>. The multi-seedlot planting was established over ten years by collecting seeds from several locations in fragmented secondary forests of Hong Kong, while the single seedlot planting was established in just one year with seeds from a single natural location. We analysed the genetic diversity and genetic structure from both plantings and compared them with natural populations. The multi-seedlot planting exhibited a higher rate of genetic recovery, greater genetic diversity (He = 0.69), and higher effective population size (Ne_p = 86.5) compared to natural populations (He = 0.66, Ne_p = 64.3, on average) and the single seedlot planting (He = 0.50, Ne_p = 30.8). The multi-seedlot planting erased the effect of seed shadows which was detected in natural populations while the single seedlot planting strengthened the effect. We conclude that capturing high levels of genetic diversity in the collection of propagules is a standard requirement to ensure the long-term viability of forest restoration. Propagule collection over multiple years is required when only a few parental trees are available to avoid founder effects.</p>
Data from: Comparing G: multivariate analysis of genetic variation in multiple populations
The additive genetic variance–covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design.
Data from: Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)
Background: Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice. Results: We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved 'hotspots' in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum. Conclusions: Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.
FIGURE 1 in Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori
FIGURE 1. Whole mount, fresh samples of Holothuria sanctori (1,2) and Holothuria polii (3,4).
FIGURE 1 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers
FIGURE 1. Distribution map of the studied populations.
Data from: Influence of a growth hormone transgene on the genetic architecture of growth-related traits: a comparative analysis between transgenic and wild-type coho salmon
Genetic engineering has been increasingly applied to many commercially important plant and animal species, generating phenotypic changes that are not observed in natural populations and creating genetic interactions that have not experienced natural selection. The degree to and way in which such human-induced genetic variation interacts with the rest of the genome is currently largely unknown. Integrating such information into ecological and risk assessment frameworks is crucial to understand the potential effects of genetically modified organisms in natural environments. Here, we performed QTL mapping to investigate the genetic architecture of growth-related traits in non-transgenic (NT) and growth hormone transgenic (T) coho salmon with large changes in growth and related physiology, with the aim of identifying how an inserted transgene might influence the opportunity for selection. These fish shared the same parental genetic background, thus allowing us to determine whether the same or different loci influence these traits within the two groups. The use of over 1700 loci, derived from Restriction site Associated DNA Sequencing, revealed that different genomic regions were linked with growth over time between the two groups. Additionally, the effect sizes of detected QTL appear to have been influenced by the transgene. Direct comparison of QTL between the T and NT fish during two size-matched periods identified little overlap in their location. Taken together, the results showed that the transgene altered the genetic basis of growth-related traits in this species. The study has important implications for effective conservation and management of wild populations experiencing introduction of transgenes. Evolutionary changes and their ecological consequences may occur at different rates and in different directions in NT versus T individuals in response to selection. Thus assessments of phenotypic change, and hence ecological risk, should be determined periodically to evaluate whether initial estimates made with founder strains remain valid.
FIGURE 14 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 14. Male Boophis obscurus (UADBA uncatalogued) from Ranomafanakely.
FIGURE 2 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 2. Male holotype of Boophis piperatus sp. nov. (ZSM 377/2004) from Ranomafana.
FIGURE 13 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 13. Male holotype of Boophis spinophis sp. nov. (ZSM 376/2004) from Ambatolahy.
FIGURE 17 in Integrative taxonomy of Malagasy treefrogs: combination of molecular genetics, bioacoustics and comparative morphology reveals twelve additional species of Boophis 2383
FIGURE 17. Female holotype of Boophis praedictus sp. nov. (ZMA 20131) from Vevembe.
Figure 7 from: Kuznetsova V, Aguin-Pombo D (2015) Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 63-93. https://doi.org/10.3897/zookeys.538.6724
Figure 7 - Histogram showing the distribution of female diploid chromosome numbers in Cicadomorpha at species and generic levels, based on analysis of 511 species and 335 genera of the families Cicadellidae, Membracidae, Ulopidae, Ledridae, Aetalionidae, Cercopidae, Aphrophoridae, Machaerotidae, Clastopteridae, Cicadidae, and Myerslopiidae.
Figure 5 from: Kuznetsova V, Aguin-Pombo D (2015) Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 63-93. https://doi.org/10.3897/zookeys.538.6724
Figure 5 - Histogram showing the distribution of female diploid chromosome numbers in Cercopoidea at species and generic levels, based on analysis of 50 species and 23 genera of the families Cercopidae, Aphrophoridae, Machaerotidae, and Clastopteridae.
Figure 1 from: Kuznetsova V, Aguin-Pombo D (2015) Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 63-93. https://doi.org/10.3897/zookeys.538.6724
Figure 1 - Histogram showing the distribution of female diploid chromosome numbers in Fulgoroidea at species and generic levels, based on analysis of 308 species and 148 genera of the families Tettigometridae, Delphacidae, Cixiidae, Kinnaridae, Meenoplidae, Derbidae, Achilidae, Achilixiidae, Dictyopharidae, Fulgoridae, Issidae, Caliscelidae, Acanaloniidae, Nogodinidae, Ricaniidae, Flatidae, Hypochthonellidae, Lophopidae, Eurybrachyidae, and Gengidae.
Figure 3 from: Kuznetsova V, Aguin-Pombo D (2015) Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 63-93. https://doi.org/10.3897/zookeys.538.6724
Figure 3 - Histogram showing the distribution of female diploid chromosome numbers in Cicadellidae at species and generic levels, based on analysis of 387 species and 263 genera.
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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.