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247 results for “genetic integration”
Data from: Causes and consequences of genetic background effects illuminated by integrative genomic analysis
The phenotypic consequences of individual mutations are modulated by the wild-type genetic background in which they occur. Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist, nor about the mechanisms underlying it. We also lack knowledge on how mutations interact with genetic background to influence gene expression, and how this in turn mediates mutant phenotypes. Furthermore, how genetic background influences patterns of epistasis remains unclear. To investigate the genetic basis and genomic consequences of genetic background dependence of the scallopedE3 allele on the Drosophila melanogaster wing, we generated multiple novel genome-level datasets from a mapping-by-introgression experiment and a tagged RNA gene expression dataset. In addition we used whole genome re-sequencing of the parental lines—two commonly used laboratory strains—to predict polymorphic transcription factor binding sites for SD. We integrated these data with previously published genomic datasets from expression microarrays and a modifier mutation screen. By searching for genes showing a congruent signal across multiple datasets, we were able to identify a robust set of candidate loci contributing to the background-dependent effects of mutations in sd. We also show that the majority of background-dependent modifiers previously reported are caused by higher-order epistasis, not quantitative non-complementation. These findings provide a useful foundation for more detailed investigations of genetic background dependence in this system, and this approach is likely to prove useful in exploring the genetic basis of other traits as well.
Data from: Integrating nonadditive genomic relationship matrices into the study of genetic architecture of complex traits
The study of genetic architecture of complex traits has been dramatically influenced by implementing genome-wide analytical approaches during recent years. Of particular interest are genomic prediction strategies which make use of genomic information for predicting phenotypic responses instead of detecting trait-associated loci. In this work, we present the results of a simulation study to improve our understanding of the statistical properties of estimation of genetic variance components of complex traits, and of additive, dominance, and genetic effects through best linear unbiased prediction methodology. Simulated dense marker information was used to construct genomic additive and dominance matrices, and multiple alternative pedigree- and marker-based models were compared to determine if including a dominance term into the analysis may improve the genetic analysis of complex traits. Our results showed that a model containing a pedigree- or marker-based additive relationship matrix along with a pedigree-based dominance matrix provided the best partitioning of genetic variance into its components, especially when some degree of true dominance effects was expected to exist. Also, we noted that the use of a marker-based additive relationship matrix along with a pedigree-based dominance matrix had the best performance in terms of accuracy of correlations between true and estimated additive, dominance, and genetic effects.
Data from: Pervasive genetic integration directs the evolution of human skull shape
It has long been unclear whether the different derived cranial traits of modern humans evolved independently in response to separate selection pressures or whether they resulted from the inherent morphological integration throughout the skull. In a novel approach to this issue, we combine evolutionary quantitative genetics and geometric morphometrics to analyze genetic and phenotypic integration in human skull shape. We measured human skulls in the ossuary of Hallstatt (Austria), which offer a unique opportunity because they are associated with genealogical data. Our results indicate pronounced covariation of traits throughout the skull. Separate simulations of selection for localized shape changes corresponding to some of the principal derived characters of modern human skulls produced outcomes that were similar to each other and involved a joint response in all of these traits. The data for both genetic and phenotypic shape variation were not consistent with the hypothesis that the face, cranial base and cranial vault are completely independent modules but relatively strongly integrated structures. These results indicate pervasive integration in the human skull and suggest a reinterpretation of the selective scenario for human evolution where the origin of any one of the derived characters may have facilitated the evolution of the others.
Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma
Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of non-degenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of variation among 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (~63%) of the mating-type (mat) chromosome in N. tetrasperma, and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six out of eight lineages show introgression into one of their mat chromosomes, with at least three other Neurospora species acting as donors. The introgressed tracts have been driven to fixation in lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one of the lineages. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.
Supplementary material 2 from: Gauthey Z, Tentelier C, Lepais O, Elosegi A, Royer L, Glise S, Labonne J (2017) With our powers combined: integrating behavioral and genetic data to estimate mating success and sexual selection. Rethinking Ecology 2: 1-26. https://doi.org/10.3897/rethinkingecology.2.14956
JAGS code for the model : Data type: Programming code.
Supplementary material 1 from: Gauthey Z, Tentelier C, Lepais O, Elosegi A, Royer L, Glise S, Labonne J (2017) With our powers combined: integrating behavioral and genetic data to estimate mating success and sexual selection. Rethinking Ecology 2: 1-26. https://doi.org/10.3897/rethinkingecology.2.14956
Data and model outputs : Data type: Body size, behavioural and genetic data, and model output.
Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
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FIGURE 2 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 2. Distribution of species of the Tropidurus spinulosus group in Paraguay.
FIGURE 1 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 1. Distribution of species of the Tropidurus torquatus group in Paraguay.
Linked collectors and determiners for: Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems.
Natural history specimen data linked to collectors and determiners held within, "Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e326c808-0236-47a8-a3a0-4bf06f2d04c1">https://bionomia.net/dataset/e326c808-0236-47a8-a3a0-4bf06f2d04c1</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e326c808-0236-47a8-a3a0-4bf06f2d04c1">https://gbif.org/dataset/e326c808-0236-47a8-a3a0-4bf06f2d04c1</a>. Formatted as a Frictionless Data package.
Data from: Phenotypic and genetic integration of personality and growth under competition in the sheepshead swordtail, Xiphophorus birchmanni
Competition for resources including food, physical space, and potential mates is a fundamental ecological process shaping variation in individual phenotype and fitness. The evolution of competitive ability, in particular social dominance, depends on genetic (co)variation among traits causal (e.g., behavior) or consequent (e.g., growth) to competitive outcomes. If dominance is heritable, it will generate both direct and indirect genetic effects (IGE) on resource-dependent traits. The latter are expected to impose evolutionary constraint because winners necessarily gain resources at the expense of losers. We varied competition in a population of sheepshead swordtails, Xiphophorus birchmanni, to investigate effects on behavior, size, growth, and survival. We then applied quantitative genetic analyses to determine (i) whether competition leads to phenotypic and/or genetic integration of behavior with life history and (ii) the potential for IGE to constrain life history evolution. Size, growth, and survival were reduced at high competition. Male dominance was repeatable and dominant individuals show higher growth and survival. Additive genetic contributions to phenotypic covariance were significant, with the G matrix largely recapitulating phenotypic relationships. Social dominance has a low but significant heritability and is strongly genetically correlated with size and growth. Assuming causal dependence of growth on dominance, hidden IGE will therefore reduce evolutionary potential.
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.
Supplementary material 7 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Historical classification of the Cuban taxa of Magnolia subsect. Talauma
Supplementary material 6 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Discriminant Analysis of Principal Components (DAPC) of Magnolia subsect. Talauma in Cuba
Supplementary material 5 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Structure results of Magnolia subsect. Talauma in Cuba without M. oblongifolia
Data from: Pervasive genetic integration directs the evolution of human skull shape
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Data from: Causes and consequences of genetic background effects illuminated by integrative genomic analysis
Open the record for dataset details and reuse information.
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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.