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479 results for “genomic evolution”
Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
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Data from: Rapid evolution and the genomic consequences of selection against interspecific mating
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Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies
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Data from: A single interacting species leads to widespread parallel evolution of the stickleback genome
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Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure
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Extreme genomic volatility characterises the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes
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Caucasian treasure: genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock
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Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution
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Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes
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Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq
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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: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
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Data from: Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species
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Accelerated mitochondrial genome evolution in parasitic barnacles driven by adaptive and non-adaptive responses
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Data from: A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
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Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
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Molecular Evolution of Tuatara Visual System Datasets: Supporting Data for the Tuatara Genome
<p>Datasets associated with the Molecular Evolution of Tuatara Visual System supplement to the paper: The Tuatara Genome: Insights into Vertebrate Evolution from the Sole Survivor of an Ancient Reptilian Order.</p>
Data from: Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modeling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380–166 kya, expansion of distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated to long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.
Evolution of Rosaceae chloroplast genomes highlights unique Cerasus diversification and independent origins of fruit cherry
<p>Rosaceae plants comprise numerous fruit crops with huge economic values. The lack of genomic characteristics has largely blocked our understanding about the Rosaceae gene and plastome evolution. Here, we analyzed 121 Rosaceae chloroplast (cp) genomes of 51 taxa from 19 genera, predominantly including the Cerasus plants and their relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Protein-coding genes of Rosaceae plastomes were characterized with high proportion (over 50%) of synonymous variants and InDels with multiple triplets. Four photosynthesis-related genes were under Darwin selection, which are unique in woody fruit trees of Rosaceae. We detected considerable variations in genome size among Rosaceae plastomes and observed trivial and obvious structural variation in the examined cp genomes of tribes Pyrodae and Amygdaleae. Phylogenomic analyses and molecular dating highlighted the independent evolution of true cherry, dwarf cherry and relatives. Our findings strongly support to taxonomically treat the monophyletic true cherry group as a separate genus excluding dwarf cherry. High levels of genomic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruit cherries, particularly between cultivated Cerasus psuedocerasus and Cerasus avium. We further proposed an evolutionary model to elucidate multiple genomic introgression events among true cherries occurring since ~15 Mya. Well-resolved maternal phylogeny suggested that the cultivated C. pseudocerasus might be originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where they have subjected to frequent genomic introgression between its presumed wild ancestors and other close relatives. In conclusion, comparative analyses of plastomes and chloroplast genes detected diverse evolutionary behaviors and divergent adaptive selection in Rosaceae. We provide robust evidences for the independent origins and domestication of fruit cherries.</p>
Data from: Genomic evolution of bacterial populations under co-selection by antibiotics and phage
Bacteria live in dynamic systems where selection pressures can alter rapidly, forcing adaptation to the prevailing conditions. In particular, bacteriophages and antibiotics of anthropogenic origin are major bacterial stressors in many environments. We previously observed that populations of the bacterium Pseudomonas fluorescens SBW25 exposed to the lytic bacteriophage SBW25Φ2 and a non-inhibitive concentration of the antibiotic streptomycin (co-selection) achieved higher levels of phage resistance compared to populations exposed to the phage alone. In addition, the phage became extinct under co-selection while remaining present in the phage alone environment. Further, phenotypic tests indicated that these observations might be associated with increased mutation rate under co-selection. In this study, we examined the genetic causes behind these phenotypes by whole-genome sequencing clones isolated from the end of the experiments. We were able to identify genetic factors likely responsible for streptomycin resistance, phage resistance and hypermutable (mutator) phenotypes. This constitutes genomic evidence in support of the observation that while the presence of phage did not affect antibiotic resistance, the presence of antibiotic affected phage resistance. We had previously hypothesized an association between mutators and elevated levels of phage resistance under co-selection. However, our evidence regarding the mechanism was inconclusive, since although with phage mutators were only found under co-selection, additional genomic evidence was lacking and phage resistance was also observed in non-mutators under co-selection. More generally, our study provides novel insights into evolution between univariate and multivariate selection (here two stressors), as well as the potential role of hypermutability in natural communities.
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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.