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212 results for “parallel evolution”
Data from: Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex
Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic diversity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic divergence in face of gene flow.
Data from: Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana
The evolutionary processes and genetics underlying local adaptation at a specieswide level are largely unknown. Recent work has indicated that a frameshift mutation in a member of a family of transcription factors, C-repeat binding factors or CBFs, underlies local adaptation and freezing tolerance divergence between two European populations of Arabidopsis thaliana. To ask whether the specieswide evolution of CBF genes in Arabidopsis is consistent with local adaptation, we surveyed CBF variation from 477 wild accessions collected across the species' range. We found that CBF sequence variation is strongly associated with winter temperature variables. Looking specifically at the minimum temperature experienced during the coldest month, we found that Arabidopsis from warmer climates exhibit a significant excess of nonsynonymous polymorphisms in CBF genes and revealed a CBF haplotype network whose structure points to multiple independent transitions to warmer climates. We also identified a number of newly described mutations of significant functional effect in CBF genes, similar to the frameshift mutation previously indicated to be locally adaptive in Italy, and find that they are significantly associated with warm winters. Lastly, we uncover relationships between climate and the position of significant functional effect mutations between and within CBF paralogs, suggesting variation in adaptive function of different mutations. Cumulatively, these findings support the hypothesis that disruption of CBF gene function is adaptive in warmer climates, and illustrate how parallel evolution in a transcription factor can underlie adaptation to climate.
Data from: Population size changes and selection drive patterns of parallel evolution in a host-virus system
Predicting the repeatability of evolution remains elusive. Theory and empirical studies suggest that strong selection and large population sizes increase the probability for parallel evolution at the phenotypic and genotypic levels. However, selection and population sizes are not constant, but rather change continuously and directly affect each other even on short time scales. Here, we examine the degree of parallel evolution shaped through eco-evolutionary dynamics in an algal host population coevolving with a virus. We find high degrees of parallelism at the level of population size changes (ecology) and at the phenotypic level between replicated populations. At the genomic level, we find evidence for parallelism, as the same large genomic region was duplicated in all replicated populations, but also substantial novel sequence divergence between replicates. These patterns of genome evolution can be explained by considering population size changes as an important driver of rapid evolution.
Data from: Parallel plumage color evolution and introgressive hybridization in wheatears
Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa – pied wheatear (O. pleschanka), Cyprus wheatear (O. cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck-sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20'000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of color phenotypes, and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage color evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.
Fig. 10 in Parallel evolution of leaf morphology in gnetophytes
Fig. 10 Supposed evolutionary relationships among Cretaceous and modern gnetophytes
Data from: How parallel is parallel evolution? A comparative analysis in fishes
Evidence of phenotypic parallelism is often used to infer the deterministic role played by natural selection. However, variation in the extent or direction of divergence is often evident among independent evolutionary replicates, raising the following question: just how parallel, overall, is parallel evolution? We answer this question through a comparative analysis of studies of fishes, a taxon where parallel evolution has been much discussed. We first ask how much of the among-population variance in phenotypic traits can be explained by different "environment" types, such as high predation versus low predation or benthic versus limnetic. We then use phenotypic change vector analysis to quantify variation in the direction (vector angles) and magnitude (vector lengths) of environment-associated divergence. All analyses show high variation in the extent of parallelism—from very high to very low, along with everything in between—highlighting the importance of quantifying parallelism rather than just asserting its presence. Interestingly, instances of low extents of parallelism represent important components of divergence in many cases, promising considerable opportunities for inferences about the factors shaping phenotypic divergence.
Data for: Predation risk and the evolution of a vertebrate stress response: parallel evolution of stress reactivity and sexual dimorphism
<p><span><span><span><span><span><span><span><span><span><span><span><span><span>Predation risk is often invoked to explain variation in stress responses. Yet, the answers to several key questions remain elusive, including: 1) how predation risk influences the evolution of stress phenotypes, 2) the relative importance of environmental versus genetic factors in stress reactivity, and 3) sexual dimorphism in stress physiology. To address these questions, we </span></span>explored variation in stress reactivity (ventilation frequency) in a post-Pleistocene radiation of live-bearing fish, where Bahamas mosquitofish (<i>Gambusia hubbsi</i>) inhabit isolated blue holes that differ in predation risk. Individuals of populations coexisting with predators exhibited similar, relatively low stress reactivity as compared to low-predation populations. We suggest that this dampened stress reactivity has evolved to reduce energy expenditure in environments with frequent and intense stressors, such as piscivorous fish. Importantly, the magnitude of stress responses exhibited by fish from high-predation sites in the wild changed very little after two generations of laboratory rearing in the absence of predators. By comparison, low-predation populations exhibited greater among-population variation and larger changes subsequent to laboratory rearing. These low-predation populations appear to have evolved more dampened stress responses in blue holes with lower food availability. Moreover, females showed a lower ventilation frequency, and this sexual dimorphism was stronger in high-predation populations. This may reflect a greater premium placed on energy efficiency in live-bearing females, especially under high predation risk where females show higher fecundities. Altogether, by demonstrating parallel adaptive divergence in stress reactivity, we highlight how energetic trade-offs may mould the evolution of the vertebrate stress response under varying predation risk and resource availability.</span></span></span></span></span></span></span></span></span></span></span></p>
Figure 3 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)
Figure 3. Morphological differentiation of the dental outline among murine rodents. A, upper molars. Group means on CA1 and 2. Dotted lines show the fossil lineages leading from Progonomys hispanicus to Occitanomys and to Stephanomys, and from Pr. cathalai to Paraethomys. Outlines correspond to some group means. B, upper molars, CA1 and 3. C, lower molars, CA1 and 2. For locality and sample abbreviations see Table 1.
Data for "A massively parallel double selection workflow for the evolution of molecular switches based on surface-display in Escherichia coli" by Givelet, et al., 2023
<p>Data related to a publication on "A massively parallel double selection workflow for the evolution of molecular switches based on surface-display in Escherichia coli"</p> <p> </p> <p>The data contains</p> <p>- FACS data for the images (organized in folders)<br> - images (tiff and jpg)<br> - sequence data (fasta)<br> - one video (mov)</p>
Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory
<p><span>What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. Additionally, pleiotropy may promote repeatability by allowing large fitness benefits of single mutations via adaptive combinations of phenotypic effects. Yet, this latter evolutionary potential may be reaped solely by specific types of mutations able to realize optimal combinations of phenotypic effects while avoiding the costs of pleiotropy. Here, we address the interaction of gene pleiotropy and mutation type on evolutionary repeatability in a meta-analysis of experimental evolution studies with <em>Escherichia coli</em>. We hypothesize that single-nucleotide polymorphisms are principally able to yield large fitness benefits by targeting highly pleiotropic genes, whereas indels and structural variants provide smaller benefits and are restricted to genes with lower pleiotropy. By using gene connectivity as proxy for pleiotropy, we show that nondisruptive single-nucleotide polymorphisms (SNPs) in highly pleiotropic genes yield the largest fitness benefits, since they contribute more to parallel evolution, especially in large populations, than inactivating SNPs, indels and structural variants. Our findings underscore the importance of considering genetic architecture together with mutation type for understanding evolutionary repeatability.</span></p>
Data from: Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species
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Data from: Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife
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Data from: Parallel evolution of behaviour during independent host-shifts following maize introduction into Asia and Europe
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Data from: Identifying drivers of parallel evolution: a regression model approach
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Data from: Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity
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Female and male song exhibit both parallel and divergent patterns of cultural evolution: a long-term study of song structure and diversity in tropical wrens
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Data from: Population size changes and selection drive patterns of parallel evolution in a host-virus system
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Data from: Genomics of parallel experimental evolution in Drosophila
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Data from: Repeated parallel evolution reveals limiting similarity in subterranean diving beetles
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Data from: More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms
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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.