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58 results for “diversification dynamics”
Data from: Biotic and abiotic factors driving the diversification dynamics of Crocodylia
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Data from: Decoupled diversification dynamics of feeding morphology following a major functional innovation in marine butterflyfishes
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Data for manuscript: Extinction pulse at Eocene–Oligocene boundary drives diversification dynamics of the two Australian temperate floras
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Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multi-scale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of extant strains, so that populations have very low similarity compared over the long term. However in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.
Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification
Colonization of novel hosts is thought to play an important role in parasite diversification, yet little consensus has been achieved about the macroevolutionary consequences of changes in host use. Here we offer a mechanistic basis for the origins of parasite diversity by simulating lineages evolved in silico. We describe an individual-based model in which (i) parasites undergo sexual reproduction limited by genetic proximity, (ii) hosts are uniformly distributed along a one-dimensional resource gradient, and (iii) host use is determined by the interaction between the phenotype of the parasite and a heterogeneous fitness landscape. We found two main effects of host use on the evolution of a parasite lineage. First, the colonization of a novel host allowed parasites to explore new areas of the resource space, increasing phenotypic and genotypic variation. Second, hosts produced heterogeneity in the parasite fitness landscape, which led to reproductive isolation and therefore, speciation. As a validation of the model, we analyzed empirical data from Nymphalidae butterflies and their host plants. We then assessed the number of hosts used by parasite lineages and the diversity of resources they encompass. In both simulated and empirical systems, host diversity emerged as the main predictor of parasite species richness.
Differential geographical and ecological dynamics allow diversification of morphologically convergent giant bromeliads in the Atlantic Forest
<p>Aim: This paper investigates evolutionary mechanisms that allow morphologically convergent lineages share the same geographical space. We compared the events occurred along the diversification of <i>Karawata</i> and <i>Aechmea</i> subgen. <i>Chevaliera</i> in Atlantic Forest by 1) verifying whether the climatic niches and habitats of <i>Karawata </i>and <i>Aechmea </i>subgen.<i> Chevaliera</i> are similar; 2) testing whether the two groups had the same pattern of colonization in the Atlantic Forest; and 3) evaluating whether they had the same evolutionary dynamics of environmental space occupation. We see the two bomeliad lineages as a model case to understand sympatric diversification in the Atlantic Forest biome.</p> <p>Location: Brazilian Atlantic Forest</p> <p>Taxon: <i>Karawata</i> and <i>Aechmea </i>subgen. <i>Chevaliera</i> (Bromeliaceae: Bromelioideae)</p> <p>Methods: We explored differences in evolutionary dynamics between the lineages analyzing the divergence times, estimating ancestral ranges and habitats, testing niche similarity and evaluating shifts in speciation dynamics.</p> <p>Results: <i>Karawata </i>and <i>A. </i>subgen. <i>Chevaliera </i>most likely originated in the Pliocene and diversified during the Pleistocene. The two clades originated in ombrophilous forests and shared a similar environmental space. However, <i>Karawata </i>and <i>A. </i>subgen. <i>Chevaliera </i>show different dynamics in the occupation of geographical and environmental spaces. Our results suggest that the São Francisco and Jequitinhonha Rivers acted as geographical barriers for <i>Karawata </i>and <i>A. </i>subgen. <i>Chevaliera</i>.</p> <p>Main Conclusions: Differences in spatial and environmental evolutionary dynamics allow the two groups to occupy similar habitats as well as environmental and geographical spaces in the Brazilian Atlantic Forest.</p>
Data from: Uncovering higher-taxon diversification dynamics from clade age and species-richness data
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Data from: The ecological dynamics of clade diversification and community assembly
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Data from: Timetree of Aselloidea reveals species diversification dynamics in groundwater
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Data from: Interspecific geographic range size–body size relationship and the diversification dynamics of Neotropical Furnariid birds
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Differential geographical and ecological dynamics allow diversification of morphologically convergent giant bromeliads in the Atlantic Forest
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Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin
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Data from: Congruent phylogenetic and fossil signatures of mammalian diversification dynamics driven by tertiary abiotic change
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Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification
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Single-Cell Decoding of the Clinical Outcome-Associated Diversification and Dynamic Changes of CAR-T Cells in Patients with B-cell ALL
GEO Series GSE162975. Homo sapiens. 196 samples. Type: Expression profiling by high throughput sequencing.
The error in Bayesian phylogenetic reconstruction under diversification dynamics with simultaneous speciation events
<p>Dataset for 'The error in Bayesian phylogenetic reconstruction under diversification dynamics with simultaneous speciation events', by Laudanno, Bilderbeek & Etienne</p>
Data from: Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica
Studies of postglacial range shifts could enhance our understanding of seaweed species' responses to climate change, and hence facilitate the conservation of natural resources. However, the distribution dynamics and phylogeographic diversification of the commercially and ecologically important kelp Saccharina japonica in the Northwest Pacific (NWP) are still poorly surveyed. In this study, we analyzed the evolutionary history of S. japonica using two mitochondrial markers and 24 nuclear microsatellites. A STRUCTURE analysis revealed two partially isolated lineages: lineage H, which is scattered along the coast of Japan; and lineage P, which occurs along the west coast of the Japan Sea. Ecological niche modeling projections to the Last Glacial Maximum (LGM) revealed that the southern coasts of the Japan Sea and the Pacific side of the Oshima and Honshu Peninsulas provided the most suitable habitats for S. japonica, implying that these regions served as ancient refugia during the LGM. Ancient isolation in different refugia may explain the observed divergence between lineages P and H. An approximate Bayesian computation analysis indicated that the two lineages experienced post‐LGM range expansion, and that postglacial secondary contact occurred in Sakhalin. Model projections into the year 2100 predicted that S. japonica will shift northwards and lose its genetic diversity center on the Oshima Peninsula in Hokkaido and Shimokita Peninsula in Honshu. The range shifts and evolutionary history of S. japonica improve our understanding of how climate change impacted the distribution range and diversity of this species and provide useful information for the conservation of natural resources under ongoing environmental change in the NWP.
Data from: Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica
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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.