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58 results for “diversification dynamics”
Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - phylogenetic data
<p>This submission supplements the manuscript entitled <em>Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification</em> by <strong>Frida A.A. Feijen, Rutger A. Vos, Jorinde Nuytinck & Vincent S.F.T. Merckx.</strong></p> <p>The contents of this submission are dating analysis results for rootings of the land plant topology. Contains the following files:</p> <ul> <li>*.log.gz BEAST logs</li> <li>*.trees.gz BEAST trees</li> <li>*.tiff screen dumps of tracer, showing the burn-in</li> <li>*.consensus.trees produced with treeannotator</li> </ul> <p><strong>For more information</strong>: https://github.com/naturalis/mycorrhiza/tree/v1.0.0</p>
Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record
<p>Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: I) manually curated genus ranges, II) published text-mined genus ranges, III) non-revised Paleobiology Database (PBDB) records, IV) revised and augmented PBDB records. All datasets revealed increased origination rates in the Albian, and a twin K-Pg and Danian extinction rate peak. High origination rates in the late Selandian-Ypresian in Dataset I indicate the onset of an ascophoran-grade radiation. Lineage-through-time plots confirm the macroevolutionary lag preceding the radiation of cheilostomes in the mid-Cretaceous, and their renewed diversification in the late Paleocene and Eocene. A multivariate birth-death model indicates that origination rates are shaped by diversity-dependent dynamics coupled with a positive correlation with sea surface temperature, while extinction rates negatively correlate with sea level. Text-mined data provide broadly similar rate dynamics as manually curated data, although discrepancies could be attributed to the omission of key literature in Dataset II, and the inclusion of new published and unpublished data, and revised ranges in Dataset I. Revision and augmentation of PBDB occurrences were necessary to generate rate profiles akin to those of Datasets I and II and highlight the risks of using unedited occurrence data. Our results support the widely held assumption that diversification dynamics are controlled by both biotic and abiotic factors and pave the way for integrating fossils with molecular phylogenies to study these processes in more detail.</p>
Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
<p>Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation likely accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.</p>
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
<p><span>Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, climate) or biotic factors (traits, interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification.</span></p> <p><span>We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and disparification over time in climate and trait space, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates.</span></p> <p><span>We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later disparification in floral trait space allowed for the exploitation of wider pollination niches (i.e., shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights important pre-adaptations to mountain colonization, specifically woody habit and larger flowers. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and pre-adapted traits were critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification.</span></p>
Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record
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Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
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Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
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Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes
<p>Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8–12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.</p>
Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography
<p>The general dynamic model (GDM) of oceanic island biogeography views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, <em>Cyrtandra </em>and inferred directionality of dispersal and founder events throughout the four biogeographical units of the Indo-Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area, followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in <em>Cyrtandra </em>follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of <em>Cyrtandra</em> in the Southeast Asian grade showed early bursts followed by a plateau, which is consistent with adaptive radiation. We did not detect signals of diversity-dependent diversification, and this is attributed to Southeast Asian cyrtandras<em> </em>occupying various niche spaces, evident by their wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model, wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.</p>
Data from "Bending the course of evolution: how mutualistic interactions affect macroevolutionary dynamics of diversification in mimetic Ithomiini butterflies"
<p>Data and codes for the analyses from Chazot et al. "Bending the course of evolution: how mutualistic interactions affect macroevolutionary dynamics of diversification in mimetic Ithomiini butterflies". Check README for more information about the files. </p>
Data from: Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation
<p><span>Adaptive radiation</span><span> is proposed to play a key role in generating differences in species richness among lineages and geographic regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analyzing <em>i</em>) the temporal patterns of diversification of Caribbean <em>Eleutherodactylus</em> frogs, and <em>ii</em>) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of <em>Eleutherodactylus</em> differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation, which gradually decreases towards the present. <em>Eleutherodactylus</em> diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, <em>Eleutherodactylus</em> shows higher carrying capacity. Our results indicate that ecological opportunity <em>per se</em> is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.</span></p>
Sims et al. A Tale of Two Pools: The Dynamic Influence of Subsurface Geological Processes on the Assembly and Diversification of Thermophilic Microbial Communities in Hydrothermal Systems - Supplementary Datasets
<p>These datasets comprise the supplementary datasets found in Sims et al. A Tale of Two Pools: The Dynamic Influence of Subsurface Geological Processes on the Assembly and Diversification of Thermophilic Microbial Communities in Hydrothermal Systems, <strong><em>Geochimica et Cosmiochimica Act </em></strong></p>
Data from: Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation
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Data from: Global diversification dynamics since the Jurassic: Low dispersal and habitat-dependent evolution explain hotspots of diversity and shell disparity in River Snails (Viviparidae)
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Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes
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Computing tree size under dynamical models of diversification
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Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography
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Scripts from: Distinct intraspecific diversification dynamics in Neotropical montane versus lowland canopy birds (Thraupidae: <em>Tangara</em>) revealed by whole-genome comparative phylogeography
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Data from: The effects of cryptic diversity on diversification dynamics analyses in Crocodylia
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Gene expression dynamics during rapid organismal diversification of African cichlid fishes
<p>Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here, we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of six different organs in 74 cichlid species representing all subclades of this radiation, we demonstrate that the rate of gene expression evolution varies among organs, transcriptome parts, and the subclades of the radiation, indicating different strengths of selection. We found that the non-coding part of the transcriptome evolved more rapidly than the coding part, and that the gonadal transcriptomes evolved more rapidly than the somatic ones, with the exception of liver. We further show that the rate of gene-expression change was not constant over the course of the radiation but accelerated at its later phase. Finally, we show that – at the per-gene level – the evolution of expression patterns is dominated by stabilizing selection.</p>
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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.