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Figure S32 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S32 (lef). Internode certainty values based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). For each node, the upper number shows the quartet-based Extended Quadripartition Internode Certainty (EQP-IC) score calculated with QuartetScores, and the lower number shows the bipartition-based Internode Certainty All score calculated with PhyParts, both rounded down to two digits. Boxes are coloured based on unrounded values: green for values ≥ 0.5, yellow for values ≥ 0 and <0.5, and red for values <0. Branch lengths are set equal for easier visualisation. Inset depicts a correlation plot between the two measures.
Figure S33 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S33 (right).'esults of ASTRAL's polytomy test based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). Node numbers are tests of the null hypothesis that a branch should be replaced by a polytomy. Only node numbers> 0.05 are shown. Branch lengths are set equal for easier visualisation.
Figure S31 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S31. Gene tree incongruence mapped onto the time-calibrated version of the phylogenomic backbone of Caesalpinioideae. Each branch is coloured to reflect the ratio of total supporting versus total conflicting gene trees as determined by PhyParts. Clades named by Koenen et al. (24) are labelled. Two recent radiations in Madagascar, one in the Dichrostachys clade and one in Albizia, are highlighted.
Figure S36 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S36. Phyloregionalization of North America using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S14 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S14. Phylogeny of Caesalpinioideae. ASTRAL species tree based on the 821 single-copy gene trees. Local posterior probability support values are only shown for nodes with a local posterior probability <1. Branch lengths are expressed in coalescent units. Terminal branches were assigned an arbitrary uniform length for visual clarity.
Fig. 2 in Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Fig. 2. Drivers of phylogenetic turnover of Mimosoid legumes across the global lowland tropics. Bars show relative fractions of phylogenetic turnover explained by predictors (rescaled to add up to one). Numbers above bars are absolute explained percentages of turnover (tables S12 and S20). (A) Phylogenetic turnover explained by climatic distance (maroon), geographic distance (blue), or their interaction (cream). Turnover is assessed across four depths in the phylogeny: with the full metachronogram (age cutoff of 0) and with all clades younger than 5, 10, and 20 Ma collapsed. Note that it was not possible to fit a model to the phylogeny collapsed at 20 Ma for the pantropical and Australian models. (B) Phylogenetic turnover explained by MAP (green) and/or annual mean temperature (orange). Turnover is expressed as phylogenetic turnover not explained by geographic distance ("geographic residuals"). (C) Geographic residuals of phylogenetic turnover explained by MAP (green) and/or precipitation seasonality (gray; left) or dry season length (DSL) (i.e., the number of consecutive months with precipitation <100 mm/month; yellow; right). See fig. S45 for results obtained with an alternative, genus-level Mimosoid phylogeny. P, MAP; T, annual mean temperature; Pseas, precipitation seasonality.
Fig. 1 in Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Fig. 1. Mimosoid evolution and diversity across precipitation gradients. (A) Phylogeny of Mimosoid legumes showing the evolution of precipitation niches and transcontinental dispersal events through time. Branch colors correspond to mean annual precipitation (MAP) estimates [see (C) for scale]. Pie charts at tips and nodes of named clades [sensu (24)] represent observed and estimated spatial distributions [based on area definitions in (D)]. Ancestral niches and areas were estimated using a complete metachronogram for Caesalpinioideae, including non-Mimosoid Caesalpinioideae taxa, but only the Mimosoid clade is shown here. Green circles on branches indicate shifts between precipitation categories [following (17)] that encompass a difference of at least 250-mm MAP; red triangles indicate postulated transcontinental dispersals according to the best-supported model. The six most species-rich genera are labeled. (B) Fractions of niche shifts and transcontinental dispersal events, averaged across multiple optimizations, relative to total phylogenetic splits plotted through time for 5-Ma bins. (E) Mimosoid growth form diversity across the tropical precipitation gradient, from deserts with <50-mm MAP (left) through savannas to rain forests with>5000-mm MAP (right). See the Supplementary Results for species names and photographers. See fig. S51 for more information.
Data for: Ecological pathways connecting drought to stream invertebrate community shifts across space and time
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Data and code for: Diversity through space and time in the Upper Jurassic Morrison Formation, western USA
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Data from: Ecological and anthropogenic drivers of waterfowl productivity are synchronous across species, space, and time
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Data from: The pace and drivers of community change vary over space and time
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A transcontinental experiment elucidates (mal)adaptation of a cosmopolitan plant to climate in space and time
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Data from: Iridescence untwined - Honey bees can separate hue variations in space and time
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Data from: Exploring thermal tolerance across time and space in a tropical bivalve, Pinctada margaritifera
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Hummingbird blood traits track oxygen availability across space and time
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Data from: Parasite transmission stage abundance varies in lakes over time and space
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Data from: A pattern-oriented simulation for forecasting species spread through time and space: A case study on an ecosystem engineer on the move
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PIE LTER location and sample dates for sites used in space for time sea level rise study, Rowley, MA.
This dataset contains the GPS-ed locations of the quadrats used for the 2017-2018 Space for Time substitution experiment in tidal creek marshes off the Rowley River and Plum Island Sound in Rowley Massachusetts. The space for time study uses an intensive and comprehensive approach to compare low elevation, Spartina alterniflora marsh areas to higher elevation Spartina patens marsh areas. Other related data files include: HTL-RO-ST-MAR-Biomass, HTL-RO-ST-MAR-Birds, HTL-RO-ST-MAR-Quads, HTL-RO-ST-MAR-Sediments, HTL-RO-ST-MAR-Bites, HTL-RO-ST-MAR-Sticky, HTL-RO-ST-MAR-Decomp, HTL-RO-ST-MAR-Traps, HTL-RO-ST-MAR-Deep_pitfalls
PIE LTER bird observations associated with marsh sites used in space for time sea level rise study, Rowley, MA.
This dataset contains observations of birds foraging at high and low tide at space for time substition plots in tidal creek marshes off the Rowley River and Plum Island Sound in Rowley Massachusetts. The space for time study uses an intensive and comprehensive approach to compare low elevation, Spartina alterniflora marsh areas to higher elevation Spartina patens marsh areas. Birds were observed using timed interval observations, with one sampling bout per tide per site. Other related data files include: HTL-RO-ST-MAR-Sites, HTL-RO-ST-MAR-Biomass, HTL-RO-ST-MAR-Quads, HTL-RO-ST-MAR-Sediments, HTL-RO-ST-MAR-Bites, HTL-RO-ST-MAR-Sticky, HTL-RO-ST-MAR-Decomp, HTL-RO-ST-MAR-Traps, HTL-RO-ST-MAR-Deep_pitfalls
PIE LTER predation and herbivory rates associated with marsh sites used in space for time sea level rise study, Rowley, MA.
This dataset contains aggregated observations of predation and herbivory rates on tethered bait in each quadrat of the space for time substitution observations in salt marsh sites in Rowley and Newbury, MA.
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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.