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Figure S18 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S18. Phylogeny of Caesalpinioideae. RAxML species tree based on the nucleotide alignment of all genes without orthology assessment. Bootstrap support values are only shown for nodes with <100% bootstrap support.
Figure S20 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S20. Phylogeny of Caesalpinioideae. RAxML species tree based on the amino acid single-copy genes alignment. Bootstrap support values are only shown for nodes with <100% bootstrap support.
Figure S17 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S17. Phylogeny of Caesalpinioideae. RAxML species tree based on the nucleotide single-copy genes alignment. Bootstrap support values are only shown for nodes with <100% bootstrap support.
Figure S16 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S16. Phylogeny of Caesalpinioideae. ASTRAL species tree based on the 821 single-copy gene trees and the 665 ortholog trees resulting from orthology assessment. 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.
Figure S15 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S15. Phylogeny of Caesalpinioideae. ASTRAL species tree based on the 821 single-copy gene trees and the 165 multi-copy gene trees without orthology assessment. 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.
Figure S29 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S29 (lef). Chloroplast gene tree for Caesalpinioideae based on analysis of 72 plastid genes using RAxML. All nodes have maximal bootstrap support except those labelled with actual support values <100%.
Figure S13 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S13 (lef).'oot-to-tip length variances per gene tree. The cut-off of 0.009 is indicated with a dashed vertical line.
Figure S26 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S26. Tanglegram comparing the ASTRAL single-copy genes phylogeny (Figure S14) with the PhyloBayes phylogeny (Figure S23).
Figure S23 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S23. Phylogeny of Caesalpinioideae. PhyloBayes species tree. Posterior probability support values are only shown for nodes with a posterior probability <1.
Figure S10 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S10 (lef). Numbers of genes with potential paralogs per sample. The eleven samples with the most potential paralogs are labelled.
Figure S25 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S25. Tanglegram comparing the ASTRAL single-copy genes phylogeny (Figure S14) with the RAxML amino acid single-copy genes phylogeny (Figure S20).
Figure S28 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S28. Levels of topological congruence between phylogenies generated in different ways, estimated as Robinson-Foulds (RF) distances between species trees. Exact values are in Table S17. Thickness of the connecting lines reflects RF distance. Abbreviations are as follows 'AS' = ASTRAL-3; 'RA' = RAxML; '997' = all genes without paralogs, '997p'= all genes with paralogs, 'SC' = single-copy genes; 'NT' = nucleotide alignment; 'AA' = amino acid alignment; 'PB' = PhyloBayes phylogeny; 'CP' = chloroplast phylogeny.
Figure S40 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S40. Phyloregionalization of Australia 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 S44 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S44. Phyloregionalization per continent using the genus-level Mimosoid phylogeny (rather than the metachronogram). Caption otherwise as for Figure 3.
Figure S41 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S41. Phyloregionalization of the global tropics 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 S39 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S39. Phyloregionalization of Asia 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 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.
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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.
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DANDI Archive for NWB datasets
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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.