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Figure S37 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S37. Phyloregionalization of South 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 S21 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S21. Phylogeny of Caesalpinioideae. RAxML species tree based on the amino acid alignment of all genes without orthology assessment. Bootstrap support values are only shown for nodes with <100% bootstrap support.
Figure S38 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S38. Phyloregionalization of Africa 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 S43 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S43. Climatic distinctiveness of phyloregions. Each subplot shows, for phyloregionalization analyses with two to eight phyloregions performed using the metachronogram, how many of the resulting phyloregions have statistically significant different climatic values from the other regions based on mean annual precipitation (P), precipitation seasonality (Pseas), and dry season length.
Figure S34 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S34. Metachronogram with the names and locations of all subtrees (coloured branches) that were grafed onto the phylogenomic backbone (black branches).
Figure S19 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S19. Phylogeny of Caesalpinioideae. RAxML species tree based on the nucleotide alignment of all genes with orthology assessment. Bootstrap support values are only shown for nodes with <100% bootstrap support.
Figure S24 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S24. Tanglegram comparing the ASTRAL single-copy genes phylogeny (Figure S14) with the RAxML nucleotide single-copy genes phylogeny (Figure S17).
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.
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