DOI: 10.5061/dryad.q573n5tqm
title: Data from: Geography and ecology shape the phylogenetic composition of Amazonian tree communities

description: Aim: Amazonia hosts more tree species, from numerous evolutionary lineages
 both young and ancient, than any other biogeographic region. Previous
 studies have shown that tree lineages colonised multiple edaphic
 environments and dispersed widely across Amazonia, leading to a
 hypothesis, which we test, that lineages should not be strongly associated
 with either geographic regions or edaphic forest types. Location:
 Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods:
 Data for the abundance of 5,082 tree species in 1,989 plots were combined
 with a mega-phylogeny. We applied evolutionary ordination to assess how
 phylogenetic composition varies across Amazonia. We used variation
 partitioning and Moran’s eigenvector maps (MEM) to test and quantify the
 separate and joint contributions of spatial and environmental variables to
 explain the phylogenetic composition of plots. We tested the indicator
 value of lineages for geographic regions and edaphic forest types and
 mapped associations onto the phylogeny. Results: In the terra firme and
 várzea forest types, phylogenetic composition varies by geographic region,
 but the igapó and white-sand forest types retain a unique evolutionary
 signature regardless of region. Overall, we find that soil chemistry,
 climate, and topography explain 24% of the variation in phylogenetic
 composition, with 79% of that variation being spatially structured (R 2 =
 19% overall for combined spatial/environmental effects). Phylogenetic
 composition also shows substantial spatial patterns not related to the
 environmental variables we quantified (R 2 = 28%). A greater number of
 lineages were significant indicators of geographic regions than forest
 types. Main conclusions: Numerous tree lineages, including some ancient
 ones (&gt;66 Ma), show strong associations with geographic regions and
 edaphic forest types of Amazonia. This shows that specialization on
 specific edaphic environments has played a long-standing role in the
 evolutionary assembly of Amazonian forests. Furthermore, many lineages,
 even those that have dispersed across Amazonia, dominate within a specific
 region, likely because of phylogenetically conserved niches for
 environmental conditions that are prevalent within regions. 
description: <strong>Geography and ecology shape the phylogenetic
 composition of Amazonian tree communities</strong>
 Data files derived from the abundance of 5,082 tree species in
 1,989 plots across Amazonia and used to support the findings described in
 Luize et al., 2024 Geography and ecology shape the phylogenetic
 composition of Amazonian tree communities, Journal of
 Biogeography. This dataset includes three
 files: 1) Data contains the location of 1,989 tree
 inventory plots in Amazonia, associated evoPCA scores, and environmental
 data for each plot. To produce the evoPCA scores, we combined the
 abundance of 5,082 tree species with the phylogenetic relationships
 between species present in each plot. The environmental data for each plot
 was extracted from referenced data sources based on the locations of the
 plots. For soil attributes, we obtained point-data from soil profiles
 available in Soterlac (Dijkshoorn et al., 2005), ISRIC wise (Batjes,
 2016), RAINFOR sites (Quesada et al., 2010), and Poels (1987), Zuquim et
 al (2019), and van Kekem et al. (1996) and created a loess model based
 (with a span of 0.2, a degree of 2, using Gaussian fitting) on all data
 available (data availability differed per parameter), to estimate the
 gradient of the soil chemical parameters across the entire Amazon
 region. File = “Table_1_Evo_Assemb_Amaz_simpleCC0.csv”
 can be opened with R, text editor, or exported to Excel.
 Rows are the values obtained for each plot
 Column headers are as follows: Axis 1 to
 Axis1983           The evoPCA scores for all axes
 PlotCode           Code of plot as in ATDN database
 Latitude           Plot latitude in decimal degrees
 Longitude        Plot longitude in decimal degrees
 2) a phylogenetic chronogram for the tree species observed in the
 tree inventories. To produce the phylogenetic hypothesis, we used the
 GBOTB phylogeny as the base topology (Smith & Brown, 2018) and the
 Scenario 3 in the V.phylomaker v.2 R package (Jin & Qian, 2022) to
 prune and bind species. File =
 “Phylo_Amazonian_trees_ATDN_1989plots.phy” can be opened with R using
 library “ape” or with the Figtree app 3) Indicator
 analysis table with the results of species and lineages (above species
 level) that were determined as indicators of geographic regions or forest
 types within Amazonia. (Table 3. Nodes and tips determined as significant
 indicators for Amazonian forest types and geographic regions. All those
 taxa determined as indicator has IndVal p.value&lt;0.01 after 999
 permutations. Indicator of: Forest types considered: TF = Terra-firme;
 PZ=White-sand forest; VA=Várzea; IG=Igapó; SW=Swamp; and Geographic
 regions considered: CA=Central Amazonia; SA=Southern Amazonia; EA=Eastern
 Amazonia; NWA=Northwestern Amazonia; SWA=Southwestern Amazonia; GS=Guiana
 Shield. ) Results are described in “Geography and ecology shape the
 phylogenetic composition of Amazonian tree communities”, Luize et al. 2024
 Journal of Biogeography. File =
 “Table_2_Evo_Assemb_Amaz.xlsx” Excel file with the results of indicator
 analysis rows are the values for each lineage or
 species columns are as follows:
 Nodes or tips   The lineages (species or higher level lineages)
 determined as indicators rank         Ranking for the
 lineages indicator values ran_test_for   If the
 indicator value was tested for geographic regions or forest
 types indicator_of          The geographic region or
 the forest type that the lineage was an indicator
 Specificity_A        The specificity statistic as described in
 Legendre & Dufrene original indicator analysis
 publication Fidelity_B              The fidelity
 statistic as described in Legendre & Dufrene original indicator
 analysis publication indval      The Indicator value
 statistic as described in Legendre & Dufrene original indicator
 analysis publication p.value      Associated p values
 for the indval statistic descendentesGenera         
  The genera that were descendants from lineages determined as
 indicators Sharing/Access information – Open
 access Links to other publicly accessible locations of
 the data:
 https://sites.google.com/naturalis.nl/amazon-tree-diversity-network/homepage?authuser=0 Data was derived from the Amazon Tree Diversity Network (ATDN) database. The abundance matrix of species per location is available upon request following ATDN agreements.
description: # Geography and ecology shape the phylogenetic composition of Amazonian
 tree communities
 [https://doi.org/10.5061/dryad.q573n5tqm](https://doi.org/10.5061/dryad.q573n5tqm) Data files derived from the abundance of 5,082 tree species in 1,989 plots across Amazonia and used to support the findings described in Luize et al., 2024 Geography and ecology shape the phylogenetic composition of Amazonian tree communities, Journal of Biogeography. ## Description of the data and file structure This dataset includes three files: 1\) Data contains the location of 1,989 tree inventory plots in Amazonia, associated evoPCA scores, and environmental data for each plot. To produce the evoPCA scores, we combined the abundance of 5,082 tree species with the phylogenetic relationships between species present in each plot. The environmental data for each plot was extracted from referenced data sources based on the locations of the plots. For soil attributes, we obtained point-data from soil profiles available in Soterlac (Dijkshoorn et al., 2005), ISRIC wise (Batjes, 2016), RAINFOR sites (Quesada et al., 2010), and Poels (1987), Zuquim et al (2019), and van Kekem et al. (1996) and created a loess model based (with a span of 0.2, a degree of 2, using Gaussian fitting) on all data available (data availability differed per parameter), to estimate the gradient of the soil chemical parameters across the entire Amazon region. File = “Table_1_Evo_Assemb_Amaz_simpleCC0.csv” can be open with R, text editor, or exported to excel. Rows are the values obtained for each plot Columns headers are as follows: Axis 1 to Axis1983           The evoPCA scores for all axes PlotCode           Code of plot as in ATDN database Latitude           Plot latitude in decimal degrees Longitude          Plot longitude in decimal degrees 2\) a phylogenetic chronogram for the tree species observed in the tree inventories. To produce the phylogenetic hypothesis, we used the GBOTB phylogeny as the base topology (Smith & Brown, 2018) and the Scenario 3 in the V.phylomaker v.2 R package (Jin & Qian, 2022) to prune and bind species. File = “Phylo_Amazonian_trees_ATDN_1989plots.phy”can be open with R using library “ape” or with Figtree app 3\) Indicator analysis table with the results of species and lineages (above species level) that were determined as indicators of geographic regions or forest types within Amazonia. (Table 3. Nodes and tips determined as significant indicators for Amazonian forest types and geographic regions. All those taxa determined as indicator has IndVal p.value&lt;0.01 after 999 permutations. Indicator of: Forest types considered: TF = Terra-firme; PZ=White-sand forest; VA=Várzea; IG=Igapó; SW=Swamp; and Geographic regions considered: CA=Central Amazonia; SA=Southern Amazonia; EA=Eastern Amazonia; NWA=Northwestern Amazonia; SWA=Southwestern Amazonia; GS=Guiana Shield. ) Results are described in “Geography and ecology shape the phylogenetic composition of Amazonian tree communities”, Luize et al. 2024 Journal of Biogeography. File = “Table_2_Evo_Assemb_Amaz.xlsx” excel file with the results of indicator analysis rows are the values for each lineage or species columns are as follows: Nodes or tips          The lineages (species or higer level lineages) determined as indicators rank             Ranking for the lineages indicator values ran_test_for   If the indicator value was tested for geographic regions or forest types indicator_of             The geographic region or the forest type that the lineage was indicator Specificity_A           The specificity statistic as described in Legendre & Dufrene original indicator analysis publication Fidelity_B                 The fidelity statistic as described in Legendre & Dufrene original indicator analysis publication indval         The Indicator value statistic as described in Legendre & Dufrene original indicator analysis publication p.value      Associated p values for the indval statistic descendentesGenera         The genera that were descendants from lineages determined as indicators ## Sharing/Access information Open access [https://sites.google.com/naturalis.nl/amazon-tree-diversity-network/homepage?authuser=0](https://sites.google.com/naturalis.nl/amazon-tree-diversity-network/homepage?authuser=0) Data was derived from the Amazon Tree Diversity Network (ATDN) database. The abundance matrix of species per location is available upon request following ATDN agreements.