DOI: 10.5061/dryad.z612jm6jd
title: Data from: Phylogenetic biogeography inference using dynamic paleogeography models and explicit geographic ranges

description: Supplementary data for the manuscript entitled "Phylogenetic
 Biogeography Inference Using Dynamic Paleogeography Models and Explicit
 Geographic Ranges". This dataset contains the supplementary figures
 as well as the basic setup for the simulation used to test the method
 described in the manuscript,and an empirical example using the plant
 family Sapindaceae, analyzed with the program PhyGeo.
description: Paleogeographic
 model The plate motion model is
 Muller
 et al. (2022). The paleolandscape model is based on an unrotated
 version of Cao et al.
 (2017) for the 0-400 Ma period, and an unrotated version of the
 PaleoMap model (Scotese and Wright 2018), for the period 405-540 Ma. Then the pixels were rotated using the Muller et al. (2022) plate motion model. Phylogeny The phylogenetic tree for the empirical dataset was built using the Sapindaceae branch from the phylogenomic analysis of the Sapindales by Joyce et al. (2023), which is quite similar in content (at genus level) to previous biogeographic analyses of the group (Buerki et al. 2011, 2013). As the original publication does not provide a machine-readable file, the relationships and ages were extracted manually from the figures. The phylogeny was augmented with a few terminals from Buerki et al. (2013), mostly to enlarge the sampling of a few genera. The species <em>Matayba tenax</em> was excluded, as it does not match any <em>Maytaba</em> species or synonym in the Plants of the World database, as this particular terminal float in a previous analysis (Buerki et al., 2021), and the genus <em>Matayba</em> did not appear as monophyletic in previous studies (Buerki et al. 2011, 2013). Distribution records Specimen data were obtained from a search of geo-referenced preserved specimens of Sapindaceae in GBIF. The initial number of records was 387.463 occurrences. Data analysis See the readme for the data analysis.
description: # Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models
 and Explicit Geographic Ranges Supplementary data for the manuscript
 entitled *"Phylogenetic Biogeography Inference Using Dynamic
 Paleogeography Models and Explicit Geographic Ranges"*. This dataset
 contains the supplementary figures as well as the basic setup for the
 simulation used to test the method described in the manuscript and an
 empirical example using the plant family
 [Sapindaceae](https://en.wikipedia.org/wiki/Sapindaceae), analyzed with
 the program [PhyGeo](https://github.com/js-arias/phygeo). Files are stored
 mostly as zip files to reduce their size and to mimic a directory
 structure. # Simulations with `PhyGeo` Files prefixed with `sim-` store
 files from the simulations. ## Projects A project is defined by a plate
 motion model and a landscape model, as well as the project files. The
 files contain the suffix `-project.zip`. Inside a zip file the projects
 are called `project.tab`, The file `terms50-100.sh` contains the bash
 script to run all the simulations and the inference. ### Geographic data
 The geographic data model is an equal area pixelation of the Earth, with
 120 pixels in the equatorial ring. ### Paleogeographic models Three
 different models were used for the simulations and inferences. The first
 is a homogeneous sphere without any geographic features, which was used
 without time stages and with time stages every 5 million years. The second
 is a model with the current geographic landscape and time stages every 5
 million years, but without any change in the landscape. The third is a
 full paleogeographic model, using the plate motion model from Müller et
 al. (2022) and the paleolandscape model of Cao et al. (2017) for the time
 stages between 0-400 Ma and from 405 to 540 from the PaleoMap model. The
 model has time stages every 5 million years. *
 `nomotion-motion-120.tab`: Motion model for the homogeneous sphere (no
 motion). * `nomotion-landscape-120.tab`: Landscape model for the
 homogeneous sphere (two pixel types, both used with the same weight). *
 `nomotion-motion-120-5.tab`: Motion model for the homogeneous sphere with
 time slices each 5 million years (no motion). *
 `nomotion-landscape-120.tab`: Landscape model for the homogeneous
 sphere with time slices each 5 million years (two pixel types, both used
 with the same weight). * `muller-motion-120-5.tab`: This file contains the
 pixelated version of the plate motion model, with e120 pixelation, and
 time slices for each 5 million years, from 600 Ma to present. *
 `muller-landscape-cao-paleomap-120-5.tab`: This file contains the
 pixelated version of the paleolandscape model, with e120 pixelation, and
 time slices for each 5 million years, from 540 Ma to present. *
 `cao-landscape-nomotion-120-5.tab`: This file contains the pixelated
 version of the paleolandscape model, with e120 pixelation, and time slices
 for each 5 million years, from 540 Ma to present, but with the present
 time stage in all time stages. ### Landscape pixel weights For the
 homogeneous sphere model, the pixel weights are all identical. | Key |
 Weight | Environment | | --- | ------ | ----------- | | 1 | 1.000 | ocean
 | | 3 | 1.000 | land | The landscape model for the full model and the
 model with the current landscape use the following pixel weights: | Key |
 Weight | Environment | | --- | ------ | ----------------- | | 1 | 0.001 |
 oceanic plateaus | | 2 | 0.005 | continental shelf | | 3 | 1.000 |
 lowlands | | 4 | 1.000 | highlands | | 5 | 0.001 | ice sheets | *
 `no-landscape/model-pix-weights.tab`: This file contains the definition of
 the pixel weights used in the analysis without landscape. *
 `no-landscape/strat/model-pix-weights.tab`: This file contains the
 definition of the pixel weights used in the analysis without landscape. *
 `muller-model/model-pix-weights.tab`: This file contains the definition of
 the pixel weights used in the analysis with a full landscape. *
 `muller-model/no-motion/model-pix-weights.tab`: This file contains the
 definition of the pixel weights used in the analysis with the current
 landscape. * `muller-model/no-landscape/model-pix-weights.tab`: This file
 contains the definition of the pixel weights used in the analysis without
 landscape. ## Simulation setup All simulations are run using the same
 setup. The simulations use the program `pgs`, which is available as part
 of [PhyGeo](https://github.com/js-arias/phygeo). The simulations are
 divided into five time periods that correspond to geological periods: the
 Neogene (23-0 Ma), the Paleogene (66-23 Ma), the Cretaceous (145-66 Ma),
 the Jurassic (201-145 Ma), and the Triassic (251-201 Ma). At each time
 period, the diffusion is divided into three groups: slow ($\lambda$
 between 100 and 1000), average (10-100), and slow (1-10). For each
 combination of time period and diffusion group, 50 trees were simulated.
 For each simulated tree, a random starting root is selected for the
 specified time period, and then a particle evolves in the tree using a
 $\lambda$ value selected at random from the diffusion group. To produce
 the ancestral particles, 100 pixels are selected at random using the
 spherical normal, with a mean equal to the simulated particle and a
 $\lambda$ of 100 (this value is used because it produces geographic points
 that are similar to the observed ones). The pixel locations are
 conditioned by the pixel weight at the time period of the particle. The
 simulation produces three output files: files with suffix `-lambda.tab`
 store the simulated $\lambda$ values; and files with suffix `-trees.tab`
 store the simulated trees, These files are stored with the suffix
 `-sim-lambda-trees.zip`. The third kind of file has suffix
 `-particles.tab` and stores the simulated particles. The compressed files
 have the suffix `-sim-particles.zip`. The files used in the inference to
 test the results are a process of these particle files, which are prefixed
 as `want-`, and contain the pixel frequencies of the simulated pixels at
 each node. The compressed files have the suffix `-want.zip`. In the
 particular case of the inference with the current landscape, this
 frequency file was rotated to the present coordinates and stored with the
 prefix `unrot-`, in this case the compressed file have the suffix
 `want-unrot.zip`. The inference phase produces a file suffixed
 `-infer-lambda.tab` for the inferred $\lambda$ values and a file suffixed
 `-infer-particles.tab` for the inferred particles. The same suffixes are
 used for the compressed files (but using the extension `.zip`). To process
 the particle files, the particles are transformed into a continuous
 distribution using a spherical normal KDE with a $\lambda$ of 1000 that
 produces files stored with the prefix `got-`. These files, the particle
 files and the KDE files are too large for the repository. The output
 results, are files prefixed `pix-`, which is a table with the total number
 of correctly inferred pixels per node (suffix as `-pix.zip`), as well as a
 graph with the proportion of retrieved nodes (prefixed `nodes-`,
 compressed with the suffix `-nodes.zip`). ## Experiments ### Homogeneous
 sphere In the experiments using the homogeneous sphere models, the
 objective is to test the inference of the $\lambda$ parameter. The first
 experiment is stored with the prefix `sim-no-land-`. In the zip files
 prefixed as `sim-no-land-strat`, the simulations used in the homogeneous
 sphere are used, but this time the inference was made with a
 time-stratified model (but not movement). The objective is to test if the
 results are modified by the use of an inference with time stratification
 (that is, by including internodes along the branches that cross each time
 stage). ### Full paleogeographic model In the experiments using the full
 paleogeographic models, the objective is to test the inference of the
 $\lambda$ parameter as well as the inference of the ancestral pixels. The
 first experiment is in the files prefixed `sim-muller-`. For the second
 experiment, stored with the prefix `sim-muller-no-motion-` the same data
 generated in the simulation with the full model is used, but the inference
 model is a time stratified model without any change in the current
 landscape. As biogeographers using such a model would argue that the
 inferred pixels should be considered pixels in a particular location,
 independent of the time stage, the simulated pixels with the full model
 are rotated to the current coordinates. For the third experiment, the data
 produced with the full data model was used, but the inference was made
 without any landscape (and therefore, without any motion). This experiment
 is stored with the files prefixed as `sim-muller-no-land`. # Phylogenetic
 biogeography of Sapindaceae This repository contains the data and results
 of a phylogenetic biogeography analysis of the plant family
 [Sapindaceae](https://en.wikipedia.org/wiki/Sapindaceae) using the
 computer program [PhyGeo](https://github.com/js-arias/phygeo). The
 compressed files are prefixed as `sap-`. ## Source data The data files
 used for the analysis are stored in the file `sap-project.zip`. ###
 Geographic data model The geographic data model is an equal area
 pixelation of the Earth, with 360 pixels in the equatorial ring. *
 `pixels-360.tab`: This file contains the pixel IDs and their associated
 geographic locations. ### Paleogeographic model The plate motion model is
 Muller et al. (2022). The paleolandscape model is based on an unrotated
 version of Cao et al. (2017) for the 0-400 Ma period, and an unrotated
 version of the PaleoMap model (Scotese and Wright 2018), for the period
 405-540 Ma. Then the pixels were rotated using the Müller et al. (2022)
 plate motion model. * `muller-motion-360-5.tab`: This file contains the
 pixelated version of the plate motion model, with e360 pixelation, and
 time slices for each 5 million years, from 600 Ma to present. *
 `muller-landscape-cao-paleomap-360-5.tab`: This file contains the
 pixelated version of the paleolandscape model, with e360 pixelation, and
 time slices for each 5 million years, from 540 Ma to present. ###
 Phylogeny The phylogenetic tree was built using the Sapindaceae branch
 from the phylogenomic analysis of the Sapindales by Joyce et al. (2023),
 which is quite similar in content (at genus level) to previous
 biogeographic analyses of the group (Buerki et al. 2011, 2013). As the
 original publication does not provide a machine-readable file, the
 relationships and ages were extracted manually from the figures. The
 phylogeny was augmented with a few terminals from Buerki et al. (2013),
 mostly to enlarge the sampling of a few genera and fossil taxa used as
 stem calibration points in Joyce et al. (2023) were added as sisters of
 the indicated clade. The species *Matayba tenax* was excluded, as it does
 not match any *Maytaba* species or synonym in the [Plants of the
 World](https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30000506-2) database, as this particular terminal float in a previous analysis (Buerki et al., 2021), and the genus *Matayba* did not appear as monophyletic in previous studies (Buerki et al., 2011, 2013). The tree was then updated with the taxonomy from [Plants of the World](https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30000506-2) in the file `term-taxonomy.tab`, removing synonyms from the tree. * `data-tree.tab`: This file contains the phylogeny as a tab-delimited table. * `tree-joyce2023.svg`: This file contains a drawing of the phylogenetic tree. A tree was edited to remove the four faster branches (*Lecanodiscus*, *Podonephelium*, *Tina*, and *Toechima*). * `tree-trim.tab`: This file contains the phylogeny with the four faster branches removed. ### Distribution records The file `sap-raw-geodata.zip` stores the raw geographic files. Specimen data were obtained from a search of geo-referenced preserved specimens of Sapindaceae in [GBIF](https://doi.org/10.15468/dl.tjpzv2). The initial number of records was 387.463 occurrences. To process the raw occurrence records in GBIF, first a taxonomy using the terminal names was built using the [GBIFer](https://github.com/js-arias/gbifer) tool: ```bash gbifer tax add --rank species --file term-taxonomy.tab &lt; terminals.txt ``` Then the taxonomy is filled with all potential taxon names from the occurrence file from GBIF that are synonyms or sub-species of the names already in the taxonomy file: ```bash gbifer tax match --file term-taxonomy.tab &lt; occurrence.txt ``` The taxonomy file was edited to correct spelling errors and match the [GBIF](https://www.gbif.org/species/6657) taxonomy with the taxonomy from the [Plants of the World](https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30000506-2). This updated taxonomy, in the file `term-taxonomy.tab`, is used to update the phylogenetic tree, removing synonyms from the tree. The taxonomy file was used to extract country information from the specimen records: ```bash gbifer country --tax term.taxonomy.tab &lt; occurrence.txt &gt; countries.tab ``` The resulting file `countries.tab` was edited by removing the countries not explicitly defined in [Plants of the World](https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30000506-2) as native. Then the occurrence table from GBIF was filtered using both the taxonomy file and the country file. ```bash gbifer filter -tax term-taxonomy.tab -country countries.tab &lt; occurrence.txt &gt; occu-in-tree-geo.txt ``` Then the filtered points are converted into a file of points to be used with the [taxRange](https://github.com/js-arias/ranges) tool: ```bash gbifer export -tax term-taxonomy.tab &lt; occu-in-tree-geo.txt &gt; raw-gbif-records.tab ``` The filtered file, contains 68.307 occurrences. As there are no geo-referenced specimen records for *Euchorium cubense*, a record file is created based on [a material citation for the taxon](https://www.gbif.org/occurrence/4135894102). Using the [taxRange](https://github.com/js-arias/ranges) tool, the filtered GBIF records are transformed into a file with presence pixels. ```bash taxrange imp.points -e 360 -f text -o raw-points.tab raw-gbif-records.tab taxrange imp.points -e 360 -f text -o raw-euchorium-points.tab raw-euchorium-records.tab ``` The resulting file is stored in `raw-points.tab`. The directory `terminals` stores the maps of the used distribution ranges. Using the references given by Joyce et al. (2023), I added some fossil records to the file `raw-fossil-records.tab`. Then these records were added to the points file after the project was created. Then fossil records were rotated to their past locations: ```bash phygeo range add -type points -format text project.tab raw-fossils-records.tab phygeo range rotate project.tab ``` ## Analysis ### Landscape | Key | Weights | Environment | | --- | ------- | ----------------- | | 1 | 0.001 | oceanic plateaus | | 2 | 0.005 | continental shelf | | 3 | 1.000 | lowlands | | 4 | 1.000 | highlands | | 5 | 0.001 | ice sheets | * `landscape-key.tab`: This file contains the keys for the landscape features of the paleolandscape model. * `model-pix-weights.tab`: This file contains the definition of the pixel weights used in the analysis. ### Project To set up a project, all input data is added to the project. Here the project is stored in the `project.tab` file: ```bash phygeo geo add -type geomotion project.tab muller-motion-360-5.tab phygeo geo add -type landscape project.tab muller-landscape-cao-paleomap-360-5.tab phygeo geo prior -add model-pix-weights.tab project.tab phygeo tree add -f data-tree.tab project.tab data-tree.tab phygeo range add -f data-points.tab -type points project.tab raw-points.tab phygeo range add -type points project.tab raw-euchorium-points.tab ``` A project using the tree without the four faster branches was created in the same way and stored as `project-trim.tab`. ## Results Inference files are defined with the prefix `sap-infer-`. ### Estimation Maximum likelihood was estimated using the command `diff ml` of `PhyGeo`. The output log is stored in `log-ml.txt` file: ```bash phygeo diff ml project.tab &gt; log-ml.txt ``` The maximum likelihood estimation of $\lambda$ was 19.5. The same procedure was used to estimate the maximum likelihood with the trimmed tree, which was stored as `log-trim-ml.txt`. The maximum likelihood estimation of $\lambda$ was 32.8. To estimate the shape of the likelihood function, the command `diff integrate` was used, estimating likelihood values for $\lambda$ between 0 and 50. The output is stored in `log-file.txt`. ```bash phygeo diff integrate -parts 100 -max 50 project.tab &gt; log-like.txt ``` The same procedure was used for the project with the trimmed tree, but for $\lambda$ values between 0 and 100. The results were stored as `log-trim-like.txt`. To estimate the conditional likelihoods on each node, the command `diff like` was used. For the final results, the $\lambda$ value used was the one estimated without the four fast branches but using the full tree. For the sake of completeness, the same procedure was also used for the maximum likelihood estimate of $\lambda$ with the full tree. ```bash phygeo diff like -lambda 32.8 -o l33 project.tab ``` The stochastic map was performed using 10,000 particles, with the command `diff particles`, and using the conditionals for a $\lambda$ value of 32.8. Again, for the sake of completeness, the same procedure was followed with the results of the maximum likelihood estimate. ```bash phygeo diff particles -p 10000 -i l33-project.tab-joyce2023-32.800000-down.tab -o p-l33 project.tab ``` ### Outputs the raw frequencies are calculated with the command `diff freq` and posted as a compressed file `freq-l33-project.tab.zip`. ```bash phygeo diff freq -i p-l33-joyce2023-32.800000x10000.tab -o freq-l33 project.tab ``` The same procedure was used for the maximum likelihood estimate of $\lambda$,stored as `freq-ml-project.tab.zip`. For the output maps, a KDE using a spherical normal with lambda 1000 was built from the particle file. The same procedure was used for the maximum likelihood estimate. ```bash phygeo diff freq -kde 1000 -i p-l33-joyce2023-32.800000x10000.tab -o kde-l33 project.tab ``` Maps are stored in files `sap-maps-`. The maps use `tree-joyce2023.svg` for the node numbers. ```bash phygeo diff map -c 1440 -key landscape-key.tab -gray -i kde-l33-project.tab-p-l33-joyce2023-32.800000x10000.tab.tab -o "maps-l33-k95/l33-k95" project.tab ``` Other maps are also generated: ```bash phygeo diff map -c 360 -key landscape-key.tab -gray -bound 0.5 -i kde-l33-project.tab-p-l33-joyce2023-32.800000x10000.tab.tab -o "maps-l33-k50/k50" project.tab ``` Maps for lineage richness are stored in the directories `maps-l33-rich` and `maps-l33-rich-u` for the maps using paleogeographic reconstructions and maps rotated to present time, respectively. ```bash phygeo diff map -c 1440 -key landscape-key -gray -richness -i kde-l33-project.tab-p-l33-joyce2023-32.800000x10000.tab.tab -o "maps-l33-rich/l33-r" project.tab phygeo diff map -c 1440 -key landscape-key -gray -richness -unrot -i kde-l33-project.tab-p-l33-joyce2023-32.800000x10000.tab.tab -o "maps-l33-rich/l33-ru" project.tab ``` Each map has the convention `--n-.png`, in which `` indicates the type of the reconstruction (for example l33-k95 for maps form $\lambda$ 32.8, and KDE of 95%), `` indicates the tree (in this case joyce2023), `` is the identifier of the node (that can be consulted in the file `tree-joyce2023.svg`), and `` is the age in million years. The speed is calculated with the command `diff speed`, a tree with the speed of branches is stored as `speed-l33-joyce2023.svg`, and a log file with the distances, the confidence interval, and the average velocity is stored in `speed-l33.tab`. ```bash phygeo diff speed -tree speed-l33 -step 5 -box 10 -i p-l33-joyce2023-32.800000x10000.tab project.tab &gt; speed-l33.tab ``` The same procedure was performed with the maximum likelihood estimate, and the results stored as `speed-ml-joyce.svg` and `speed-ml.tab`. # Sapindaceae data exploration Exploratory data analysis were stored in the files `sap-exp-`. The files used the same nomenclature of the main analysis. ## Source data ### Geographic data model The geographic data model is an equal area pixelation of the Earth, with 120 pixels in the equatorial ring. * `pixels-ids-120.tab`: This file contains the pixel IDs and their associated geographic locations. ### Paleogeographic model Three paleogeographic models are used for the data exploration. The full plate motion model is Muller et al. (2022). The paleolandscape model is based on an unrotated version of Cao et al. (2017) for the 0-400 Ma period, and an unrotated version of the PaleoMap model (Scotese and Wright 2018), for the period 405-540 Ma. Then the pixels were rotated using the Müller et al. (2022) plate motion model. * `muller-motion-120-5.tab`: This file contains the pixelated version of the plate motion model, with e120 pixelation, and time slices for each 5 million years, from 600 Ma to present. * `muller-landscape-cao-paleomap-120-5.tab`: This file contains the pixelated version of the paleolandscape model, with e120 pixelation, and time slices for each 5 million years, from 540 Ma to present. A time-staged model using the current landscape was based on the landscape from the Cao model at the present time stage, but without any movement between time stages and no changes in the geography. * `no-motion-motion-120-5.tab`: This file contains a single plate that is immobile in all time stages. It uses e120 pixelation and time slices for each 5 million years, from 600 Ma to the present. * `cao-landscaoe.nomotion-120-5.tab`: This file contains the pixelated version of the paleolandscape model, with e120 pixelation, and time slices for each 5 million years, from 540 Ma to present, but using the present landscape for all time stages. A model without any movement and any landscape (i.e., a homogeneous sphere) is also used. * `no-motion-motion-120.tab`: This file contains a single plate and a single time stage. It uses e120 pixelation. * `no-motion-landscape-120.tab`: This file contains two landscape features defined for all pixels (used only for drawing) without any time stage. It uses e120 pixelation. ### Phylogeny The same phylogeny as in the main study was used. * `data-tree.tab`: This file contains the phylogeny as a tab-delimited table. The tree was edited to remove the four faster branches (*Lecanodiscus*, *Podonephelium*, *Tina*, and *Toechima*). * `tree-trim.tab`: This file contains the phylogeny with the four faster branches removed. ### Distribution records The same distribution records used for the main study were used, but pixelated into an e120 pixelation. * `data-points.tab`: The file with the pixelated records, using an e120 pixelation. ## Analysis ### Landscape The landscape model for the full model and the model with the current landscape use the same weights as the main study. | Key | Weights | Environment | | --- | ------- | ----------------- | | 1 | 0.001 | oceanic plateaus | | 2 | 0.005 | continental shelf | | 3 | 1.000 | lowlands | | 4 | 1.000 | highlands | | 5 | 0.001 | ice sheets | * `landscape-key.tab`: This file contains the keys for the landscape features of the paleolandscape model. * `model-pix-weights.tab`: This file contains the definition of the pixel weights used in the analyses with landscape. For the homogeneous sphere, only two pixel types are defined; both were set with a weight of 1.0. | Key | Weight | Environment | | --- | ------ | ----------- | | 1 | 1.000 | ocean | | 3 | 1.000 | land | * `noland-pix-weights.tab`: This file contains the definition of the pixel weights used in the analysis without landscape. ### Project Projects are created in the same way as in the main study. * `project-120.tab`: Project for the full model. * `project-landscape-nomotion.tab`: Project for the current landscape. * `project-120-noland.tab`: Project for the homogeneous sphere. * `project-trim.tab`: The same as `project-120.tab`, but using the tree without the four faster branches. ## Results ### Estimation The procedure for estimation is the same as used for the main study. Here only the likelihood estimates are reported, as the resulting files are too large. | Project | MLE Lambda | LogLike | | ------------------ | ---------- | -------- | | Full model | 20.0 | -1135.61 | | Current landscape | 17.1 | -1162.10 | | Homogeneous sphere | &lt;0.005 | -1247.75 | | Trimmed tree | 39.0 | -1015.63 | ### Output The output is too large to be posted here, but as the general results from the full model are cursorily compared with the model with only the current landscape, the result from all nodes is posted here in the directories `maps-full` (for the full model) and `maps-curr` (for the current landscape). # References References are also available as BiBTeX in the file `biblio.bib`. Buerki, S. et al. (2011) An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae. Journal of Biogeography, 38, 531-550. DOI: [10.1111/j.1365-2699.2010.02432.x](https://doi.org/10.1111/j.1365-2699.2010.02432.x). Buerki, S. et al. (2013) The abrupt climate change at the Eocene–Oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages. Annals of Botany, 112, 151-160. DOI: [10.1093/aob/mct106](https://doi.org/10.1093/aob/mct106). Buerki, S. et al. (2021) An updated infra-familial classification of Sapindaceae based on targeted enrichment data. American Journal of Botany, 108, 1234-1251. DOI: [10.1002/ajb2.1693](https://doi.org/10.1002/ajb2.1693). Cao, W. et al. (2017) Improving global paleogeography since the late Paleozoic using paleobiology. Biogeosciences, 14, 5425-5439. DOI: [10.5194/bg-14-5425-2017](https://doi.org/10.5194/bg-14-5425-2017). GBIF.org (2023) GBIF occurrence download. DOI: [10.15468/dl.tjpzv2](https://doi.org/10.15468/dl.tjpzv2). Joyce, E. M. et al. (2023) Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication. Frontiers in Plant Science 14: 1063174. DOI: [10.3389/fpls.2023.1063174](https://doi.org/10.3389/fpls.2023.1063174) Müller, R. D. et al. (2022) A tectonic-rules-based mantle reference frame since 1 billion years ago – implications for supercontinent cycles and plate–mantle system evolution. Solid Earth, 12, 1127-1159. DOI: [10.5194/se-13-1127-2022](https://doi.org/10.5194/se-13-1127-2022). PoWO (2023) Plants of the World Online. URL: [http://www.plantsoftheworldonline.org/](http://www.plantsoftheworldonline.org/). Scotese, C.S., Wrigth, N. (2018) PALEOMAP Paleodigital elevation models (PaleoDEMs) for Phanerozoic. URL: [https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018/](https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018/).