This repository contains the data and results of a phylogenetic biogeography analysis of the plant family Sapindaceae using the computer program PhyGeo.
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.
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.
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 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
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.
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.
To process the raw occurrence records in GBIF, first a taxonomy using the terminal names was built using the GBIFer tool:
gbifer tax add --rank species --file term-taxonomy.tab < terminals.txtThen 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:
gbifer tax match --file term-taxonomy.tab < occurrence.txtThe taxonomy file was edited to correct spelling errors
and match the GBIF taxonomy
with the taxonomy from the Plants of the World.
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:
gbifer country --tax term.taxonomy.tab < occurrence.txt > countries.tabThe resulting file countries.tab was edited
by removing the countries not explicitly defined in Plants of the World
as native.
Then the occurrence table from GBIF was filtered using both the taxonomy file and the country file.
gbifer filter -tax term-taxonomy.tab -country countries.tab < occurrence.txt > occu-in-tree-geo.txtThen the filtered points are converted into a file of points to be used with the taxRange tool:
gbifer export -tax term-taxonomy.tab < occu-in-tree-geo.txt > raw-gbif-records.tabThe filtered file,
stored as raw-gbif-records.tab,
contains 68.307 occurrences.
As there are no geo-referenced specimen records for Euchorium cubense,
a record file based on a material citation for the taxon
is stored in the file raw-euchorium-records.tab.
Using the taxRange tool, the filtered GBIF records are transformed into a file with presence pixels.
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.tabThe 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:
phygeo range add -type points -format text project.tab raw-fossils-records.tab
phygeo range rotate project.tab | Key | Prior | 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-prior.tab: This file contains the definition of the pixel priors used in the analysis.
To set up a project,
all input data is added to the project.
Here the project is stored in the project.tab file:
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-prior.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.
Maximum likelihood
was estimated using the command diff ml of PhyGeo.
The output log is stored in log-ml.txt file:
phygeo diff ml project.tab > log-ml.txtThe maximum likelihood estimation of
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
To estimate the shape of the likelihood function,
the command diff integrate was used,
estimating likelihood values for log-file.txt.
phygeo diff integrate -parts 100 -max 50 project.tab > log-like.txtThe same procedure was used for the project with the trimmed tree,
but for log-trim-like.txt.
To estimate the conditional likelihoods on each node,
the command diff like was used.
For the final results,
the
phygeo diff like -lambda 32.8 -o l33 project.tabThe stochastic map was performed using 10,000 particles,
with the command diff particles,
and using the conditionals for a
phygeo diff particles -p 10000 -i l33-project.tab-joyce2023-32.800000-down.tab -o p-l33 project.tabWhile the file with the particles is too large to be posted here,
the raw frequencies are calculated with the command
diff freq
and posted as a compressed file freq-l33-project.tab.zip.
phygeo diff freq -i p-l33-joyce2023-32.800000x10000.tab -o freq-l33 project.tabThe same procedure was used for the maximum likelihood estimate of 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.
phygeo diff freq -kde 1000 -i p-l33-joyce2023-32.800000x10000.tab -o kde-l33 project.tabEven as KDE,
the files are too large to be posted in this repository,
so the maps for all the reconstructions are provided.
And stored in the directory maps-l33-k95.
Use tree-joyce2023.svg
for the node numbers.
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.tabMaps
(in lower resolution)
with 50% of the KDE are stored
in the directory maps-l33-k50.
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.
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.tabEach map has the convention
<type>-<tree>-n<node id>-<age>.png,
in which <type>
indicates the type of the reconstruction
(for example l33-k95 for maps form <tree> indicates the tree
(in this case joyce2023),
<node id> is the identifier of the node
(that can be consulted in the file tree-joyce2023.svg),
and <age> 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.
phygeo diff speed -tree speed-l33 -step 5 -box 10 -i p-l33-joyce2023-32.800000x10000.tab project.tab > speed-l33.tabThe same procedure was performed
with the maximum likelihood estimate,
and the results stored as speed-ml-joyce.svg
and speed-ml.tab.
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.
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.
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.
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.
GBIF.org (2023) GBIF occurrence download. DOI: 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
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.
PoWO (2023) Plants of the World Online. URL: 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/.