Data and scripts accompanying the PhyloNext manuscript

Pipeline documentation: https://phylonext.github.io/
Pipeline source code: https://github.com/vmikk/PhyloNext

Directory Data contains:

• Acacia_2013_parquet.7z - the original dataset (based on DOI:10.5061/dryad.33kn3) converted into Parquet format
• Acacia_2022Dec_parquet.7z - the subset of Acacia species occurrences deposited in GBIF (as of December 2022)
• Acacia_2013_tree.nwk - the original phylogenetic tree used in González-Orozco et al. (2013)
• Acacia_2022_OTT_tree.nwk - phylogenetic tree fetched from the Open Tree of Life (does not contain tree tips imputed based on taxonomic data only)
• Acacia_GBIF_speciesKeys.txt - GBIF species keys used to obtain a data subset comparable to the original dataset.
• Acacia_2022Dec_Dataset_DOIs.txt - DOIs of datasets with Australian Acacia species occurrences

Directory Scripts contains:

• Acacia_PhyloNext.txt - the main script that performs the analysis

Directory Results contains:

• the obtained diversity estimates in tabular format (Biodiverse_results_merged.txt)
• interactive choropleth maps (Choropleth.html)
• results in GeoPackage format (Diversity_estimates.gpkg)
• biodiversity estimates, along with the phylogenetic tree, in the native Biodiverse format (Biodiverse.bds)

The test included:
a) a nearly identical analysis of the original spatial dataset and phylogeny,
b) analysis of original phylogeny with new filtered GBIF occurrence data with the original phylogeny,
c) analysis of the original occurrence data with a custom synthetic phylogeny from OpenTree,
d) analysis of new filtered GBIF occurrence data with a custom synthetic phylogeny from OpenTree.

Acacia_2013_parquet.7z

To make the dataset compatible with PhyloNext, it was converted into Apache Parquet file format. In the original dataset, species occurrences are in Lambert Conformal Conic projection for Australia, which was converted into latitude and longitude coordinates (EPSG:4326).
In addition, several Acacia species were renamed according to the current classification system:

Name in the original dataset	Updated name
Acacia bancroftii	Acacia bancroftiorum
Acacia bartleana	Acacia microbotrya
Acacia centrinervia	Acacia lineata
Acacia cometes	Acacia lachnophylla
Acacia cunninghamii	Acacia cummingiana
Acacia diphylla	Acacia blakei
Acacia eglandulosa	Acacia cyclops
Acacia homalophylla	Acacia omalophylla
Acacia hunteriana	Acacia boormanii
Acacia jutsonii	Acacia heteroneura
Acacia leichardtii	Acacia leichhardtii
Acacia microcephala	Acacia microcybe
Acacia perangusta	Acacia fimbriata
Acacia stowardii	Acacia chamaeleon
Acacia vincentii	Acacia deltoidea

Citation:

Acacia 2013 dataset:

González-Orozco CE, Laffan SW, Knerr N, Miller JT. (2013) Data from: A biogeographical regionalisation of Australian Acacia species. Dryad, Dataset DOI:10.5061/dryad.33kn3

González-Orozco CE, Laffan SW, Knerr N, Miller JT. (2013) A biogeographical regionalization of Australian Acacia species. The Journal of Biogeography, 40: 2156-2166. DOI:10.1111/jbi.12153

Mishler BD, Knerr N, González-Orozco CE, Thornhill AH, Laffan SW, Miller JT. (2014). Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nature Communications, 5(1), 4473. DOI:10.1038/ncomms5473

Acacia 2022 dataset:

See the Data/Acacia_2022Dec_Dataset_DOIs.txt file.

Acacia phylogenetic trees:

Mishler BD, Knerr N, González-Orozco CE, Thornhill AH, Laffan SW, Miller JT. (2014) Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nature Communications, 5(1), 4473. DOI:10.1038/ncomms5473

Miller JT, Murphy DJ, Ho SYW, Cantrill DJ, Seigler D. (2013) Comparative dating of Acacia: Combining fossils and multiple phylogenies to infer ages of clades with poor fossil records. Australian Journal of Botany, 61(6), 436–445. DOI:10.1071/BT13149

Miller JT, Seigler D, Miller JT, Seigler D. (2012) Evolutionary and taxonomic relationships of Acacia s.l. (Leguminosae: Mimosoideae). Australian Systematic Botany, 25(3), 217–224. DOI:10.1071/SB11042

Miller JT, Terra V, Riggins C, Ebinger JE, Seigler DS (2017) Molecular Phylogenetics of Parasenegalia and Pseudosenegalia (Fabaceae: Mimosoideae). Systematic Botany, 42(3), 465–469. DOI:10.1600/036364417X696140

Williams AV, Miller JT, Small I, Nevill PG, Boykin LM. (2016) Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia. Molecular Phylogenetics and Evolution, 96, 1–8. DOI:10.1016/j.ympev.2015.11.021