DOI: 10.5061/dryad.69329
title: Data from: On the Biogeography of Centipeda: A Species Tree Diffusion Approach

description: The deserts of Australia together constitute one of the world’s largest
 continuous arid zones, where precipitation is low and access to water
 limited and/or sometimes restricted to temporal and unpredictable
 flooding. In this environment, a wide variety of plants and animals have
 evolved, many of which are morphologically adapted to ephemeral water and
 fire regimes. Reconstructing the biogeographic history of groups present
 in such landscapes is challenging, due to the difficulties in defining
 discrete areas for analyses, and even more so when species largely overlap
 both in terms of geography and habitat preference. In this study, we use a
 novel approach to estimate ancestral areas for the small plant genus
 Centipeda. Our analysis applies continuous diffusion of geography by a
 relaxed random walk, where each species is sampled from its extant
 distribution on an empirical distribution of time calibrated species
 trees. Using a distribution of previously published substitution rates of
 ITS for the Asteraceae, we show how the evolution of Centipeda correlates
 with the temporal increase of aridity in the arid zone since the Pliocene.
 Geographic estimates of ancestral species show a consistent pattern of
 speciation of early lineages in the Lake Eyre region, with a division in
 more northerly and southerly groups since approximately 840 ka.
 Summarising the geographic slices of species trees at timing of latest
 speciation event (~20 ka), indicates no presence of the genus in Australia
 west of the combined desert belt of the Nullabor Plain, the Great Victoria
 Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main
 continental shelf of Australia. The result indicates all western
 occurrences of the genus to be a result of recent dispersal, rather than
 ancient vicariance. This study contributes to our understanding of the
 spatiotemporal processes shaping the flora of the arid zone, and offers a
 significant improvement in inference of ancestral areas for any organismal
 group distributed where it remains difficult to describe geography in
 terms of discrete areas.
description: Centipeda_continuous_diffusion_analysis_fileAnalysis file for BEAST - place in directly and make sure the polygon files and species tree file are referenced correctlyCentipeda_continuous_diffusion.xmlCentipeda_pruned_species_treesEmpirical distribution of time calibrated species trees, with pruned outgroup. Place in same directory as xml and polygon files.Centipeda_pruned_species.treesC_aotearoana_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_aotearoana.kmlC_borealis_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_borealis.kmlC_crateriformis_ssp_compacta_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_crateriformis_ssp_compacta.kmlC_crateriformis_ssp_crateriformis_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_crateriformis_ssp_crateriformis.kmlC_cunninghamii_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_cunninghamii.kmlC_elatinoides_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_elatinoides.kmlC_minima_ssp_macrocephala_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_minima_ssp_macrocephala.kmlC_minima_ssp_minima_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_minima_ssp_minima.kmlC_nidiformis_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_nidiformis.kmlC_pleiocephala_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_pleiocephala.kmlC_racemosa_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_racemosa.kmlC_thespidioides_polygon_fileGoogle Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.C_thespidioides.kmlSupplementary Figure S1Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.Fig. S1.jpgSupplementary Figure S2Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.Fig. S2.jpgSupplementary Figure S3Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.Fig. S3.jpgSupplementary Figure S4Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.Fig. S4.jpgSupplementary Figure S5Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.Fig. S5.jpgTutorialTutorial on how to set up and modify a species tree diffusion analysisAppendix - Specimens listFull list of specimens used for species tree inference with additional information on collection localities in decimal grades