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.
Centipeda_continuous_diffusion_analysis_file
Analysis file for BEAST - place in directly and make sure the polygon files and species tree file are referenced correctly
Centipeda_continuous_diffusion.xml
Centipeda_pruned_species_trees
Empirical distribution of time calibrated species trees, with pruned outgroup. Place in same directory as xml and polygon files.
Centipeda_pruned_species.trees
C_aotearoana_polygon_file
Google 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.kml
C_borealis_polygon_file
Google 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.kml
C_crateriformis_ssp_compacta_polygon_file
Google 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.kml
C_crateriformis_ssp_crateriformis_polygon_file
Google 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.kml
C_cunninghamii_polygon_file
Google 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.kml
C_elatinoides_polygon_file
Google 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.kml
C_minima_ssp_macrocephala_polygon_file
Google 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.kml
C_minima_ssp_minima_polygon_file
Google 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.kml
C_nidiformis_polygon_file
Google 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.kml
C_pleiocephala_polygon_file
Google 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.kml
C_racemosa_polygon_file
Google 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.kml
C_thespidioides_polygon_file
Google 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.kml
Supplementary Figure S1
Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
Fig. S1.jpg
Supplementary Figure S2
Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
Fig. S2.jpg
Supplementary Figure S3
Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
Fig. S3.jpg
Supplementary Figure S4
Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
Fig. S4.jpg
Supplementary Figure S5
Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
Fig. S5.jpg
Tutorial
Tutorial on how to set up and modify a species tree diffusion analysis
Appendix - Specimens list
Full list of specimens used for species tree inference with additional information on collection localities in decimal grades