Accounting for extinction dynamics unifies the geological and biological histories of Indo-Australian Archipelago

Biogeographical reconstructions of the Indo-Australian Archipelago (IAA) have suggested recent spread across the Sunda and Sahul shelves of lineages with diverse origins, which appears to be congruent with a geological history of recent tectonic uplift in the region. However, this scenario is challenged by new geological evidence suggesting that the Sunda shelf was never submerged prior to the Pliocene, casting doubt on the interpretation of recent uplift and the correspondence of evidence from biogeography and geology. A mismatch between geological and biogeographical data may occur if analyses ignore the dynamics of extinct lineages, because this may add uncertainty to timing and origin of clades in biogeographical reconstructions. We revisit the historical biogeography of multiple IAA taxa and explicitly allow for the possibility of lineage extinction. In contrast to models assuming zero extinction, we find that all of these clades, including plants, invertebrates, and vertebrates, h..., , , # Code and data for: Accounting for extinction dynamics unifies the geological and biological histories of Indo-Australian Archipelago

[https://doi.org/10.5061/dryad.0vt4b8h70](https://doi.org/10.5061/dryad.0vt4b8h70)

Code to re-run the analysis in the manuscript entitled: \"Accounting for extinction dynamics unifies the geological and biological histories of Indo-Australian Archipelago\". It also includes some datasets re-visited in the manuscript. We have permission by the original authors of those datasets to make them public. 

Geologists and biogeographers have worked together to characterize the consequences of large-scale events on species formation and extinction. Until very recently, complementary evidence from both disciplines has been used to describe the evolution of species diversity in Southeast Asia. However, fresh geological findings show a completely different scenario of island connectivity that sets an evolutionary stage impossible to match the biological inferences m...