DOI: 10.5061/dryad.5tb2rbp75
title: Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies

description: Australia was predominantly tropical for most of the early Cenozoic, then
 transitioned to a cooler and drier climate in the Oligocene. In response
 to this increasing aridity, some lineages adapted to more xeric
 ecosystems, contracted, or became restricted to increasingly fragmented
 mesic refugia, or went extinct. Yet, the lack of macroevolutionary studies
 at a continental scale precludes a better understanding of Australian
 biodiversity patterns and processes during the Cenozoic. Here, we infer a
 robust dated phylogenomic tree for a radiation of Australian endemic
 butterflies, the Trapezitinae skippers, to test the impact of biotic and
 abiotic drivers on Cenozoic diversification dynamics in Australia. These
 butterflies originated during the Eocene (ca. 42 Ma) in the mesic biome of
 Australia. Trapezitinae exploded in diversity during a cool, dry period in
 the late Oligocene and early Miocene, then experienced a sharp
 deceleration in speciation. Xeric ecosystems appear to have been colonized
 more recently, supporting the hypothesis of arid and semi-arid biomes as
 evolutionary sinks. Temperature-dependent and phytophagy-dependent
 diversification models received little support. Instead, we find evidence
 for diversity-dependent processes with a declining diversification in
 Trapezitinae likely linked to limited ecological opportunities following a
 rapid initial burst of diversification.
description: ----------------------------------------------------------------------------------------------------------<br><br>README File for Dryad repository on "Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies"<br><br>----------------------------------------------------------------------------------------------------------<br>Number of files: 10<br>----------------------------------------------------------------------------------------------------------<br><br>Description:<br><br>Paper appendices / supplementary information<br><br>File S1 - IQ-TREE Best Scoring ML tree.tre<br>File S2 - wASTRAL MSC tree.tre<br>File S3 - BEAST MCC 14ULRC BDeath.tre<br><br>Table S1 - Taxon Sampling.xlsx<br>Table S2 - Genomic Matrix Composition.xlsx<br>Table S3 - Biogeography Data.xlsx<br>Table S4 - BEAST Results.xlsx<br>Table S5 - TreePar Results.xlsx<br>Table S6 - RPANDA Results.xlsx<br>Table S7 - HiSSE Results.xlsx<br><br>See the paper for more descriptions of these files<br><br>----------------------------------------------------------------------------------------------------------<br><br>ADDITIONAL DATA FILES<br><br>Trapezitinae Final Concatenated Matrix for IQ-TREE<br><br>This is the final concatenated matrix used for the IQ-TREE analyses including all AHE loci.<br>You can split it into loci using the partitions indicated in Table S2<br>You can also reproduce the analyses using the partitioning file from ModelFinder (see below)<br><br>----------------------------------------------------------------------------------------------------------<br><br>Trapezitinae Final Partitioning Scheme for IQ-TREE.nex<br><br>This is the partitioning file from ModelFinder used to conduct the IQ-TREE analyses<br><br>----------------------------------------------------------------------------------------------------------<br><br>Trapezitinae Final Sortadate Dataset for BEAST<br><br>This is the final concatenated matrix used for the BEAST analyses including loci selected using SortaDate.<br>The file includes models and partitions at the bottom when opened in a text editor<br><br>----------------------------------------------------------------------------------------------------------<br><br>IMPORTANT<br><br>If you need access to raw data or other data format please send a request to emmanuel.toussaint@ville-ge.ch OR kawahara@flmnh.ufl.edu <br><br>----------------------------------------------------------------------------------------------------------