DOI: 10.5061/dryad.5qfttdzgp
title: Data from: Repeated evolution of storage root and invasions of alpine biome drove replicated radiations of the megadiverse Corydalis (Papaveraceae) in the Qinghai–Tibet Plateau

description: The interplay of key innovation and ecological opportunity is commonly
 recognized to be the catalyst for rapid radiation. Underground storage
 organs (USOs), as a vital ecological trait, are advantageous for
 adaptation of plants to extreme environments, but receive less attention
 compared to aboveground organs. Repeated evolution of various USOs has
 occurred across the plant tree of life. However, whether repeated
 occurrences of a USO in different clades of a group can promote its
 replicated radiations in combination with the invasion of similar
 environments remains poorly known. Corydalis is a megadiverse genus in
 Papaveraceae and exhibits remarkable variations in USO morphology and
 biome occupancy. Here, we first generated a robust phylogeny for Corydalis
 with wide taxonomic and genomic coverage based on plastome and nuclear
 ribosomal DNA sequence data. By dating the branching events,
 reconstructing ancestral ranges, evaluating diversification dynamics, and
 inferring evolutionary patterns of USOs and biomes and their correlations,
 we then tested whether the interplay of USO evolution and biome shifts has
 driven rapid diversification of some Corydalis lineages. Our results
 indicate that Corydalis began to diversify in the Qinghai–Tibet Plateau
 (QTP) at ca. 41 Ma, and 88% of dispersals happened through forests,
 suggesting that forests served as important dispersal corridors for range
 expansion of the genus. The storage root has originated independently at
 least six times in Corydalis since the Miocene, and its acquisition could
 have operated as a key innovation towards the adaptation to the alpine
 biome in the QTP. Repeated evolution of this game-changing trait and
 invasions of alpine biome, in combination with geoclimatic changes, could
 have jointly driven independent radiations of the two clades of Corydalis
 in the QTP at ca. 6 Ma. Our study provides new insights into the joint
 contribution of USO repeated evolution and biome shifts to replicated
 radiations, hence increasing our ability to predict evolutionary
 trajectories in plants facing similar environmental pressures.
description: # Data from: Repeated evolution of storage root and invasions of alpine
 biome drove replicated radiations of the megadiverse Corydalis
 (Papaveraceae) in the Qinghai–Tibet Plateau ## Description of the data and
 file structure ## Data.zip The compressed master directory
 "Data.zip", contains a total of two directories and 85 files:
 The first directory "Alignments" includes 79 files, which are
 sequence alignments in NEXUS format for each locus used in phylogenetic
 analyses. These 79 loci are three nuclear ribosomal DNA regions (nrDNA;
 18S, ITS, 26S) and 76 coding regions from plastomes. The second directory
 "Trees" includes 6 files, which are: BI-combined.tre:
 Phylogenetic tree inferred by the combined nrDNA and plastome dataset
 using Bayesian inference; BI-nrDNA.tre: Phylogenetic tree inferred by the
 nrDNA dataset using Bayesian inference; BI-plastome.tre: Phylogenetic tree
 inferred by the plastome dataset using Bayesian inference;
 ML-combined.tre: Phylogenetic tree inferred by the combined nrDNA and
 plastome dataset using the maximum likelihood method; ML-nrDNA.tre:
 Phylogenetic tree inferred by the nrDNA dataset using the maximum
 likelihood method; ML-plastome.tre: Phylogenetic tree inferred by the
 plastome dataset using the maximum likelihood method. ## Supplementary
 Material.pdf This file contains supplementary tables and figures that
 support results in the published article
 ([https://doi.org/10.1093/sysbio/syaf014](https://doi.org/10.1093/sysbio/syaf014)).