DOI: 10.5061/dryad.298d0
title: Data from: Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci

description: Premise of the study: The use of multiple genetic regions from the nuclear
 genome, including low-copy markers, has long been recognized as essential
 to robust phylogenetic construction, addressing gene tree incongruence,
 and allowing increased resolution to test current taxonomy and resolve
 basic hypotheses about character evolution, biogeography, and other
 organismal traits of interest to biologists. Heuchera, the largest genus
 of Saxifragaceae endemic to North America, has presented an unusually
 difficult case for systematists with limited sampling in previous
 molecular studies. We used morphological and multilocus molecular
 phylogenetic data to test the monophyly of Heuchera, better resolve
 hypotheses of relationships, and test hypotheses of character evolution,
 biogeography, and diversification rates. Methods: Phylogenetic
 relationships were inferred using sequences from six nuclear loci and 39
 morphological characters using concatenation and coalescent analysis.
 Ancestral state reconstruction, diversification, and correlated evolution
 of morphological traits were performed using parsimony, BiSSE, and Pagel’s
 method, respectively. Key results: The concatenation and species tree
 analyses gave confident support to the monophyly of Heuchera and suggested
 several well-supported subclades. The addition of morphological data
 significantly improved support numbers. Ancestral character reconstruction
 suggested frequent homoplasy and reversal of floral characters and a
 complex biogeographical history. Conclusions: Heuchera is a natural genus;
 however, the current subgeneric classification is artificial and requires
 revision. Biogeographic reconstructions suggest a Pacific Northwest origin
 for the genus; morphological shifts in stamen exsertion and hypanthium
 length are hypothesized to have driven diversification in Heuchera in
 concert with possible pollinator shifts.
description: Concatenated DNA +
 morphology tree, maximum likelihoodThis tree corresponds to
 the maximum likelihood tree of Figure 1. The tree was inferred in RAxML
 using a partitioned GTR-GAMMA model. Please note for interpretation of
 taxon labels: Heuchera cuneata = Heuchera rubescens var.
 truncata.RAxML_bipartitions.DNAmorph.treDNA + morphology matrixThis file includes all data used for phylogenetic inference. Alignments were performed in MAFFT. The ribosomal and DNA only analysis can be replicated by deleting partitions. Please note for interpretation of taxon labels: Heuchera cuneata = Heuchera rubescens var. truncata.alllocimorph.phyPartition fileThis is a partition file, in RAxML format, for the entire phylogenetic dataset. The analyses for subsets of data can be replicated by deactivating partitions.morphdnapartition.txtRibosomal DNA + morphology tree, maximum likelihoodThis tree corresponds to Figure 2. The tree was inferred in RAxML using a partitioned GTR-GAMMA model.RAxML_bipartitions.ribosomalmorph.treConcatenated DNA tree, maximum likelihoodThis tree corresponds to Supplement S5. The tree was inferred in RAxML using a partitioned GTR-GAMMA model.RAxML_bipartitions.DNAonly.treRibosomal DNA tree, maximum likelihood.This tree corresponds to supplement S6. The tree was inferred in RAxML using a partitioned GTR-GAMMA model.RAxML_bipartitions.ribosomalonly.treData file for Mesquite.This includes the characters used for diversification analyses as well as the reduced tree file.mesquitefinalfile.nex