DOI: 10.5061/dryad.6k1s9d4
title: Data from: Integrative identification of incipient lineages in Heuchera longiflora (Saxifragaceae)

description: Following on emerging understanding of the diversification process, many
 recent workers have considered infraspecific taxa as valuable for formally
 recognizing incompletely speciated entities. The distinction between a
 species and an infraspecific taxon represents a fundamentally subjective
 weighting of evidence, yet this points further to the need for an
 evidential basis for these decisions. We explore these concepts in
 Heuchera longiflora (Saxifragaceae), which is morphologically variable and
 has a disjunct range across several physiographic provinces in the eastern
 U.S. using a tiered sampling approach and a combination of Sanger and next
 generation sequencing (NGS) techniques. We investigated 56 populations
 with seven markers to investigate population structure, and for a subset
 of 12 representative populations we sequenced 277 nuclear markers to
 characterize gene tree discord. Using a variety of methods to overcome
 high levels of gene conflict, we find evidence for the traditionally
 recognized taxa H. longiflora var. longiflora and H. longiflora var.
 aceroides in molecular and morphological data partitions. Our results
 comprise a case study on the use of multiple sources of data and
 analytical methods to delimit infraspecific taxa.
description: Alignments of phased
 Sanger dataSample codes follow the
 main text. "a" and "b" refer to reconstructed alleles.
 Numbers preceded by the caret symbol refer to assignments to a priori
 groupings used by BPP.phased_loci.zipAlignments of unphased Sanger dataSample codes follow the main text. Numbers preceded by the caret symbol refer to assignments to a priori groupings used by BPP.unphased_loci.zipFloral morphometric dataSample codes give the herbarium (Index Herbariorum codes), collector, and collector number. Floral number is sequential where multiple flowers were available on a specimen. For area codes, refer to text. All units are in centimeters except Floral length/width and Zygomorphy, which are unitless ratios.floral_dimensions_final.xlsxLeaf landmark dataThe landmark file is in TPS format. Sample codes give the herbarium (Index Herbariorum codes), collector, and collector number. For area codes in the classifier file, refer to text.leaf_landmarks_final.zipNGS_gene_alignmentsAlignments for the 277 gene alignments generated from NGS data.Best ML trees from NGS dataThe best ML trees for the 277 NGS genes, used for ASTRAL-II analysesallbest.tre.renamed.treBootstrapped ML trees from NGS dataThe bootstrapped ML trees for the 277 NGS genes, used for ASTRAL-II analyses.bootstraps.zipAllele tableThe allele table used to assign population samples to putative species for ASTRAL-II.allele_table_longiflora.txtConcatenated Sanger data with gaps codedThe seven Sanger loci concatenated, with a final binary partition for gap characters.all_longiflora_trimmed_concatenated_gaps.phyPartition file for concatenated Sanger data with gaps codedPartition file, with gene-wise partitions and a single separate partition for gap data.partitionlongifloratest_edited_gaps.txtRAxML best tree: 7 Sanger loci, unpartitionedThe best tree with with boostrap frequencies, using the full Sanger dataset without gaps or partitions. Population codes follow the text; note this is an unrooted tree.RAxML_bipartitions.longiflora_unpartitioned_julian.tre.renamed.treRAxML best tree: 7 Sanger loci, partitionedThe best tree with with boostrap frequencies, using the full Sanger dataset without gaps but with seven partitions. Population codes follow the text; note this is an unrooted tree.RAxML_bipartitions.longiflora_partitioned_julian.tre.renamed.treRAxML best tree: 7 Sanger loci, unpartitioned, reduced missing dataThe best tree with with boostrap frequencies, using reduced Sanger dataset without gaps or partitions. Sites with higher missing data were removed as described in the text. Population codes follow the text; note this is an unrooted tree.RAxML_bipartitions.all_longiflora_30_missing_unpartitioned.tre.renamed.treRAxML best tree: 7 Sanger loci, partitioned, reduced missing dataThe best tree with with boostrap frequencies, using the reduced Sanger dataset without gaps but with seven partitions. Sites with higher missing data were removed as described in the text. Population codes follow the text; note this is an unrooted tree.RAxML_bipartitions.all_longiflora_30_missing_partitioned.tre.renamed.treRAxML best tree: 7 Sanger loci, partitioned, gap codingThe best tree with with boostrap frequencies, using the full Sanger dataset with gaps and with eight partitions. Population codes follow the text; note this is an unrooted tree.RAxML_bipartitions.longiflora_partitioned_gaps_julian.tre.renamed.treRAxML best tree: 7 Sanger loci, partitioned, gap codingThe best tree with with boostrap frequencies, using the reduced Sanger dataset with gaps and with eight partitions. Sites with higher missing data were removed as described in the text. Population codes follow the text; note this is an unrooted tree.RAxML_bipartitions.longiflora_partitioned_gaps_julian.tre.renamed.tre