Data from: Integrative identification of incipient lineages in Heuchera longiflora (Saxifragaceae)

Folk RF, Ginori JC, Soltis DE, Floden AJ

Date Published: May 2, 2018

DOI: https://doi.org/10.5061/dryad.6k1s9d4

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Title Alignments of phased Sanger data
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Description Sample 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.
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Title Alignments of unphased Sanger data
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Description Sample codes follow the main text. Numbers preceded by the caret symbol refer to assignments to a priori groupings used by BPP.
Download unphased_loci.zip (10.1 Kb)
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Title Floral morphometric data
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Description Sample 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.
Download floral_dimensions_final.xlsx (64.80 Kb)
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Title Leaf landmark data
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Description The 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.
Download leaf_landmarks_final.zip (11.6 Kb)
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Title NGS_gene_alignments
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Description Alignments for the 277 gene alignments generated from NGS data.
Download NGS_gene_alignments.zip (573.0 Kb)
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Title Best ML trees from NGS data
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Description The best ML trees for the 277 NGS genes, used for ASTRAL-II analyses
Download allbest.tre.renamed.tre (378.0 Kb)
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Title Bootstrapped ML trees from NGS data
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Description The bootstrapped ML trees for the 277 NGS genes, used for ASTRAL-II analyses.
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Title Allele table
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Description The allele table used to assign population samples to putative species for ASTRAL-II.
Download allele_table_longiflora.txt (535 bytes)
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Title Concatenated Sanger data with gaps coded
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Description The seven Sanger loci concatenated, with a final binary partition for gap characters.
Download all_longiflora_trimmed_concatenated_gaps.phy (238.5 Kb)
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Title Partition file for concatenated Sanger data with gaps coded
Description Partition file, with gene-wise partitions and a single separate partition for gap data.
Download partitionlongifloratest_edited_gaps.txt (185 bytes)
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Title RAxML best tree: 7 Sanger loci, unpartitioned
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Description The 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.
Download RAxML_bipartitions.longiflora_unpartition...ed.tre (6.925 Kb)
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Title RAxML best tree: 7 Sanger loci, partitioned
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Description The 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.
Download RAxML_bipartitions.longiflora_partitioned...ed.tre (6.926 Kb)
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Title RAxML best tree: 7 Sanger loci, unpartitioned, reduced missing data
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Description The 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.
Download RAxML_bipartitions.all_longiflora_30_miss...ed.tre (2.668 Kb)
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Title RAxML best tree: 7 Sanger loci, partitioned, reduced missing data
Downloaded 2 times
Description The 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.
Download RAxML_bipartitions.all_longiflora_30_miss...ed.tre (2.67 Kb)
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Title RAxML best tree: 7 Sanger loci, partitioned, gap coding
Description The 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.
Download RAxML_bipartitions.longiflora_partitioned...ed.tre (4.189 Kb)
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Title RAxML best tree: 7 Sanger loci, partitioned, gap coding
Downloaded 1 time
Description The 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.
Download RAxML_bipartitions.longiflora_partitioned...ed.tre (2.674 Kb)
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When using this data, please cite the original publication:

Folk RA, Ginori JC, Soltis DE, Floden AJ (2018) Integrative identification of incipient lineages in Heuchera longiflora (Saxifragaceae). Botanical Journal of the Linnean Society 187(2): 327-345. https://doi.org/10.1093/botlinnean/boy012

Additionally, please cite the Dryad data package:

Folk RF, Ginori JC, Soltis DE, Floden AJ (2018) Data from: Integrative identification of incipient lineages in Heuchera longiflora (Saxifragaceae). Dryad Digital Repository. https://doi.org/10.5061/dryad.6k1s9d4
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