Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms

Folk RA, Mandel JR, Freudenstein JV

Date Published: September 8, 2016

DOI: http://dx.doi.org/10.5061/dryad.cd546

 

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Title Concatenated nuclear alignment, 70 taxa
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Download nuclearAlignment.phy.reduced (27.76 Mb)
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Title Concatenated nuclear tree, unpartitioned
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Download NuclearTreeUnpartitioned.tre (3.781 Kb)
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Title Concatenated nuclear tree, partitioned by gene
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Download NuclearTreePartitionedByGene.tre (3.755 Kb)
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Title Concatenated nuclear tree, partitioned by splice site
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Download NuclearTreePartitionedBySpliceSite.tre (3.757 Kb)
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Title Chloroplast alignment, 70 taxa
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Download chloroplastAlignment.phy.reduced (11.36 Mb)
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Title Chloroplast tree, unpartitioned
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Download ChloroplastOneIRunpartitioned.tre (3.783 Kb)
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Title Chloroplast tree, partitioned
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Download ChloroplastOneIRpartitioned.tre (3.812 Kb)
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Title Chloroplast alignment of Sanger loci
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Download sangerAlignment.phy.reduced (244.2 Kb)
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Title Chloroplast tree of Sanger loci
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Download ChloroplastSangerTree.tre (4.854 Kb)
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Title Mitochondrial alignment, 66 taxa
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Download MitochondrionAlignment66taxa.phy (31.34 Mb)
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Title Mitochondrial tree, unpartitioned
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Download MitochondrionTree66taxaUnpartitioned.tre (3.614 Kb)
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Title Mitochondrial tree, partitioned
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Download MitochondrionTree66taxaPartitioned.tre (3.588 Kb)
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Title Mitochondrial tree, upper 50% of taxa in terms of coverage
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Download MitochondrionTreeUpper50.tre (1.903 Kb)
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Title RAxML nuclear partition file, by gene
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Download NuclearPartitionByGene.txt (7.835 Kb)
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Title RAxML nuclear partition file, by splice site
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Download NuclearPartitionBySpliceSite.txt (26.72 Kb)
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Title RAxML chloroplast partition file, coding vs. non-coding
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Download ChloroplastPartitionCoding-NonCoding.txt (3.785 Kb)
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Title RAxML chloroplast partition file, Sanger loci, by gene
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Download ChloroplastSangerPartitionByGene.txt (64 bytes)
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Title RAxML mitochondrial partition file, coding vs. non-coding
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Download MitochondrionPartitionCoding-NonCoding.txt (2.189 Kb)
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Title ASTRAL tree
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Download ASTRALtree.txt (2.705 Kb)
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Title SVDquartets tree
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Download SVDquartetstree.txt (877 bytes)
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Title ASTRAL optimal gene trees (in one file) and boostraps (separate files in subdirectory)
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Download ASTRAL_OptimalGeneTreesandBootstraps.zip (24.46 Mb)
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Title BUCKy gene MCMC distributions, with individual gene alignments
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Download BUCKyGeneDistributions.zip (452.0 Mb)
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Title Online Appendix 1
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Description Table of voucher information, collection localities, SRA accession numbers, and coverage values for nuclear, plastid, and mitochondrial contigs, as well as individual low-copy nuclear genes. A translate table for phylogenetic files in the online appendices is also provided.
Download Appendix1_Coverage statistics and voucher ....xlsx (63.79 Kb)
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Title Online Appendix 2
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Description Sanger phylogeny of three plastid regions (trnL-F, rpl32-trnL, and rps16-trnK), included in order to increase outgroup sampling (n =15; added samples summarized in Methods). Bootstrap proportions are plotted on all branches of non-zero length; branch coloration follows Fig. 1.
Download Appendix2_SangerChloroplastTree.pdf (26 Kb)
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Title Online Appendix 3
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Description All 277 analyzed gene trees as inferred in RAxML. The loci are labeled and arranged by descending order of locus length. All clade bootstraps ≥ 50 are plotted on branches.
Download Appendix3_MLgenetrees.pdf (2.035 Mb)
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Title Online Appendix 4
Downloaded 15 times
Description All 277 analyzed Bayesian MCM distributions from MrBayes, summarized as 50% majority consensus trees. The loci are labeled and arranged by decreasing length. All clade posterior probabilities ≥ 50 are plotted on branches.
Download Appendix4_Bayesgenetrees.pdf (1.836 Mb)
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Title Online Appendix 5
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Description Species-genotype association file in ASTRAL-II format, also used for SVDquartets and MP-EST.
Download Appendix5_ASTRALalleletable.txt (854 bytes)
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Title Online Appendix 6
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Description ASTRAL-II analysis performed with individual sequences treated as species to assess potential issues with uncertain species limits. Note that these results strongly resemble the concatenation topology and are highly congruent with the ASTRAL-II topology assigning multiple sequences to putative species.
Download Appendix6_ASTRALnoallelemap.pdf (24.75 Kb)
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Title Online Appendix 7
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Description Table of results for the φ tests for recombination.
Download Appendix7_RecombinationTests.pdf (44.63 Kb)
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Title Online Appendix 8
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Description NeighborNet split network inferred using the concatenated nuclear data, showing conflict among nuclear loci. The currently recognized sections are indicated by colored circles: orange = sect. Holochloa; blue = sect. Heuchera; green = sect. Bracteatae; pink = sect. Rhodoheuchera.
Download Appendix8_NeighborNet.pdf (29.89 Kb)
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Title Online Appendix 9
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Description Comparison of coalescent branch length estimates in BUCKy (with individual sequences treated as species, using all 277 loci, subsampled MCMC, and α = 1) and MP-EST (with multiple sequences assigned to putative species). Only internal branches are shown since infraspecific sampling is required to reliably estimate external branch lengths, causing these to misleadingly take on the maximum possible values when there is only one individual per species. The outgroup branch is not to scale.
Download Appendix9_CoalescentBranchLengths.pdf (638.9 Kb)
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Title Online Appendix 10
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Description Table of thermocycler programs and PCR primers for PCR and Sanger sequencing.
Download Appendix10_PCRprogramsandprimers.xlsx (40.35 Kb)
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Title Online Appendix 11
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Description Summary of taxa included in the analysis of Sanger-sequenced loci, including voucher information and GenBank accession numbers.
Download Appendix11_SangerGenbank and voucherinform....xlsx (50.18 Kb)
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Title Online Appendix 12
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Description Gene trees simulated under the coalescent using the MP-EST tree.
Download Appendix12_MPESTsimulatedGeneTrees1000.txt (184.4 Kb)
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Title Online Appendix 13
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Description Summary of bipartitions in the gene trees of online Appendix 12, plotted on the MP-EST species tree estimate.
Download Appendix13_MP_ESTGeneTreeSimulationSummar...ee.pdf (148.3 Kb)
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Title Online Appendix 14
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Description Gene trees simulated under the coalescent using the BUCKy tree.
Download Appendix14_BUCKysimulatedGeneTrees1000.txt (2.400 Mb)
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Title Online Appendix 15
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Description Summary of bipartitions in the gene trees of online Appendix 14 using the plastid tree.
Download Appendix15_BUCKyGeneTreeSimulationSummary...ee.pdf (292.3 Kb)
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Title Online Appendix 16
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Description Comparison of BUCKy concordance factors for a completely sampled MCMC analysis (last 90% of samples) and a subsampled analysis (last 10% of samples), using the longest 50 low-copy nuclear loci. Branch labels are concordance factors; all factors ≥ 0.1 are in bold. Only internal branches are shown with concordance factors, as in online Appendix 4.
Download Appendix16_BUCKyBurnIn.pdf (850.1 Kb)
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Title Online Appendix 17
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Description Comparison of BUCKy concordance factors for different alpha values in the subsampled MCMC analyses. Branch labels are concordance factors; all factors ≥ 0.1 are in bold. External branch concordance factors are not shown; all external branches (those leading to single OTUs) must have 100% concordance since every group containing one OTU must be present in all trees, and hence these numbers may be misleading.
Download Appendix17_BUCKyAlphaValues.pdf (1.272 Mb)
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Title Online Appendix 18
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Description Analysis of the low-copy nuclear concatenated dataset with no partitioning scheme.
Download Appendix18_NuclearTree70taxa_scale.pdf (44.18 Kb)
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Title Online Appendix 19
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Description Analysis of the low-copy nuclear concatenated dataset with each genetic locus treated as a separate partition.
Download Appendix19_Partitionednuclear-bygene_scale.pdf (39.82 Kb)
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Title Online Appendix 20
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Description Concatenated low-copy nuclear phylogeny inferred in RAxML without partitioning, with four rogue taxa pruned as suggested by RogueNaRok. Branch support in sect. Rhodoheuchera (magenta) are dramatically improved with only the position of H. rubescens var. versicolor remaining uncertain. Labeling and coloring of branches follow Fig. 1.
Download Appendix20_NuclearTreeNoRogues_scale.pdf (43.58 Kb)
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Title Online Appendix 21
Downloaded 47 times
Description Analysis of the plastid genome dataset with coding and noncoding regions treated as separate partitions and the second copy of the inverted repeat region (IR) deleted. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
Download Appendix21_Partitionedchloroplast_scale.pdf (44.45 Kb)
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Title Online Appendix 22
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Description Analysis of the plastid genome dataset with no partitioning scheme and the second copy of the inverted repeat region (IR) deleted. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
Download Appendix22_Unpartitionedchloroplasttree.pdf (44.20 Kb)
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Title Online Appendix 23
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Description Analysis of the mitochondrial genome dataset with coding and noncoding regions treated as separate partitions. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
Download Appendix23_Partitionedmitochondrion_scale.pdf (39.56 Kb)
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Title Online Appendix 24
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Description Analysis of the mitochondrial genome dataset with no partitioning scheme. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
Download Appendix24_Unpartitionedmitochondrion_scale.pdf (48.69 Kb)
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Title Online Appendix 25
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Description Mitochondrial phylogeny including only samples in upper 50th percentile in terms of coverage (unpartitioned). The topology is largely congruent with the tree containing 66 taxa, indicating that the topology is not sensitive to low-coverage samples. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
Download Appendix25_MitochondrionUpper50_scale.pdf (36.27 Kb)
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Title Online Appendix 26
Downloaded 22 times
Description Cluster network depicting conflict between plastid and nuclear topologies; blue branches represent reticulation, while black branches show tree-like relationships held in common between the two phylogenies. The topological conflict is so extreme and involves such distantly related taxa that almost no clades are held in common between the two datasets. In the two input trees, all clades with < 70% bootstrap support were collapsed.
Download Appendix26_chloroplastclusternetwork.pdf (15.67 Kb)
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Title Online Appendix 27
Downloaded 17 times
Description Tanglegram comparing mitochondrial and concatenated nuclear phylogenies, optimized in Dendroscope to minimize line crossings. Again, the concatenation tree is used to represent the nuclear phylogeny in order to maintain comparability and to show divergent placement of subspecific samples in the mitochondrial tree. In order to minimize spurious disagreement between phylogenies due to estimation error, all clades with < 70% bootstrap support have been collapsed.
Download Appendix27_Tanglegram_mitochondron_nucleus.pdf (32.33 Kb)
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Title Online Appendix 28
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Description Proposed introgression events (from Table 2) mapped onto the ASTRAL topology as a visual representation of hypothesized gene flow. Solid red arrows represent proposed hybridization ancestral to a clade; dotted lines represent hybridization among species or populations only; asterisks mark taxa where there was evidence for introgression but the source of the organellar DNA was unresolved.
Download Appendix28_ASTRALintrogressionEvents.pdf (18.47 Kb)
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Title Online Appendix 29
Downloaded 52 times
Description The mitochondrial tree (see Fig. 3), pruned to only mitochondrial clade A, and rerooted with Mitella pentandra to match the plastid tree. This figure demonstrates that the mitochondrial tree differs from the plastid tree in ways that cannot be explained simply by subtree misrooting.
Download Appendix29_MitochondrialcladeArerooted.pdf (257.9 Kb)
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Title Online Appendix 30
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Description Four mitochondrial regions that were conserved, easily aligned among taxa, and generally were represented by complete sequences in the main alignment (of which were used, respectively: positions 103,060-129,653; 132,480-142,279; 416; 224-428,828; 452,332-467,783).
Download Appendix30_MitochondrialConservedRegions.pdf (1.354 Mb)
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Title Online Appendix 31
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Description ASTRAL-II tree, including only those loci for which ϕ-tests could not detect recombination. Methods were otherwise identical to the main ASTRAL-II analysis.
Download Appendix31_ASTRAL_norecombination.pdf (284.1 Kb)
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When using this data, please cite the original publication:

Folk RA, Mandel JR, Freudenstein JV (2017) Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms. Systematic Biology 66(3):320-337. http://dx.doi.org/10.1093/sysbio/syw083

Additionally, please cite the Dryad data package:

Folk RA, Mandel JR, Freudenstein JV (2016) Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cd546
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