Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms
Data files
Sep 08, 2016 version files 559.53 MB
-
Appendix1_Coverage statistics and voucher information.xlsx
63.80 KB
-
Appendix10_PCRprogramsandprimers.xlsx
40.36 KB
-
Appendix11_SangerGenbank and voucherinformation.xlsx
50.18 KB
-
Appendix12_MPESTsimulatedGeneTrees1000.txt
184.46 KB
-
Appendix13_MP_ESTGeneTreeSimulationSummaryPlottedOnSpeciesTree.pdf
148.39 KB
-
Appendix14_BUCKysimulatedGeneTrees1000.txt
2.40 MB
-
Appendix15_BUCKyGeneTreeSimulationSummaryPlottedOnChloroplastTree.pdf
292.32 KB
-
Appendix16_BUCKyBurnIn.pdf
850.17 KB
-
Appendix17_BUCKyAlphaValues.pdf
1.27 MB
-
Appendix18_NuclearTree70taxa_scale.pdf
44.19 KB
-
Appendix19_Partitionednuclear-bygene_scale.pdf
39.82 KB
-
Appendix2_SangerChloroplastTree.pdf
26 KB
-
Appendix20_NuclearTreeNoRogues_scale.pdf
43.59 KB
-
Appendix21_Partitionedchloroplast_scale.pdf
44.45 KB
-
Appendix22_Unpartitionedchloroplasttree.pdf
44.20 KB
-
Appendix23_Partitionedmitochondrion_scale.pdf
39.56 KB
-
Appendix24_Unpartitionedmitochondrion_scale.pdf
48.69 KB
-
Appendix25_MitochondrionUpper50_scale.pdf
36.28 KB
-
Appendix26_chloroplastclusternetwork.pdf
15.68 KB
-
Appendix27_Tanglegram_mitochondron_nucleus.pdf
32.34 KB
-
Appendix28_ASTRALintrogressionEvents.pdf
18.47 KB
-
Appendix29_MitochondrialcladeArerooted.pdf
257.91 KB
-
Appendix3_MLgenetrees.pdf
2.04 MB
-
Appendix30_MitochondrialConservedRegions.pdf
1.35 MB
-
Appendix31_ASTRAL_norecombination.pdf
284.14 KB
-
Appendix4_Bayesgenetrees.pdf
1.84 MB
-
Appendix5_ASTRALalleletable.txt
854 B
-
Appendix6_ASTRALnoallelemap.pdf
24.75 KB
-
Appendix7_RecombinationTests.pdf
44.64 KB
-
Appendix8_NeighborNet.pdf
29.90 KB
-
Appendix9_CoalescentBranchLengths.pdf
638.94 KB
-
ASTRAL_OptimalGeneTreesandBootstraps.zip
24.47 MB
-
ASTRALtree.txt
2.70 KB
-
BUCKyGeneDistributions.zip
452.04 MB
-
chloroplastAlignment.phy.reduced
11.36 MB
-
ChloroplastOneIRpartitioned.tre
3.81 KB
-
ChloroplastOneIRunpartitioned.tre
3.78 KB
-
ChloroplastPartitionCoding-NonCoding.txt
3.78 KB
-
ChloroplastSangerPartitionByGene.txt
64 B
-
ChloroplastSangerTree.tre
4.85 KB
-
MitochondrionAlignment66taxa.phy
31.34 MB
-
MitochondrionPartitionCoding-NonCoding.txt
2.19 KB
-
MitochondrionTree66taxaPartitioned.tre
3.59 KB
-
MitochondrionTree66taxaUnpartitioned.tre
3.61 KB
-
MitochondrionTreeUpper50.tre
1.90 KB
-
nuclearAlignment.phy.reduced
27.76 MB
-
NuclearPartitionByGene.txt
7.84 KB
-
NuclearPartitionBySpliceSite.txt
26.73 KB
-
NuclearTreePartitionedByGene.tre
3.76 KB
-
NuclearTreePartitionedBySpliceSite.tre
3.76 KB
-
NuclearTreeUnpartitioned.tre
3.78 KB
-
sangerAlignment.phy.reduced
244.27 KB
-
SVDquartetstree.txt
877 B
Abstract
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord.