10.5061/DRYAD.FF749
Straub, Shannon C. K.
Moore, Michael J.
Oberlin College
Soltis, Pamela S.
University of Florida
Soltis, Douglas E.
University of Florida
Liston, Aaron
Oregon State University
Livshultz, Tatyana
Drexel University
Straub, Shannon C.K.
Oregon State University
Data from: Phylogenetic signal detection from an ancient rapid radiation:
effects of noise reduction, long-branch attraction, and model selection in
crown clade Apocynaceae
Dryad
dataset
2015
Anodendron oblongifolium
Oncinotis tenuiloba
Rhabdadenia biflora
Next-generation sequencing
Nerium oleander
Aganosma cymosa
Pentalinon luteum
Apocynaceae
Neobracea bahamensis
long-branch attraction
pollen aggregation
Echites umbellatus
Epigynum auritum
Asclepias syriaca L.
Secamone afzelli
Periploca sepium
Wrightia natalensis
2015-08-13T00:00:00Z
en
https://doi.org/10.1016/j.ympev.2014.07.020
41009991 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs,
and herbs with a diversity of pollen aggregation morphologies including
monads, tetrads, and pollinia, making them an ideal group for
investigating the evolution and function of pollen packaging. Traditional
molecular systematic approaches utilizing small amounts of sequence data
have failed to resolve relationships along the spine of the crown clade, a
likely ancient rapid radiation. The previous best estimate of the
phylogeny was a five-way polytomy, leaving ambiguous the homology of
aggregated pollen in two major lineages, the Periplocoideae, which possess
pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae),
which possess pollinia. To assess whether greatly increased character
sampling would resolve these relationships, a plastome sequence data
matrix was assembled for 13 taxa of Apocynaceae, including nine newly
generated complete plastomes, one partial new plastome, and three
previously reported plastomes, collectively representing all primary crown
clade lineages and outgroups. The effects of phylogenetic noise,
long-branch attraction, and model selection (linked versus unlinked branch
lengths among data partitions) were evaluated in a hypothesis-testing
framework based on Shimodaira–Hasegawa tests. Discrimination among
alternative crown clade resolutions was affected by all three factors.
Exclusion of the noisiest alignment positions and topologies influenced by
long-branch attraction resulted in a trichotomy along the spine of the
crown clade consisting of Rhabdadenia + the Asian clade, Baisseeae +
milkweeds, and Periplocoideae + the New World clade. Parsimony
reconstruction on all optimal topologies after noise exclusion
unambiguously supports parallel evolution of aggregated pollen in
Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic
approach has greatly advanced the resolution of one of the most perplexing
radiations in Apocynaceae, providing the basis for study of convergent
floral morphologies and their adaptive value.
Read me first, translation key for taxon names in
filesDryad_readme_first.rtfStarting alignment of 13 plastomesStarting
alignment of 13 plastomes (including partial Anodendron plastome), 145,064
base pairs long, Phylip format.infileStarting alignment of 12
plastomesStarting alignment of 12 plastomes (excluding partial Anodendron
plastome) 144,864 base pairs long, created from the 145,064 alignment by
1) deletion of Anodendron plastome and 2) deletion of all gap and all “N”
characters, Phylip format.infile_144864.reducedRaxML partition file for 13
plastome, 145,064 base pair, alignment from Partition Finder
analysis.partRaxML partition file for 12 plastome, 144,864 base pair
alignment from Partition Finder analysis.part_144864.reducedRaxML exclude
file for 13 plastome, 145,064 base pair alignment; 1075 segments excluded
based on GBLOCKS analysis.exclRaxML exclude file for 12 plastome, 144,864
base pair alignment; 1065 segments excluded based on GBLOCKS
analysis.Gblocks_exclude_20131001.txtRaxML input matrix
“Allsites_alltaxa”Anodendron included; 125,369 aligned base pairs,
undetermined and ambiguously aligned sites identified by GBLOCKS removed;
Phylip format.infileRaxML partition file for matrix
“Allsites_alltaxa”Anodendron included, 125,369 aligned base pairs,
undetermined and ambiguously aligned sites identified by GBLOCKS
removed.partMaximum likelihood bootstrap tree for matrix
“Allsites_alltaxa” analyzed with linked branch
lengths.RAxML_bipartitions.resultMaximum likelihood bootstrap tree for
matrix “Allsites_alltaxa” analyzed with unlinked branch
lengths.RAxML_bipartitions.resultMost parsimonious tree for matrix
“Allsites_alltaxa”, Winclada tree file.125369_names.treMaximum likelihood
bootstrap tree for matrix “Allsites_alltaxa” with Rhabdadenia excluded,
linked branch lengths.RAxML_bipartitions.resultMaximum likelihood
bootstrap tree for matrix “Allsites_alltaxa” with Rhabdadenia excluded,
unlinked branch lengths.RAxML_bipartitions.resultMost parsimonious trees
for matrix “Allsites_alltaxa” with Rhabdadenia excluded, Winclada tree
file.125369_rhab_names.treMaximum likelihood bootstrap tree for matrix
“Allsites_alltaxa” with Periploca excluded, linked branch
lengths.RAxML_bipartitions.resultMaximum likelihood bootstrap tree for
matrix “Allsites_alltaxa” with Periploca excluded, unlinked branch
lengths.RAxML_bipartitions.resultMost parsimonious trees for matrix
“Allsites_alltaxa” with Periploca excluded, Winclada
format.125369_peri_names.treRaxML input matrix “Allsites_noAno”RaxML input
matrix “Allsites_noAno”, Anodendron excluded, 126,430 aligned base pairs,
undetermined and ambiguously aligned sites identified by GBLOCKS removed,
Phylip format.infileRaxML partition file for matrix “Allsites_noAno”,
Anodendron excluded, 126,430 aligned base pairs, undetermined and
ambiguously aligned sites identified by GBLOCKS removed.partMaximum
likelihood bootstrap tree for matrix “Allsites_noAno” analyzed with linked
branch lengths.RAxML_bipartitions.resultMaximum likelihood bootstrap tree
for matrix “Allsites_noAno” analyzed with unlinked branch
lengths.RAxML_bipartitions.resultMost parsimonious trees for matrix
“Allsites_noAno”, Winclada format.126430_names.treMaximum likelihood
bootstrap tree for matrix “Allsites_noAno” with Rhabdadenia excluded,
branch lengths linked.RAxML_bipartitions.resultMaximum likelihood
bootstrap tree for matrix “Allsites_noAno” with Rhabdadenia excluded,
branch lengths unlinked.RAxML_bipartitions.resultMost parsimonious trees
for matrix “Allsites_noAno” with Rhabdadenia excluded, Winclada
format.126430_rhab_names.treMaximum likelihood bootstrap tree for matrix
“Allsites_noAno” with Periploca excluded, branch lengths
linked.RAxML_bipartitions.resultMaximum likelihood bootstrap tree for
matrix “Allsites_noAno” with Periploca excluded, branch lengths
unlinked.RAxML_bipartitions.resultMost parsimonious trees for matrix
“Allsites_noAno” with Periploca excluded, Winclada
format.126430_peri_names.treRaxML input matrix “>3.4_excluded”RaxML
input matrix “>3.4_excluded”, Anodendron excluded, created from
matrix “Allsites_noAno” by exclusion of sites with AIR rates > 3.4,
125,871 base pairs retained, 559 base pairs excluded, Phylip
format.infileRaxML exclusion file, sites excluded from “Allsites_noAno” to
create matrix “>3.4_excluded”.AIR_exclude_559_7tre.txtMaximum
likelihood bootstrap tree for matrix “>3.4_excluded” analyzed with
linked branch lengths.RAxML_bipartitions.resultMaximum likelihood
bootstrap tree for matrix “>3.4_excluded” analyzed with unlinked
branch lengths.RAxML_bipartitions.resultMost parsimonious trees for matrix
“>3.4_excluded”125871_names.treRaxML input matrix
“>3.3_excluded”RaxML input matrix “>3.3_excluded”,
Anodendron excluded, created from matrix “Allsites_noAno” by exclusion of
sites with AIR rates > 3.3, 125,487 base pairs retained, 943 base
pairs excluded, Phylip format.infileRaxML exclusion file, sites excluded
from “Allsites_noAno” to create matrix
“>3.3_excluded”.AIR_exclude_943_7treA.txtMaximum likelihood
bootstrap tree for matrix “>3.3_excluded” analyzed with linked
branch lengths.RAxML_bipartitions.resultMaximum likelihood bootstrap tree
for matrix “>3.3_excluded” analyzed with unlinked branch
lengths.RAxML_bipartitions.resultMost parsimonious trees for matrix
“>3.3_excluded”125487_names.treRaxML input matrix
“>3.0_excluded”RaxML input matrix “>3.0_excluded”,
Anodendron excluded, created from matrix Allsites_noAno (4b) by exclusion
of sites with AIR rates > 3.0, 123,995 base pairs retained, 2,435
base pairs excluded.infileRaxML exclusion file, sites excluded from
“Allsites_noAno” to create matrix
“>3.0_excluded”.AIR_exclude_2435_7tre.txtMaximum likelihood
bootstrap tree for matrix “>3.0_excluded” analyzed with linked
branch lengths.RAxML_bipartitions.resultMaximum likelihood bootstrap tree
for matrix “>3.0_excluded” analyzed with unlinked branch
lengthsRAxML_bipartitions.resultMost parsimonious trees for matrix
“>3.0_excluded”, Winclada tree file format123995_names.treRaxML
partition file for matrix “>3.4_excluded”partRaxML partition file
for matrix “>3.3_excluded”partRaxML partition file for matrix
“>3.0_excluded”partRaxML input matrix, inverse exclusion matrix for
matrix “>3.4_excluded”, includes only 559 sites with AIR rate
>3.4, analyzed without partitionsinfileMaximum likelihood bootstrap
tree for inverse exclusion matrix for matrix
“>3.4_excluded”RAxML_bipartitions.resultRaxML input matrix, inverse
exclusion matrix for matrix “>3.3_excluded”, includes only 943
sites with AIR rate >3.3infileMaximum likelihood bootstrap tree for
inverse exclusion matrix for matrix
“>3.3_excluded”RAxML_bipartitions.resultRaxML input matrix, inverse
exclusion matrix for matrix “>3.0_excluded”, includes only 2,435
sites with AIR rate >3.0infileMaximum likelihood bootstrap tree for
inverse exclusion matrix for matrix
“>3.0_excluded”RAxML_bipartitions.resultRaxML input tree file of
105 topologies for SH test of matrix
“Allsites_alltaxa”.topologies_file.treResult of SH test on matrix
“Allsites_alltaxa” with linked branch lengths.tab delimited text
file125369_SH_linked.txtResult of SH test on matrix “Allsites_alltaxa”
with unlinked branch lengths.tab delimited text
file.125369_SH_unlinked.txtAlternative topologies (105) for SH test of
matrices “Allsites_noAno”, “>3.4_excluded”, “>3.3_excluded”,
“>3.0_excluded”.tab delimited text file.105_topologies.txtResult of
SH test on matrix “Allsites_noAno” with linked branch
lengths.SH_linked_2013_10_01.txtResult of SH test on matrix
“Allsites_noAno” with unlinked branch
lengths.SH_unlinked_2013_10_01.txtResult of SH test on matrix
“>3.4_excluded” with linked branch
lengths.SH_linked_AIR559excl_3.4_7tr.txtResult of SH test on matrix
“>3.4_excluded” with unlinked branch
lengths.SH_unlinked_AIR559excl_3.4_7tr.txtResult of SH test on matrix
“>3.3_excluded” with linked branch lengths.Tab delimited text
file.SH_linked_AIR943excl_3.3_7tr.txtResult of SH test on matrix
“>3.3_excluded” with unlinked branch
lengths.SH_unlinked_AIR943excl_3.3_7tr.txtResult of SH test on matrix
“>3.0_excluded” with linked branch lengths.tab delimited text
file.SH_linked_AIR2435excl_3_7tr.txtResult of SH test on matrix
“>3.0_excluded” with unlinked branch
lengths.SH_unlinked_AIR2435excl_3_7tr.txtAIR analysis output, based on 7
treesAIR analysis output, average rates for each site in matrix
“Allsites_noAno” for 7 trees with p>0.05 from SH test of
“Allsites_noAno” with linked branch lengths. Tab delimited text
file.AIR7trees.txtAIR analysis output, based on 12 treesAIR analysis
output, average rates for each site in matrix “Allsites_noAno” for 12
trees with p>0.05 from SH test of “Allsites_noAno” with unlinked
branch lengths. Tab delimited text file.AIR12trees.txtSites removed by
GBLOCKS and AIR sorted by genomic featureGenomic features associated with
sites excluded from the alignment of 12 full plastomes by GBLOCKS to
produce matrix Allsites_noAno and by AIR to produce matrix
>3.0_excluded, data for Figure 4. Tab delimited text
file.summary_sorted_for_graph.txtMorphological character matrix: pollen
aggregation.character_matrix.outAnodendron oblongifolium partial plastome
assemblyfasta fileAnodendron_oblongifolium_plastome_assembly.fasta
global