New Phytologist Supporting Information
Rapid report
Independent allopolyploidization events preceded speciation in the temperate and tropical
woody bamboos
Jimmy K. Triplett, Lynn G. Clark, Amanda E. Fisher and Jun Wen.
Article acceptance date: 17 July 2014
The following Supporting Information is available for this article:
Figs S1–S9 and Tables S1–S4
1
Fig. S1 Comparison of the gene phylogenies for gpa1, pabp1, and pvcel1, highlighting the backbone phylogeny for genomes A, B, C,
D, E, and H and the composite nature of several putative hybrid species. Colored lines are used to indicate the phylogenetic positions
of multiple sequences recovered from a given hybrid individual. For example, Pseudosasa japonica has four sequence types of gpa1
(two in clade A and two in clade B). Each of the gene trees is consistent with gene duplication prior to the diversification of temperate
and tropical woody bamboos, suggesting allopolyploidization preceded speciation in these bamboos.
2
Fig. S2 Phylogram of the majority rule consensus tree from the Bayesian analysis of the abridged
and concatenated three-region data set (gpa1, pabp1, and pvcel1). Codes after the species name
indicate voucher, clade assignment (A, B, etc), allele (e.g., A1 or A2), and number of sequences
recovered in cloning experiments. Posterior probabilities are indicated above the branches. Clade
labels correspond to genome groups associated with the temperate woody bamboos
(Arundinarieae: A and B), the tropical woody bamboos (Bambuseae: C, D, and E), and the
herbaceous bamboos (Olyreae: H).
3
Fig. S3 Bootstrap consensus tree from a parsimony analysis of the abridged and concatenated
three-region data set (gpa1, pabp1, and pvcel1). Codes after the species name indicate voucher,
clade assignment (A, B, etc), allele (e.g., A1 or A2), and number of sequences recovered in
cloning experiments. Bootstrap values are indicated above the branches. Clade labels correspond
to genome groups associated with the temperate woody bamboos (Arundinarieae: A and B), the
tropical woody bamboos (Bambuseae: C, D, and E), and the herbaceous bamboos (Olyreae: H).
4
Fig. S4 Phylogram of the majority rule consensus tree from the Bayesian analysis of the
complete gpa1 data set. Codes after the species name indicate voucher, clade assignment (A, B,
etc), allele (e.g., A1 or A2), and number of sequences recovered in cloning experiments.
Posterior probabilities are indicated above the branches. Clade labels correspond to genome
groups associated with the temperate woody bamboos (Arundinarieae: A and B), the tropical
woody bamboos (Bambuseae: C and D), and the herbaceous bamboos (Olyreae: H). Note the
absence of clade E in this gene tree.
5
Fig. S5 Bootstrap consensus tree from a parsimony analysis of the complete gpa1 data set. Codes
after the species name indicate voucher, clade assignment (A, B, etc), allele (e.g., A1 or A2), and
number of sequences recovered in cloning experiments. Bootstrap values are indicated above the
branches. Clade labels correspond to genome groups associated with the temperate woody
bamboos (Arundinarieae: A and B), the tropical woody bamboos (Bambuseae: C, D, and E), and
the herbaceous bamboos (Olyreae: H). Note the absence of clade E in this gene tree.
6
Fig. S6 Phylogram of the majority rule consensus tree from the Bayesian analysis of the
complete pabp1 data set. Codes after the species name indicate voucher, clade assignment (A, B,
etc), allele (e.g., A1 or A2), and number of sequences recovered in cloning experiments.
Posterior probabilities are indicated above the branches. Clade labels correspond to genome
groups associated with the temperate woody bamboos (Arundinarieae: A and B), the tropical
woody bamboos (Bambuseae: C and D), and the herbaceous bamboos (Olyreae: H).
7
Fig. S7 Bootstrap consensus tree from a parsimony analysis of the complete pabp1 data set.
Codes after the species name indicate voucher, clade assignment (A, B, etc), allele (e.g., A1 or
A2), and number of sequences recovered in cloning experiments. Bootstrap values are indicated
above the branches. Clade labels correspond to genome groups associated with the temperate
woody bamboos (Arundinarieae: A and B), the tropical woody bamboos (Bambuseae: C, D, and
E), and the herbaceous bamboos (Olyreae: H).
8
Fig. S8 Phylogram of the majority rule consensus tree from the Bayesian analysis of the
complete pvcel1 data set. Codes after the species name indicate voucher, clade assignment (A, B,
etc), allele (e.g., A1 or A2), and number of sequences recovered in cloning experiments.
Posterior probabilities are indicated above the branches. Clade labels correspond to genome
groups associated with the temperate woody bamboos (Arundinarieae: A and B), the tropical
woody bamboos (Bambuseae: C and D), and the herbaceous bamboos (Olyreae: H).
9
Fig. S9 Bootstrap consensus tree from a parsimony analysis of the complete pvcel1 data set.
Codes after the species name indicate voucher, clade assignment (A, B, etc), allele (e.g., A1 or
A2), and number of sequences recovered in cloning experiments. Bootstrap values are indicated
above the branches. Clade labels correspond to genome groups associated with the temperate
woody bamboos (Arundinarieae: A and B), the tropical woody bamboos (Bambuseae: C, D, and
E), and the herbaceous bamboos (Olyreae: H).
10
Table S1 Taxa included in this study. Voucher abbreviations: LA – Lakshmi Attigala; GSK –
Gabriel Sanchez-Ken; JT – Jimmy Triplett; LC – Lynn Clark; PA – Patricio Asimbaya; SD –
Soejatmi Dransfield; WZ – Weiping Zhang; XL – Ximena Londoño. All voucher specimens are
at ISC except SD 1365, which is at K.
Higher Level Taxonomy Taxon
Voucher
Pooideae
Brachyelytrum erectum (Schreb.)
JT 199
P. Beauv.
Ehrhartoideae
Oryza sativa L.
GenBank NC 0013201
Tribe Olyreae: Subtribe
Buergersiochloa bambusoides
SD 1365
Buergersiochloinae
Pilg.
Tribe Olyreae: Subtribe
Olyra latifolia L.
XL and LC 911
Olyrinae
Tribe Olyreae: Subtribe
Sucrea maculata Soderstr.
LC and WZ 1345
Olyrinae
Tribe Bambuseae:
Aulonemia queko Goudot
LC 1445
Subtribe Arthrostylidiinae
Tribe Bambuseae:
Chusquea bambusoides (Raddi)
LC 1029
Subtribe Chusqueinae
Hack.
Tribe Bambuseae:
Chusquea scandens Kunth
LC and XL 1235
Subtribe Chusqueinae
Tribe Bambuseae:
Neurolepis aperta (Munro) Pilg.
LC 919
Subtribe Chusqueinae
[= Chusquea spectabilis L.G.
Clark]
Tribe Bambuseae:
Neurolepis elata (Kunth) Pilg. [=
LC and PA 1409
Subtribe Chusqueinae
Chusquea elata (Kunth) L.G.
Clark]
Tribe Bambuseae:
Guadua angustifolia Kunth
LC and XL 931
Subtribe Guaduinae
Tribe Bambuseae:
Otatea acuminata (Munro) C.
LC et al. 1312
Subtribe Guaduinae
Calderón & Soderstr.
Tribe Bambuseae:
Bambusa vulgaris Schrad.
GSK 666
Subtribe Bambusinae
Tribe Bambuseae:
Dendrocalamus latiflorus Munro
JT 332
Subtribe Bambusinae
Tribe Bambuseae:
Oxytenanthera abyssinica (A.
LC and JT 1664
Subtribe Bambusinae
Rich.) Munro
Tribe Bambuseae:
Schizostachyum dumetorum
JT 647
Subtribe Melocanninae
(Hance) Munro
Tribe Bambuseae:
Melocanna baccifera (Roxb.)
XL and LC 930
Subtribe Melocanninae
Kurz
Tribe Arundinarieae
Arundinaria densifolia Munro
LA 126
[= Kuruna densifolia (Munro)
Attigala, Kaththriarachchi & L. G.
Clark]
Tribe Arundinarieae
Arundinaria gigantea (Walter)
JT 197
Muhl.
11
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Tribe Arundinarieae
Arundinaria tecta (Walt.) Muhl
Chimonocalamus montanus J.R.
Xue & T.P. Yi
Hibanobambusa tranquillans
(Koidzumi) Maruyama and H.
Okamura
Phyllostachys bambusoides
Siebold and Zucc.
Pleioblastus chino (Franchet and
Savatier) Makino
Pleioblastus gozadakensis Nakai
Pleioblastus hindsii (Munro)
Nakai
Pleioblastus maculatus (McClure)
C.D. Chu and C.S. Chao
Pseudosasa amabilis (McClure)
P.C. Keng
Pseudosasa japonica (Siebold and
Zuccarini ex Steudel) Makino ex
Nakai
Sasa veitchii (Carrière) Rehder
Sasaella bitchuensis (Makino)
Makino ex Koidzumi
Sasaella ramosa (Makino) Makino
Sasamorpha borealis (Hackel)
Nakai
Semiarundinaria makinoi Hisauti
and Muroi
Semiarundinaria fastuosa (Marliac
ex Mitford) Makino ex Nakai
Semiarundinaria yashadake
(Makino) Makino
Shibataea chinensis Nakai
Thamnocalamus tessellatus (Nees)
Soderstr. and R.P. Ellis
[= Bergbambos tessellata (Nees)
Stapleton]
12
JT 24
JT 261
JT 205
JT 121
JT 420
JT 344
JT 411
JT 252
JT 545
JT 320
JT 126
JT 128
JT 118
JT 294
JT 135
JT 138
JT 137
JT 231
JT 202
Table S2 DNA primers and PCR parameters used for amplification and sequencing. Chromosomal locations of nuclear genes are
based on rice.
Region Location
Primer Sequences (5' to 3')
PCR Parameters
Reference
Chromosome GPA1-FF: GCAAGAGTACGGACAAATGGTG
95C, 5m; 35x (95C, 38; this study
gpa1
5
GPA1-14R: GCTTGCTGCTCTGGAAGTAG
30s; 49C, 45s; 72C, (copy-specific
Copy-specific primers:
1m 20s); 72C, 15m
primers).
C copy.
g1c_mb1721R: AAATTTGTTGAGAAACAGCATG
(used with GPA1-FF)
pabp1
pvcel1
Chromosome pabp1_for: GCTTGTCCGTAGAAGAGTTG
4
pabp1_rev2: GTGTTAGCAAAGGGTCTGGATTT
Copy-specific primers
B copy.
pa1b_786R: GTGGCTGACATGTTTTCCTTG
(used with pabp1_for)
E copy.
pa1e_2557R: ATTACTAGTGCCCAATTATAGATTA
(used with pabp1_for)
95C, 5m; 35x (95C,
30s; 49C, 45s; 72C,
1m 20s); 72C, 15m
This study.
Chromosome pvcel1_for: GCCAACATGGTTCAGTTGG
9
pvcel1_rev: CGCCCCTCTGTGGTGTAC
Copy-specific primers
C copy.
cel1c_157F: ATGGGACTCAAAATGTATAGAGACACTGC
(used with pvcel1_rev or cel1c_1228R)
95C, 5m; 35x (95C,
30s; 49C, 45s; 72C,
1m 20s); 72C, 15m
This study.
cel1c_1228R: CCGACCAAAATAGTCATAGATTCGTA
(used with pvcel1_for or cel1c_157F)
D copy.
cel1d_10F: TGTGAATTCCCTTAGCAGGGTTA
(used with cel1d_918R or pvcel1_rev)
13
cel1d_918R: CACAACAGATTAGAAAGTTACACC
(used with pvcel1_for or cel1d_10F)
E copy.
cel1e_440F: ATAATTTTAACGCAGGAGGATTGGTGTGGA
(used with pvcel1_rev)
cel1e_877R: CCAAGACAACAGAAATATCGTCCAAAGTC
(used with pvcel1_for)
14
Table S3 Statistics and evolutionary models for separate data partitions. PIC = parsimony
informative characters. PIC parenthetical indicates the number of parsimony informative
characters within the temperate clade. MP = maximum parsimony; CI = consistency index,
excluding uninformative characters; RI = retention index.
Partition
Sequences Total
Indels PIC
MP
MP
CI
char.
Trees
Length
gpa1
66
2248
55
438
448
1396
0.7092
pabp1
76
2955
51
549
20
1355
0.7852
pvcel1
102
1773
66
488
6528
1430
0.6790
combined
54
6535
164
1121
8
3758
0.7360
data
15
RI
0.8616
0.8959
0.9070
0.8384
Table S4 Hypotheses regarding clades and relationships among them. All hypotheses were
tested under Maximum Parsimony using the Kishino-Hasegawa test. We report the difference
between the MP trees and those consistent with the constraint (percent difference is calculated
relative to lengths of the MP trees).
Hypothesis
H (Olyreae) is sister to ABCDE
(Bambuseae). Data set: pvcel1
H is sister to D. Data set: combined
C is monophyletic. Data set: gpa1
C is monophyletic. Data set:
combined
One origin of tetraploidy in the
woody bamboos, prior to split b/w
temperate and tropical lineages
[(A+D) is sister to (B+C)]. Data
set: combined
Results of Test
Reject (+9 steps, 0.6%, t = 2.0666, p = 0.0389)
Reject (+22 steps, 0.6%, t = 2.7514, p = 0.0060)
Reject (+15 steps, 1.1%, t = 2.7896, p = 0.0053)
Cannot reject (+3 steps, 0.1%, t = 0.5071, p = 0.6121)
Reject (+38 steps, 1.0%, t = 3.9662, p = 0.0001)
16