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Vol. 65 (3) • June 2016
International Journal of Taxonomy, Phylogeny and Evolution
Electronic Supplement to
Cynanchum (Apocynaceae: Asclepiadoideae): A pantropical Asclepiadoid genus revisited
Electr. Suppl. to: Khanum & al. • Cynanchum revisitedTAXON 65 (3) • June 2016
S1
0.01 expected subst./site
*/*
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90/0.97*/*
*/*
*/**/*
32/0.5834/0.62
85/*93/*
60/0.99
37/0.9021/0.28
46/0.97
86/*28/0.999
21/0.7447/0.55
16/0.24
44/0.71 */*
99/**/*
98/*
4280.5888/0.91
81/*
37/0.84
86/*
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64/*
98/*
*/*73/0.99
57/0.41
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39/0.62
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99/*
30/0.95
32/0.91
31/0.87
27/0.97
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*/**/*
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39/0.5462/0.54
53/0.39
65/0.94
84/0.99969/0.86
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*/*
*/**/*
99/*
*/**/* */*
98/*
87/*
96/*76/*
59/0.99
49/<0.2
*/*85/*
83/*
97/*
97/*
77/*
89/0.998*/*
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*/*
*/**/*
*/*41/0.9140/0.73
*/*72/.097
*/* 82/0.78
75/*
97/0.99
88/0.99
54/0.58
*/*88/0.84
91/*99/*
*/*
*/*
52/0.74
29/0.59
64/0.99
*/*
*/**/*
*/**/*
*/*
*/0.996
*/*64/0.82
*/*
44/0.47
88/0.82
75/0.89
53/0.81
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C. repandumC. obovatum
C. pachycladonC. analamazaotrense
Schizostephanus alatusCalciphila galgalensis 6205
Ca. galgalensis 9433Ca. gillettii
Calotropis proceraPs. nivalis
Ps. madagascariensisPs. sp. 20905
C. papillatumC. cucullatum
C. sessili�orumC. erythranthum
C. itremenseC. lineareC. moramangense
C. angavokelienseC. leucanthum
C. danguyanumC. comorense
C. phillipsonianumC. madagascariense
C. grandidieriC. mariense
C. arenariumC. verrucosumC. macranthum
C. perrieriC. descoingsii
C. crassipedicellatumC. hardyi
C. rauhianumC. toliari
C. marnieranumC. appendiculatopsis
C. insigneC. compactum
C. a�. compactumC. folotsioides
C. implicatumC. messeri
C. mahafalenseC. pycnoneuroides
C. rossii
C. gerrardii Newton 6206C. gerrardii 962C. gerrardii 2797
C. juliani marnieriC. radiatum
C. ampanihenseC. sigridiae
C. mevei
C. viminale brunonianum Liede 3272C. arabicum
C. viminale suberosumC. mulanjense
C. viminale UM 1441C. viminale viminaleC. antsiranense
C. membranaceumC. pearsonianum
C. meyeriC. natalitium
C. ellipticumC. altiscandens
C. obtusifoliumC. africanum
C. rungweenseC. chouxii
C. orangeanum 347C. orangeanum 4537
C. praecox
C. crassiantheraeC. rubricoronae
C. blyttioidesC. hastifolium 21213C. hastifolium 3226
C. giraldiiC. wilfordii
C. purpureumC. lysimachioides
C. auriculatumC. petrense
C. �oribundumC. corymbosumC. dalhousiae
C. tunicatumC. callialatum
C. acutum LisboaC. acutum 36516
C. chinenseC. abyssinicum
C. ovalifoliumC. physocarpum
C. formosanumGraphistemma pictum
C. longipesC. adalinae
C. taiwanianumC. boudieri
C. o�cinaleC. maximoviczii
C. wallichii
Metaplexis japonica NankingMp. japonica Tartu
C. thesioides QingruC. thesioides Wang
C. sinoracemosumRaphistemma pulchellum
Holostemma annulariumSeshagiria sahyadrica
P. somaliense 4238P. somaliense 3225
P. gonoloboidesOdontanthera radians
Glossonema revoiliiG. varians
C. polyanthumC. falcatum 3169
C. falcatum 21226C. schistoglossum
P. abyssinicumP. insipidum
P. ledermannii
Cynanchum montevidenseC. a�. montevidense
C. blandumMetalepis albi�ora
M. pera�nisC. roulinioides
C. foetidumC. racemosum
C. ligulatumC. laeve
Calciphila
PentatropisCalotropis
Schizostephanus
Clade 1: Madagascan and all succulent Cynanchum
Clade 2: S./E. African Cynanchum
Clade 3: African Cyanchum
Clade 4: Eurasian-Australian Cynanchum
Clade 4b
Clade 4a
Clade 7: Asian Cynanchum andmonospeci�c genera
Clade 9: New World Cynanchumand Metalepis
Clade 9a
Clade 9b
Clade 8: Glossonema, Odontanthera, and Pentarrhinum
Clade 5: C. falcatum-schistoglossum
Clade 6: C. adalinae-longipes
Clade 1b
Clade 1a
45/0.83
Fig. S1. Comprehensive version of the outgroup-rooted maximum likelihood (ML) tree for the Cynanchinae shown in Fig. 2 of the main paper. Numbers at branches indicate support as estimated from non-parametric bootstrapping under ML (BSML) and Bayesian-inferred posterior probabilities (PP). Asterisks refer to unambiguous support by both methods (BSML = 100, PP = 1).
Electr. Suppl. to: Khanum & al. • Cynanchum revisitedTAXON 65 (3) • June 2016
S2
ML-BS = 100
Clade 1
Clade 2
Clade 3Clade 7
Clade 99b: N. America
4a4a
4b
9a: S. America(incl. Metalepis)
Clade 8
Clade 6
Clade 5
Clade 4
Outgroup
1a: Non-succulentMadagascanCynanchum
1b: SucculentCynanchum
C. pachycladon
C. analam.
C. chouxii
C. polyan.
Pentarrhinum
GlossonemaOdontanthera
C. abyss.
Schizostephanus
Calotropis
Calciphila
Pentatropis
75/0.8953/0.81
52/0.74
65/0.94
75/*
42/0.4221/0.2621/-
84/0.999
21/<0.2
25/<0.1
99.7/*
*/*
*/*
99.7/**/*
98/*
97/0.999
88/0.84
64/0.99
54/0.58
99/*
31/0.51
99.7/*
*/*
*/**/*
*/*
90/0.97
57/0.49
74/0.999
42/0.51
63/0.94
*/*
50/0.49
43/<0.2
72/0.80
97/*42/0.89
44/<0.1
88/0.82
87/*
96/*
Fig. S2Fig. S2. Signal compatibility in the concatenated data. This bipartition network based on 350 maximum likelihood bootstrap replicates illustrates compatibility of backbone signals in the concatenated data. Edges correspond to potential branches in phylogenetic trees; their lengths are proportional to the occurrence frequency of the corresponding bipartition (edge/branch) in the bootstrap replicate tree sample. For better comparison, ML bootstrap support (BSML) values are also shown as values in addition to the Bayesian-inferred (BI) posterior probabilities (PP) of the according edge; asterisks indicate unambigu-ous support (BSML = 100, PP = 1). Bipartitions with frequencies < 20% are not shown; terminal subtrees are represented by triangles (version with all leaves can be found in the electronic supplement Fig. S3).
Electr. Suppl. to: Khanum & al. • Cynanchum revisitedTAXON 65 (3) • June 2016
S3
ML-BS = 100
Raphistemma pulchellumHolostemma annularium
C. pachycladon
C. toliari
C. arenariumC. verrucosum
C. rossiiC. pynoneuroides
C. repandumC. obovatum
C. arabicum
C. pear-
C. mahafalense.C. folotsioides
C. mevei
C. ampanihenseC. gerrardii
C. juliani-marnieri
C. appendiculatopsisC. marnieranum
C. compactum
C. antsira-
C. viminale
C. viminale
C. mulanjense
C. membranaceum
C. madagascariense
C. leucanthum
C. lineareC. angavokeliense
C. moramangense
C. itremense
C. cucullatumC. papillatum
C. sessili�orum
C. danguyanumC. comorense
C. phillipsonianum
C. erythranthum
C. a�. compactum
C. insigne
C. radiatum
C. sigridiae
C. implicatumC. messeri
C. rauhianum
C. hardyi
C. macranthum
C. crassipedicellatum
C. mariense
C. descoingsii
C. grandidieri
C. perrieri
C. analamazaotrense
C. chouxii
C. obtusifolium
C. schistoglossum
C. crassiantherae
C. altiscandens
C. ellipticum
C. natalitium
C. hastifolium
C. falcatum
Seshagiria sahyadrica
C. physocarpumC. formosanum
C. adalinaeC. longipes
C. polyanthumC. laeve
C. roulinioides
C. blandum
Metalepis albi�orumM. pera�nis
C. montevidenseC. a�. montevidense
P. somaliense
P. ledermannii
Pentarrhinum insipidum P. abyssinicum
Glossonema revoilii
G. varians
C. callialatum
C. dalhousiae
C. corymbosumC. �oribundum
C. acutum
C. purpureum
C. o�cinale
C. taiwanianumC. boudieri
C. giraldii
C. auriculatumC. lysimachioides
C. wilfordii
C. chinense
C. maximovicziiC. wallichii
C. tunicatum
Odontanthera radians
P. gonoloboides
C. ligulatum
C. foetidumC. racemosum
C. abyssinicumC. ovalifoliumGraphistemma pictum
Schizostephanus
Calotropis
Calciphila galgalensis
Pentatropis
Pentatropis nivalisP. madagascariense
C. thesioides
C. sinoracemosum
Metaplexis
C. petrense
C. rungweense
C. africanum
C. blyttioidesC. orangeanum
C. praecox
C. rubricoronae
C. meyeri
Clade 1
Clade 2
Clade 3
Clade 5
Clade 7
Clade 9
Clade 8
Clade 6
Clade 4
4a
9a
9b
4bOutgroup
1a: Non-succulentMadagascanCynanchum
1b: SucculentCynanchum
japonicum
nense
sonianum
sp. 20905
alatus
procera
Fig. S3
Calciphila gillettii
Fig. S3. Comprehensive bipartition network based on 350 maximum likelihood (ML) bootstrap (BS) replicates illustrating compatibility of phylogenetic signal in the concatenated data. Edges correspond to potential branches in phylogenetic trees; their lengths are proportional to the occurrence frequency of the corresponding bipartition (edge/branch) in the bootstrap replicate tree sample. See Fig. S2 for a version focussing on backbone topological alternatives providing support values from non-parametric bootstrapping under ML and Bayesian inference; Table S2 for a graphically enhanced tabulation of ML-BS support for ML-preferred and alternative bipartitions based on the concatenated data and one- or two-partition datasets.
Electr. Suppl. to: Khanum & al. • Cynanchum revisitedTAXON 65 (3) • June 2016
S4
PP = 1.00
Raphistemma pulchellumHolostemma annularium
C. pachycladonC. toliari
C. arenarium
C. verrucosum
C. rossii
C. pynoneuroides
C. repandumC. obovatum
C. arabicum
C. pearsonianum
C. mahafalense
C. folotsioides
C. meveiC. ampanihense
C. gerrardii
C. juliani-
C. appendiculatopsisC. marnieranum
C. compactum
C. antsiranense C. viminale
C. viminaleC. mulanjense
C. membranaceum
C. mada-
C. leucanthum
C. lineare
C. angavokeliense
C. moramangense
C. itremenseC. cucullatumC. papillatum C. sessili�orum
C. danguyanumC. comorense
C. phillipsonianum
C. erythranthum
C. a�. compactum
C. insigne
C. radiatumC. sigridiae
C. implicatum
C. messeri
C. rauhianum
C. hardyi
C. macranthum
C. crassipedicellatum
C. mariense
C. descoingsii
C. grandidieri
C. perrieri
C. analamazaotrense
C. chouxii
C. obtusifolium
C. schistoglossum
C. crassiantherae
C. altiscandens
C. ellipticumC. natalitium
C. hastifolium
C. falcatum
Seshagiria sahyadrica
C. physocarpum
C. formosanum
C. adalinaeC. longipes
C. polyanthum
C. laeve
C. roulinioides
C. blandum
Metalepis albi�orumM. pera�nis
C. montevidenseC. a�. montevidense P. somaliense
P. ledermannii
Pentarrhinum insipidum P. abyssinicum
Glossonema revoilii
G. varians
C. callialatum
C. dalhousiae
C. corymbosumC. �oribundum
C. acutum
C. purpureum
C. o�cinale
C. taiwanianumC. boudieri
C. giraldii
C. auriculatumC. lysimachioides
C. wilfordii
C. chinense
C. maximoviczii C. wallichii
C. tunicatum
Odontanthera radians
P. gonoloboides
C. ligulatum
C. foetidumC. racemosum
C. abyssinicum
C. ovalifolium
Graphistemma pictum
Schizostephanus
Calotropis
Calciphila gillettii
Calciphila galgalensis
Pentatropis sp. 20905
Pentatropis nivalisP. madagascariense
C. thesioides
C. sinoracemosum
Metaplexis
C. petrense
C. rungweense
C. africanum
C. blyttioides
C. orangeanum
C. praecox
C. rubricoronae
C. meyeri
Clade 1
Clade 2
Clade 3
Clade 5
Clade 7
Clade 9
Clade 8
Clade 6
Clade 4
4a
9a
9b
4b
Outgroup
1a: Non-succulentMadagascanCynanchum
1b: SucculentCynanchum
marnieri
gascariense
alatus
procera
japonicum
Fig. S4Fig. S4. Comprehensive bipartition network based on 2000 Bayesian-inferred sampled topologies (BIST) illustrating compatibility of phylogenetic signal in the concatenated data. Edges correspond to potential branches in phylogenetic trees; their lengths are proportional to the occurrence frequency of the corresponding bipartition (edge/branch) in the BIST tree sample. The posterior probabilities cal-culated from this sample are shown in Fig. 2 of the main paper and Figs. S1 and S2, and included in Table S2 for direct comparison with maximum likelihood non-parametric bootstrap support.
Electr. Suppl. to: Khanum & al. • Cynanchum revisitedTAXON 65 (3) • June 2016
Clade 9a (South America into Central America) 100 1.00 95 0.97 ₮ 98 1.00 <20 0.33 99.5 1.00 90 1.00 <20 <0.2 <20 <0.2Clade 9b (North and Central America) 99.7 1.00 <20 <0.2 99 0.97 35 0.35 38 0.46 43 0.59 <20 <0.2 63 0.95 ₩
* Single species♯ One accession (Pentatropis sp. 20905) with ambiguous affinity to other outgroup accessions† C. pachycladon nested in Clade 1b‡ In contrast to the C. hastifolium accessions that group with the outgroup, the other two representatives of Clade 3 group are resolved as sister taxa with BSML/PP = 99.8/1.0, and are placed according to the concatenated tree§ C. chouxii grouped with all Clade 1 members save C. analamazaonese and C. purpurense , the latter two unresolved₱ C. chouxii grouped with all Clade 1 members save C. analamazaonese , the latter unresolved. Under BI, C. erythrantum is only indicated as potential relative of some Clade 1 members, but not all.$ C. calliatum grouping with 1+5 (BSML = 47/38; PP = 0.59/0.37), C. corymbosum unresolved¥ C. corymbosum nested in Clade 4b, C. officinale groups with members of Clade 4a¶ C. rungweense (Clade 2) grouped with Clade 1, C. africanum unresolved; remainder BSML/PP = 91/0.75, placed as sister to rest of ingroup‼ C. orangeanum 4537 unresolved£ Several taxa with predominant polymorphic base calls group with Clade 2; an according (artificial) clade would receive BSML/PP = 86/0.87₩ Only two species out of six covered (three without data, forth polymorphic£)₡ Includes C. pycnoneuroides₦ In the BIST sample, C. anamalazotrense nests within Clade 1a; a corresponding clade would receive a BSML = 35€ Including C. leucanthum (Clade 1a)ℓ Glossonema+Odanthera unresolved₪ C. purpureum unresolved₮ C. roulinoides unresolved₰ Excluding the two C. hastifolium accessions
NUC2137 127 137 92 106 134 104 96
tHpA trnTLF rps16i 5' ETS ITS NUC1
Table S2. Tabulation of ML-BS support for ML-preferred and alternative bipartitions based on the concatenated data and single-region datasets.
Continued next page
Electr. Suppl. to: Khanum & al. • Cynanchum revisitedTAXON 65 (3) • June 2016
Clade 9a (South America into Central America) 100 1.00 95 0.97 ₮ 98 1.00 <20 0.33 99.5 1.00 90 1.00 <20 <0.2 <20 <0.2Clade 9b (North and Central America) 99.7 1.00 <20 <0.2 99 0.97 35 0.35 38 0.46 43 0.59 <20 <0.2 63 0.95 ₩
* Single species♯ One accession (Pentatropis sp. 20905) with ambiguous affinity to other outgroup accessions† C. pachycladon nested in Clade 1b‡ In contrast to the C. hastifolium accessions that group with the outgroup, the other two representatives of Clade 3 group are resolved as sister taxa with BSML/PP = 99.8/1.0, and are placed according to the concatenated tree§ C. chouxii grouped with all Clade 1 members save C. analamazaonese and C. purpurense , the latter two unresolved₱ C. chouxii grouped with all Clade 1 members save C. analamazaonese , the latter unresolved. Under BI, C. erythrantum is only indicated as potential relative of some Clade 1 members, but not all.$ C. calliatum grouping with 1+5 (BSML = 47/38; PP = 0.59/0.37), C. corymbosum unresolved¥ C. corymbosum nested in Clade 4b, C. officinale groups with members of Clade 4a¶ C. rungweense (Clade 2) grouped with Clade 1, C. africanum unresolved; remainder BSML/PP = 91/0.75, placed as sister to rest of ingroup‼ C. orangeanum 4537 unresolved£ Several taxa with predominant polymorphic base calls group with Clade 2; an according (artificial) clade would receive BSML/PP = 86/0.87₩ Only two species out of six covered (three without data, forth polymorphic£)₡ Includes C. pycnoneuroides₦ In the BIST sample, C. anamalazotrense nests within Clade 1a; a corresponding clade would receive a BSML = 35€ Including C. leucanthum (Clade 1a)ℓ Glossonema+Odanthera unresolved₪ C. purpureum unresolved₮ C. roulinoides unresolved₰ Excluding the two C. hastifolium accessions