Table S1. Source Phylogenies for Supertree Building

Supplementary information for: Jenkins, CE and Keller SR (2010) A phylogenetic comparative study of preadaptation for invasiveness in the genus Silene (Caryophyllaceae) Biological Invasions

Table S1. Source phylogenies for supertree building.

Source / Genomic Region / Genome / N1
1 / Burleigh and Holtsford, 2003 / ITS / Nuclear / 19
2 / Desfeux et. al., 1996 / ITS / Nuclear / 28
3 / Egens et. al., 2007 / ITS / Nuclear / 54
4 / Egens et. al., 2007 / rps16 / Chloroplast / 53
5 / Egens et. al., 2007 / RPB2 / Nuclear / 50
6 / Ironside and Filatov, 2005 / DD44Y / Nuclear / 4
7 / Oxelman and Liden, 1995 / ITS / Nuclear / 21
8 / Oxelman and Liden, 1995 / ITS / Nuclear / 64
9 / Oxelman et. al., 1997 / rps16 / Chloroplast / 48
10 / Oxelman et. al., 2000 / ITS, rps16 / Nuclear, chloroplast / 32
11 / Popp and Oxelman, 2004 / rps16 / Chloroplast / 30
12 / Popp and Oxelman, 2004 / ITS / Nuclear / 28
13 / Popp and Oxelman, 2004 / RPA2 / Nuclear / 29
14 / Popp and Oxelman, 2004 / RPB2 / Nuclear / 33
15 / Popp and Oxelman, 2004 / RPD2a / Nuclear / 31
16 / Popp and Oxelman, 2004 / RPD2b / Nuclear / 23
17 / Popp et. al., 2005 / cpDNA / Nuclear / 23
18 / Popp and Oxelman 2007 / psbE-petL, rps 16 / Chloroplast / 69
19 / Popp and Oxelman 2007 / ITS / Nuclear / 82
20 / Popp and Oxelman 2007 / RPA2 / Nuclear / 61
21 / Popp and Oxelman 2007 / RPB2 / Nuclear / 75
22 / Popp and Oxelman 2007 / RPD2a / Nuclear / 46
23 / Popp and Oxelman 2007 / RPD2b / Nuclear / 50

1Number of taxa in the source tree.

Table S2. Non-parametric analysis of phylogenetic independent contrasts using the brunch algorithm of CAIC. N refers to the number of contrasts in the model, n the number of contrasts with non-zero values, and T the test statistic from a Wilcoxon signed-rank test. In all cases, significant T values indicate a positive association between contrasts in traits and invasiveness. Values in bold indicate significant relationships.

GCW / USDA
N / n / T / P / N / n / T / P
Pollen:ovule ratio / 19 / 18 / 74.5 / 0.6095 / 19 / 12 / 36.5 / 0.8501
Ovule number / 19 / 18 / 58.5 / 0.2645 / 19 / 12 / 13.0 / 0.0425
Stem height / 63 / 36 / 150.5 / 0.0035 / 43 / 19 / 41.5 / 0.0323
Leaf size / 52 / 28 / 79.5 / 0.0041 / 30 / 14 / 10.0 / 0.0052
Seed size / 48 / 26 / 136.5 / 0.3403 / 31 / 15 / 56.5 / 0.8904
Germination time / 9 / 8 / 17.0 / 0.9453 / 8 / 6 / 7.0 / 0.5625
Germination temperature range / 7 / 6 / 8.0 / 0.5625 / 7 / 7 / 0.0 / 0.0156
Number of months flowering / 33 / 23 / 90.0 / 0.1511 / 24 / 13 / 17.5 / 0.0574
Flower number / 34 / 20 / 42.0 / 0.0172 / 20 / 10 / 2.0 / 0.0059
Native geographic range size / 50 / 32 / 61.5 / <0.0001 / 34 / 17 / 21.0 / 0.0067

Table S3. Spearman rank correlations on the raw (species-level) trait data. Numbers above the diagonal are Spearman’s ρ; numbers below the diagonal are degrees of freedom. Values in bold are significant after Bonferroni correction.

GCW index / USDA index / Range size / Pollen: ovule / Ovule number / Stem height / Leaf size / Seed size / Germ. time / Germ. temp. / Months flower / Flower number
GCW index / 0.70**** / 0.70**** / -0.21 / 0.24 / 0.27** / 0.03 / -0.11 / -0.36 / 0.30 / 0.30** / 0.22
USDA index / 113 / 0.64**** / 0.07 / 0.27 / 0.34*** / 0.30* / 0.19 / -0.15 / 0.24 / 0.33** / 0.27
Range size / 67 / 64 / -0.20 / 0.34 / 0.44*** / 0.38* / 0.12 / -0.13 / 0.29 / 0.22 / 0.07
Pollen:ovule / 40 / 39 / 36 / -0.49** / -0.01 / -0.11 / 0.01 / 0.08 / 0.08 / -0.29 / -0.60**
Ovule number / 40 / 39 / 36* / 40 / 0.34* / 0.54** / -0.02 / 0.40 / 0.18 / 0.00 / 0.30
Stem height / 133 / 90 / 64 / 40 / 40 / 0.59**** / 0.17 / 0.20 / 0.03 / 0.17 / 0.17
Leaf size / 107 / 64 / 44 / 32 / 32 / 105 / 0.26* / -0.13 / -0.04 / 0.03 / 0.19
Seed size / 105 / 65 / 54 / 34 / 34 / 103 / 87 / -0.20 / -0.63* / 0.18 / -0.06
Germ. time / 18 / 17 / 15 / 13 / 13 / 18 / 13 / 12 / -0.69* / 0.04 / 0.01
Germ. range / 16 / 16 / 14 / 9 / 9 / 16 / 11 / 12 / 12 / -0.21 / -0.12
Months flower / 97 / 71 / 49 / 36 / 36 / 95 / 85 / 80 / 16 / 14 / 0.16
Flower number / 72 / 44 / 34 / 19 / 19 / 70 / 64 / 59 / 11 / 9 / 54

*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001

Figure S1. Supertree of Silene and related genera. Taxa marked with black circles have >5 citations in Randall’s Global Compendium of Weeds. Major recognized taxonomic subsections within the Sileneae are labeled. Scale is estimated divergence time in millions of years.

Supertree topology in standard Newick format. Topology isthe majority-rule consensus tree from a parsimony heuristic search. Branch lengths are scaled to estimated divergence times in millions of years.

((((((((Silene_aellenii:3.64000000,(Silene_burchellii:3.12000000,(Silene_pseudoatocion:2.60000000,(Silene_nocturna:2.08000000,((Silene_bergiana:0.78000000,Silene_turbinata:0.78000000):0.78000000,((Silene_colorata:0.52000000,Silene_niceensis:0.52000000):0.52000000,(Silene_fuscata:0.52000000,Silene_gallica:0.52000000):0.52000000):0.52000000):0.52000000):0.52000000):0.52000000):0.52000000):0.52000000,(((Silene_brevistaminea:2.94141400,(Silene_ampullata:2.52121200,(Silene_cappadocica:2.10101000,(Silene_repens:1.68080800,(Silene_linicola:1.26060600,((Silene_moorcroftiana:0.42020200,Silene_schafta:0.42020200):0.42020200,Silene_boryi:0.84040400):0.42020200):0.42020200):0.42020200):0.42020200):0.42020200):0.42020200,Silene_italica:3.36161600):0.42020200,(((((Silene_hawaiiensis:0.87522100,Silene_struthioloides:0.87522100):0.87522100,(Silene_lanceolata:1.16696100,(Silene_perlmanii:0.58348000,Silene_alexandri:0.58348000):0.58348000):0.58348100):0.58348000,Silene_antirrhina:2.33392200):0.58348100,((Silene_linearis:1.94493500,(Silene_arenosa:1.45870100,((Silene_austroiranica:0.48623400,Silene_exsudans:0.48623400):0.48623400,Silene_leyseroides:0.97246700):0.48623400):0.48623400):0.48623400,((Silene_cuatrecasasii:0.91168800,Silene_inaperta:0.91168800):0.91168800,(Silene_martyri:1.21558400,(Silene_reticulata:0.60779200,Silene_muscipula:0.60779200):0.60779200):0.60779200):0.60779200):0.48623400):0.48623400,((Silene_cretica:2.59324700,((Silene_subcretacea:1.72883100,(Silene_cariensis:1.29662300,(Silene_marschallii:0.86441600,(Silene_longipetala:0.43220800,Silene_bupleuroides:0.43220800):0.43220800):0.43220800):0.43220800):0.43220800,((Silene_echinospermoides:0.86441600,Silene_reinwardtii:0.86441600):0.86441600,(Silene_ungeri:1.29662300,(Silene_corinthiaca:0.86441600,(Silene_pinetorum:0.43220800,Silene_echinosperma:0.43220800):0.43220800):0.43220800):0.43220800):0.43220800):0.43220800):0.43220800,((Silene_mentagensis:1.32363600,Silene_portensis:1.32363600):1.32363600,((Silene_tatarica:1.51272700,(Silene_acaulis:0.75636400,Silene_nivalis:0.75636400):0.75636400):0.75636400,((((Silene_fortunei:0.75636400,(Silene_macrostyla:0.37818200,Silene_stenophylla:0.37818200):0.37818200):0.37818200,Silene_otites:1.13454500):0.37818200,Silene_pseudotites:1.51272700):0.37818200,(((Silene_gigantea:0.75636400,(Silene_falcata:0.37818200,Silene_nemoralis:0.37818200):0.37818200,Silene_waldsteinii:0.75636400):0.37818200,Silene_saxifraga:1.13454500):0.37818200,((Silene_tanakae:0.50424200,Silene_nutans:0.50424200):0.50424200,Silene_roemeri:1.00848500,Silene_fruticosa:1.00848500):0.50424200):0.37818200):0.37818200):0.37818200):0.37818200):0.37818200):0.37818200):0.37818200):8.34714300,(Silene_foetida:10.43142900,((((Silene_littorea:3.71365100,(Silene_sedoides:1.85682500,Silene_integripetala:1.85682500):1.85682500):1.85682600,((Silene_insularis:2.78523800,(Silene_pentelica:1.39261900,Silene_cryptoneura:1.39261900):1.39261900):1.39261900,Silene_dichotoma:4.17785700):1.39261900):1.39261900,(Silene_samia:5.57047700,((Silene_williamsii:2.78523800,(Silene_seelyi:1.39261900,Silene_menziesii:1.39261900):1.39261900):1.39261900,(Silene_nivea:2.08892900,Silene_baccifera:2.08892900):2.08892900):1.39261900):1.39261900):1.39261900,(((Silene_multinervia:2.69142900,Silene_nana:2.69142900):2.69142900,((Silene_elisabethae:2.24285700,Silene_noctiflora:2.24285700):2.24285700,((Silene_latifolia:2.69142900,(Silene_heuffelii:1.79428600,(Silene_dioica:0.89714300,Silene_diclinis:0.89714300):0.89714300):0.89714300):0.89714300,Silene_conica:3.58857200):0.89714300):0.89714300):0.89714300,((((Silene_reinholdii:1.47159100,Silene_fabaria:1.47159100):1.47159100,Silene_pendula:2.94318200):1.47159100,(Silene_vulgaris:2.20738600,Silene_uniflora:2.20738600):2.20738600):1.47159100,(Silene_sordida:5.49272700,(Silene_furcata:5.09909100,((Silene_scopulorum:2.35272700,Silene_oblanceolata:2.35272700):2.35272700,(Silene_viscosa:4.31181800,(Silene_zawadskii:3.91818200,(((Silene_aprica:2.34969700,((Silene_involucrata:1.17484900,(Silene_ostenfeldii:0.58742400,Silene_sorensenis:0.58742400):0.58742400):0.58742400,(Silene_linnaeana:0.88113600,Silene_ajanensis:0.88113600):0.88113600):0.58742400):0.58742400,Silene_keiskei:2.93712100):0.58742400,(((Silene_hookeri:1.95681800,((Silene_lemmonii:0.65227300,Silene_invisa:0.65227300):0.65227300,(Silene_parryi:0.65227300,Silene_drummondii:0.65227300):0.65227300):0.65227300):0.65227300,(Silene_parishii:2.08727300,((Silene_suksdorfii:0.78272700,Silene_uralensis:0.78272700):0.78272700,(Silene_thysanodes:1.04363600,(Silene_ovata:0.52181800,Silene_nigrescens:0.52181800):0.52181800):0.52181800):0.52181800):0.52181800):0.52181800,((Silene_nuda:2.34363700,(((Silene_scaposa:0.97500000,(Silene_sargenti:0.48750000,Silene_scouleri:0.48750000):0.48750000):0.48750000,Silene_bernardina:1.46250000):0.48750000,Silene_douglasii:1.95000000):0.39363600):0.39363600,(((Silene_oregana:1.27739400,(Silene_laciniata:0.63869700,Silene_campanulata:0.63869700):0.63869700):0.63869700,(Silene_andersonii:1.43706800,((Silene_occidentalis:0.47902300,Silene_verecunda:0.47902300):0.47902300,(Silene_chubutensis:0.47902300,Silene_mandonii:0.47902300):0.47902300):0.47902300):0.47902300):0.47902300,((Silene_subciliata:1.02647700,Silene_regia:1.02647700):1.02647700,(Silene_petersonii:1.71079500,((Silene_polypetala:1.02647700,(Silene_stellata:0.68431800,(Silene_virginica:0.34215900,Silene_caroliniana:0.34215900):0.34215900):0.34215900):0.34215900,Silene_rotundifolia:1.36863600):0.34215900):0.34215900):0.34215900):0.34215900):0.39363600):0.39363600):0.39363600):0.39363600):0.39363700):0.39363600):0.39363600):0.39363700):0.39363600):2.07571500):2.07571400):2.07571400):2.07571400,(((Lychnis_lagrangei:3.64571500,Lychnis_flos-cuculi:3.64571500):3.64571500,Lychnis_abyssinica:7.29142900):3.64571400,(Lychnis_chalcedonica:7.29142900,(Lychnis_coronaria:3.64571400,Lychnis_flos-jovis:3.64571400):3.64571400):3.64571500):3.64571400):2.07571400,Petrocoptis_pyrenaica:16.65857100):2.07571400,((Eudianthe_coeli-rosa:7.49371400,Eudianthe_laeta:7.49371400):7.49371400,((Atocion_rupestre:7.49371400,(Atocion_lerchenfeldiana:3.74685700,Atocion_armeria:3.74685700):3.74685700):3.74685700,(Silene_pusilla:5.62028600,Viscaria_vulgaris:5.62028600):5.62028600):3.74685800):3.74685700):2.07571400,Agrostemma_githago:20.80999900):10.89000100,(Saponaria_ocymoides:15.85000000,Dianthus_seguieri:15.85000000):15.85000000);

Assumption tests of phylogenetic independent contrasts in CAIC.ns=not significant, *P < 0.05, **P < 0.01, *** P < 0.001. Refer to CAIC User’s manual for more information on each assumption test.

Part A. Equal branch length model:

Index / Identifier / %Outliers / Largest resid / b{x vs x@node} / b{x vs SD} / b{y vs y@node} / b{y vs SD} / b{x vs Resids}
GCW / # of flowers / 7.04 / 3.7256 / 0.5189*** / ns / 0.4960*** / ns / 0.0858***
GCW / Days to germination / 11.76 / 2.2264 / 0.4218*** / ns / 0.2466*** / -3.9370* / ns
GCW / Geographic range size / 5 / 4.7706 / ns / -0.6680*** / 0.5004*** / -2.3619** / 0.4141***
GCW / Germination temp range / 6.67 / -2.8148 / ns / -0.8225* / 0.3062*** / neg / pos
GCW / Height / 6.92 / 3.3476 / 0.4299*** / ns / 0.1559** / -7.8194** / ns
GCW / Leaf size / 7.55 / 4.03 / 0.3431*** / ns / 0.1993*** / neg / ns
GCW / Months flowering / 7.37 / -3.735 / ns / ns / 0.3801*** / ns / 0.8621**
GCW / Ovule number / 7.89 / 2.641 / 0.2057*** / -2.4808* / 0.2602*** / -19.9046* / 0.0623*
GCW / Pollen/Ovule ratio / 13.16 / -2.7014 / 0.2057*** / -2.4808* / 0.3197*** / ns / ns
GCW / Seed diameter / 6.8 / 3.8064 / 0.3616*** / ns / 0.1591*** / ns / ns
USDA / # of flowers / 4.65 / 3.5188 / 0.5514*** / -2.3938* / 0.4139*** / -0.1418* / ns
USDA / Days to germination / 6.25 / -2.4421 / 0.3224*** / ns / 0.2113* / ns / ns
USDA / Geographic range size / 5.88 / -2.9549 / ns / -0.3792* / 0.3629*** / -0.0986* / 0.2917**
USDA / Germination temp range / 6.67 / -2.3008 / ns / -0.8225* / 0.1865** / ns / ns
USDA / Height / 9.2 / 2.9154 / 0.1298* / -7.4706** / 0.3911*** / ns / 0.0213**
USDA / Leaf size / 9.52 / 2.5687 / 0.2598*** / -0.8381* / 0.2727*** / ns / 0.1653**
USDA / Months flowering / 7.25 / -2.5134 / ns / -0.2016* / 0.3322*** / ns / 0.6389*
USDA / Ovule number / 5.41 / -2.3081 / 0.2560*** / neg / 0.1940*** / ns / ns
USDA / Pollen/Ovule ratio / 2.7 / 1.9675 / 0.4284*** / neg / 0.1940*** / ns / ns
USDA / Seed diameter / 6.35 / -2.5393 / 0.1659*** / ns / 0.3040*** / ns / ns

Part 2. Scaled branch length model:

Index / Identifier / %Outliers / Largest resid / b{x vs x@node} / b{x vs SD} / b{y vs y@node} / b{y vs SD} / b{x vs Resids}
GCW / # of flowers / 9.86 / 3.8637 / 0.1858*** / ns / 0.1498*** / pos / 0.2735***
GCW / Days to germination / 5.88 / 2.5385 / 0.2441*** / ns / 0.0917*** / neg / ns
GCW / Geographic range size / 4 / 5.1299 / ns / -0.0366*** / 0.1780*** / ns / 1.0366***
GCW / Germination temp range / 13.33 / -2.3838 / ns / -0.0543* / 0.1028*** / ns / ns
GCW / Height / 6.15 / -5.8534 / 0.1030*** / -0.5315*** / 0.1554*** / ns / ns
GCW / Leaf size / 6.6 / 4.9953 / 0.0691*** / -0.0513** / 0.1204*** / ns / ns
GCW / Months flowering / 6.32 / 4.161 / ns / -0.0162*** / 0.1460*** / ns / 2.8578***
GCW / Ovule number / 2.63 / -4.1614 / 0.0971*** / neg / 0.0784*** / ns / ns
GCW / Pollen/Ovule ratio / 5.26 / -3.7357 / 0.2617*** / -4.4871** / 0.0784*** / ns / ns
GCW / Seed diameter / 6.8 / 5.2574 / 0.0746*** / -0.0060* / 0.1358*** / ns / ns
USDA / # of flowers / 4.65 / 3.179 / 0.1553*** / ns / 0.1293*** / ns / ns
USDA / Days to germination / 6.25 / -2.4674 / 0.0823*** / ns / ns / ns / ns
USDA / Geographic range size / 8.82 / -2.6024 / ns / -0.0305*** / 0.1286*** / ns / 0.8410***
USDA / Germination temp range / 6.67 / -2.3898 / ns / -0.0543* / ns / ns / ns
USDA / Height / 4.6 / -3.6981 / 0.0752* / -0.4629*** / 0.1261*** / ns / 0.0420**
USDA / Leaf size / 11.11 / 2.7517 / 0.0933*** / -0.0407* / 0.0886*** / ns / ns
USDA / Months flowering / 8.7 / -2.8562 / ns / -0.0209*** / 0.1138*** / ns / 2.3081***
USDA / Ovule number / 2.7 / -3.0036 / 0.0997*** / neg / 0.0468** / ns / ns
USDA / Pollen/Ovule ratio / 2.7 / -2.8043 / 0.2762*** / -3.9131* / 0.0468** / ns / ns
USDA / Seed diameter / 7.94 / 3.1482 / pos / -0.0040* / 0.1008*** / ns / ns

References

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Desfeux C, Maurice S, Henry J-P, Lejeune B,Gouyon P-H (1996) Evolution of reproductive systems in the genus Silene. Proc Roy Soc London Ser B 263:409-414.

Egens F, Popp M, Nepokroeff M, Wagner WL, Oxelman B (2007) The origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae). Am J Bot 94:210-218.

Ironside J, Filatov D(2005) Extreme population structure and high interspecific divergence of the Silene Y chromosome. Genetics 171:705-713.

Oxelman B, Lidén M(1995) Generic boundaries in the tribe Sileneae (Caryopyllaceae) as inferred from nuclear rDNA sequences. Taxon 44:525-542.

Oxelman B, Lidén M, Berglund D (1997) Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Pl Syst Evol 206:393-410.

Oxelman B, Lidén M, Rabeler RK, Popp M (2000) A revised generic classification of the tribe Sileneae (Caryophyllaceae). Nord J Bot 20:743-748.

Popp M, Oxelman B(2004) Evolution of a RNA polymerase gene family in Silene (Caryophyllaceae) – Incomplete concerted evolution and topological congruence among paralogues. Syst Biol 53:914-932.

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Popp M, Erixon P, Eggens F, Oxelman B (2005) Origin and evolution of a circumpolar polyploidy species complex in Silene (Caryophyllaceae) inferred from low copy nuclear RNA polymerase introns, rDNA, and chloroplast DNA. Syst Bot 30:302-313.