species selection maintains...
TRANSCRIPT
reduction in chemical potential by forming thecrystalline phase. In the second scenario, weassume that oxygen has first adsorbed to theLS interface, driven by the reduction in inter-face energy (24, 28), having diffused along theinterface from the triple junction. Once oxygenadsorbs, a critical-size nucleus (in the form ofa step) forms at the triple junction and sweepsacross the LS (0001) interface, forming a new(0006) layer of a-Al2O3 in its wake. Oxygen thenagain adsorbs to the new LS interface, suppliedfrom the dissolving outer rim of the nanowire.The nucleation rate of steps is relatively low un-der the present experimental conditions, leadingto single steps that sweep across the interface (nodefects resulting from the intersection of stepsor multiple nucleation events were detected).Both of these reactions would be very fast; theformation of a new (0006) layer after oxygendiffusion has started requires only ~0.16 s. Ourexperimental observations cannot distinguishbetween these two scenarios.
Our in situ HRTEM observations have re-vealed an oscillatory growth process that is notobvious from ex situ observations of grown nano-wires. These observations provide an explanationfor the (0001) growth mechanism and why it isnot continuous. What distinguishes this reactionfrom most VLS processes is that the catalystdroplet is not directly involved in supplying allthe necessary components for growth. Instead,oxygen for the new (0006) layer is supplied bytransient sacrificial dissolution of the top rim ofthe nanowires via facet formation. The compo-nents of interface tensions at the triple junctionalso promote formation of the facets and probablydrive the nucleation of steps of solid (0006),which sweep across the LS (0001) interface, re-sulting in growth of a new (0006) layer. Forma-tion of the (0006) layer is relatively fast becausethe Al atoms on the liquid side of the LS surface
are already in positions similar to those in the un-derlying bulk sapphire. The oxygen collectedon the LV surface is used to eradicate the facetsat the outer, top rim of the nanowires once acomplete (0006) layer is formed. It is this processthat is the rate-limiting step.
References and Notes1. E. I. Givargizov, J. Cryst. Growth 31, 20 (1975).2. F. M. Ross, J. Tersoff, M. C. Reuter, Phys. Rev. Lett. 95,
146104 (2005).3. Y. Hao, G. Meng, Z. L. Wang, C. Ye, L. Zhang, Nano Lett.
6, 1650 (2006).4. L. E. Jensen et al., Nano Lett. 4, 1961 (2004).5. S. Kodambaka, J. Tersoff, M. C. Reuter, F. M. Ross,
Science 316, 729 (2007).6. V. Valcárcel, A. Souto, F. Guitián, Adv. Mater.
10, 138 (1998).7. W. F. Li et al., Phys. Stat. Sol. A 203, 294 (2006).8. T. Kuykendall et al., Nat. Mater. 3, 524 (2004).9. E. A. Stach et al., Nano Lett. 3, 867 (2003).10. Y. Wu, P. Yang, J. Am. Chem. Soc. 123, 3165
(2001).11. S. Hofmann et al., Nat. Mater. 7, 372 (2008).12. G. Lee et al., Angew. Chem. 48, 7366 (2009).13. B. Tian, P. Xie, T. J. Kempa, D. C. Bell, C. M. Lieber,
Nat. Nanotechnol. 4, 824 (2009).14. S. H. Oh, Y. Kauffmann, C. Scheu, W. D. Kaplan, M. Rühle,
Science 310, 661 (2005); published online6 October 2005 (10.1126/science.1118611).
15. See supporting material on Science Online.16. V. Laurent, D. Chatain, C. Chatillon, N. Eustathopoulos,
Acta Metall. 36, 1797 (1988).17. D. Chatain, W. C. Carter, Nat. Mater. 3, 843
(2004).18. E. J. Siem, W. C. Carter, D. Chatain, Philos. Mag. 84,
991 (2004).19. H. Wang, G. S. Fischman, J. Appl. Phys. 76, 1557
(1994).20. H. Saka, K. Sasaki, S. T. Tsukimoto, S. Arai, J. Mater. Res.
20, 1629 (2005).21. D. J. Siegel, L. G. Hector Jr., J. B. Adams, Phys. Rev. B 65,
085415 (2002).22. W. D. Kaplan, Y. Kauffmann, Annu. Rev. Mater. Res. 36,
1 (2006).23. A. Hashibon, J. Adler, M. W. Finnis, W. D. Kaplan,
Interface Sci. 9, 175 (2001).24. G. Levi, W. D. Kaplan, Acta Mater. 50, 75 (2002).
25. The reaction volume was calculated by assuming a ringof triangular cross section. Calculation of the volumeyields ~1.7 × 10−20 cm3. Given that the number ofoxygen atoms per unit volume of a-Al2O3 is 8.63 × 1022
atoms cm−3, the number of oxygen atoms containedwithin the reaction volume is ~1.46 × 103 atoms. Thenumber of oxygen atoms needed to deposit a monolayerof close-packed oxygen at the LS (0001) interface wascalculated by assuming a square and a circular shapeof the interfaces. The area density of a hexagonal close-packed oxygen layer is 1.6 × 1015 atoms cm−2. Theamount of oxygen needed to deposit a monolayer ofclose-packed oxygen is ~1.6 × 103 and ~1.2 × 103
atoms for the square and the circular interfaces,respectively.
26. S. M. Roper et al., J. Appl. Phys. 102, 034304(2007).
27. K. W. Schwarz, J. Tersoff, Phys. Rev. Lett. 102,206101 (2009).
28. G. Levi, W. D. Kaplan, J. Am. Ceram. Soc. 85, 1601(2002).
29. The in situ TEM experiments were carried out using theStuttgart high-voltage microscope (JEM-ARM 1250) at theMax-Planck-Institut für Metallforschung. We thankF. Phillipp, R. Höschen, and U. Salzberger for technicalsupport, and D. Chatain and the participants of the 3Phase, Interface, Component Systems (PICS3) meeting forstimulating discussions. Supported by the GermanScience Foundation via the Graduiertenkolleg InnereGrenzflächen (GRK 285/3), the German-Israel Fund(grant I-779-42.10/2003), the Nano and Steel FusionResearch Program funded by the POSCO (S.H.O.) BasicScience Research Institute grant 2.0006028 (S.H.O.), theBasic Science Research Program through the NationalResearch Foundation funded by the Ministry ofEducation, Science and Technology (grant 2010-0005834) (S.H.O.), the excellence cluster NanosystemsInitiative Munich (C.S. and S.H.O.), and the MaterialsSciences and Engineering Division of the U.S.Department of Energy (M.F.C. and W.L.).
Supporting Online Materialwww.sciencemag.org/cgi/content/full/330/6003/489/DC1SOM TextFigs. S1 to S5ReferencesMovies S1 to S3
7 April 2010; accepted 16 September 201010.1126/science.1190596
Species Selection MaintainsSelf-IncompatibilityEmma E. Goldberg,1 Joshua R. Kohn,2 Russell Lande,3 Kelly A. Robertson,1Stephen A. Smith,4 Boris Igic 1*Identifying traits that affect rates of speciation and extinction and, hence, explain differences inspecies diversity among clades is a major goal of evolutionary biology. Detecting such traits isespecially difficult when they undergo frequent transitions between states. Self-incompatibility,the ability of hermaphrodites to enforce outcrossing, is frequently lost in flowering plants, enablingself-fertilization. We show, however, that in the nightshade plant family (Solanaceae), specieswith functional self-incompatibility diversify at a significantly higher rate than those without it.The apparent short-term advantages of potentially self-fertilizing individuals are therefore offsetby strong species selection, which favors obligate outcrossing.
Theastonishing diversity of flowering plantshas led to numerous hypotheses linkingthe propensity for diversification to mor-
phological, life history, and physiological char-
acteristics (1–4). Although it is clear that nosingle character can entirely explain the variationin plant diversity (2, 4), many traits potentiallyassociated with an increase in species richness
may have been overlooked because of method-ological shortcomings (5, 6).
The overwhelming majority of floweringplants function as both males and females, butdespite the potential for self-fertilization in her-maphrodites, most of these plants predominantlyor exclusively mate with other individuals (out-cross) (7, 8). Outcrossing is often enforced byself-incompatibility (SI): the ability of individualplants to recognize and reject their own pollen.Each SI system characterized to date relies on
1Department of Biological Sciences, University of Illinois atChicago, 840 West Taylor Street, M/C 067, Chicago, IL 60607,USA. 2Division of Biological Sciences, University of California atSan Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.3Division of Biology, Imperial College London, Silwood ParkCampus, Ascot, Berkshire, SL5 7PY, UK. 4National EvolutionarySynthesis Center 2024 West Main Street, Durham, NC 27705,USA.
*To whom correspondence should be addressed. E-mail:[email protected]
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complex genetic mechanisms (9). Their value isprimarily attributed to the avoidance of inbreed-ing depression (10), but the short-term disad-vantages of SI, which limits an individual plant'sability to reproduce if outcross pollen is not avail-able, is expected to result in frequent transitions toself-compatibility (SC) (8). Mate limitation andthe automatic advantage of selfing (10, 11) eachfavor the spread of mutants that break down SI.Indeed, angiosperm families in which SI is foundalso contain significant proportions of SC species(12). The two states are commonly interspersedwithin clades, implying frequent evolutionary tran-sitions. Independent data, both genetic and phylo-genetic (12, 13), suggest that the transition fromSI to SC is one of the most common evolutionaryshifts in flowering plants (14). Studies of the ge-netic basis of SI indicate that novel SI systemsoriginate very rarely (9, 15). The combined evi-dence implies that SI is frequently lost by speciesand that an identical form of SI is only rarely, ifever, regained (12).
In Solanaceae species with SI, strong negativefrequency-dependent selection maintains dozensof alleles at the locus controlling self-recognition(S-locus), where it has preserved ancestral poly-morphism over 40 million years (13, 16, 17). Afterpollination, if the haploid pollen allele matcheseither allele of the diploid female reproductiveorgan, fertilization is prevented. Individuals withcommon alleles therefore have fewer potentialmates, and those with rare alleles more, so thatalleles ordinarily lost by drift are instead main-tained over long time scales (16). The outcome isa pattern of ancestral polymorphism shared notonly across species boundaries but among distant-ly related genera. Randomly sampled alleles fromdifferent SI species of Solanaceae are often moreclosely related than those within species (16, 17).This provides strong evidence that a polymorphicand therefore functional S-locus was present inthe common ancestor and passed on to descend-ent SI species in the family (17).
Although the SI mechanism has been fre-quently lost and not regained within Solanaceae(13), it occurs at an intermediate frequency. Theproportion of SI species is declining with eachtransition to SC, so SI may be destined for ex-tinction. But the SI mechanism of Solanaceae is~90 million years old, nearly as old as eudicots(15), and SI may instead persist if the diversifi-cation rate of SI lineages exceeds that of SClineages by at least the SI-to-SC transition rate(17). In this scenario, the loss of SI may be count-ered by a greater difference between speciationand extinction rates associated with the presenceof SI relative to SC. A strong association betweenSI and increased diversification would provideunusually compelling evidence for a causal re-lationship, because frequent character changes toSC uncouple the evolution of the focal characterfrom others and reduce the chance that an inferredconnection is spurious (18).
We examined the effect of SI on diversifi-cation in Solanaceae. The nightshades contain
many agriculturally important species (such astomato, potato, chile, and tobacco), so phyloge-netic and breeding system data are extensive.Among the estimated 2700 species in the fam-ily, approximately 57% are SC, 41% are SI, andless than 2% have separate male and femaleplants (19).
We constructed a phylogeny through an ini-tial alignment matrix of 998 species and eightgenes, and we assigned character states (SI or SC)for 616 species (19). Subsequent analyses con-centrated on a monophyletic clade termed “x =12” for its uniform base chromosome number,containing approximately 2300 species, includingthe subfamilies Solanoideae and Nicotianoideae(20) [we also conducted analyses on the wholefamily (19)]. Both character states and phylo-genetic data are better sampled in this clade thanin the rest of the family, yielding 356 speciespresent in the tree andwith knownmating systems
(Fig. 1). This sample did not statistically differ inSI frequency from the total available data set of616 species (P > 0.3), and our analyses accountedfor sampling incompleteness (21).
Irreversible loss of SI in Solanaceae willcause the frequency of SI to decline to zero if rI ≤rC + qIC, where rI and rC are net diversificationrates (the difference between speciation andextinction rates) for SI and SC lineages, respec-tively, and qIC is the per-lineage rate of transitionfrom SI to SC. Alternatively, the loss of SI maybe offset by more rapid diversification of SIlineages when rI > rC + qIC. In this latter case,the equilibrium proportion of SI species, pSI, ispositive and equal to 1 − qIC/(rI − rC) (17).
We analyzed character evolution and diversi-fication on the maximum likelihood tree (Fig. 1)and also on 100 bootstrap trees to assess robust-ness to phylogenetic uncertainty (19). Rates ofspeciation (lI and lC; the subscripts denote SI
Fig. 1. Maximum likelihood tree of phylogenetic relationships among 356 species of Solanaceae.Higher ranks are indicated around the perimeter of the tree. Purple and turquoise tip colors denote SIand SC extant species, respectively. The root age is 36 million years. Inset panels display posteriorprobability distributions and 95% credibility intervals of reconstructed rates of character evolution (thetime unit is millions of years). (A) BiSSE estimates of transition, speciation, and extinction parameters(qIC << mI < lI << lC < mC). (B) Net diversification rate—the difference between speciation andextinction rates—associated with each state. (C) Schematic summary of estimated rate parameters. Formethods, species names, character states, and further results, see (19).
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and SC states, respectively), extinction (mI and mC),and loss of SI (qIC) were estimated with Markovchain Monte Carlo analyses under the binary-state speciation and extinction (BiSSE) model(19, 22), which explicitly incorporates differingspeciation and extinction rates associated withthe two states of a binary character. Because SIhas apparently not been regained in this clade(13), we fixed the rate of transitions from SC toSI, qCI, to be zero in our main analyses [althoughwe also considered bidirectional transitions (19)].
We find a higher rate of speciation for SCthan SI lineages, but this apparent advantage iserased by an SC extinction rate that exceeds thatof SI lineages and even the SC speciation rate[mI < lI < lC < mC, with posterior probability 0.99(Fig. 1A)]. SI lineages consequently show asubstantially higher rate of net diversificationthan do SC lineages [rI > rC, with posterior prob-ability 1.0 (Fig. 1B)]. Furthermore, this diversi-fication difference is large enough to counter theirreversible loss of SI [rI > rC + qIC, with posteriorprobability 1.0 (Fig. 2A)]. The equilibrium fre-quency of SI is therefore positive [pSI > 0.25,with posterior probability 0.99 (Fig. 2B)], demon-strating that the macroevolutionary advantage ofSI is enough for it to persist indefinitely, despiteits loss through transitions to SC. These resultsare robust to phylogenetic uncertainty and againstthe assumption that SI is not regained (19).
The higher rate of diversification associatedwith SI means that selection is acting amongspecies, which can produce trends that are notpredictable from studies of selection among in-dividuals within species. Natural selection can actonmany levels of evolutionary hierarchy (includ-ing genes, individuals, populations, and species),with the potential for cascading effects of se-lection from any level to those above and below(18, 23–26). Species, as units, may vary in her-itable traits associated with different rates of mul-tiplication. A higher form of selection may thusbe manifested as a trait-dependent net diversifica-tion rate. There is wide acceptance of the existenceof higher-order selection (18, 25, 26) but rela-tively sparse data on its importance (25, 26).
Our results point to a strong role for speciesselection in determining the evolutionary dynam-ics and distribution of mating systems amongspecies. Both theoretical and empirical studies onthe shape of outcrossing rate distributions haveoverlooked the possibility that species selectionmay produce an arbitrary proportion of selfing,mixed-mating, and outcrossing species (8, 27).
It remains unknown why strict avoidance ofself-fertilization yields such strong long-term evo-lutionary advantages. Outcrossing plants, whichgenerallymaintain high effective population sizesand recombination rates, may have increased poly-morphism, lower linkage disequilibrium, moreefficient response to purifying selection, moreextensive geographic distribution of genetic di-versity, and lower rates of extinction (28–31).Various mechanisms other than SI, such as thephysical and temporal separation of sexes withinhermaphrodite flowers, or single-sex individuals,can effect outcrossing in the absence of SI (3).Moreover, although SI may be a relatively ef-ficient mechanism for obligate outcrossing (32),delayed selfing ability and plastic sex expressionafforded by other breeding systems may addi-tionally provide reproductive assurance (7).
At short time scales, the expression of inbreed-ing depression can oppose the spread of muta-tions that break down SI, but many ecologicalfactors favor their rapid and frequent fixation (7).This is problematic because natural selectioncannot maintain features slated for future use(18). We find that SC is associated with a macro-evolutionary disadvantage from high extinctionrates, despite its high speciation rates relative toSI. Both theoretical and empirical evidence linkinbreeding with an increased probability of ex-tinction (27,29,31). Self-fertilization and increasedinbreeding are also closely tied to higher among-population differentiation (30), which may in turnlead to escalating speciation rates.
We conclude that species selection opposesthe short-term advantages provided by the abilityof flowering plants to self-fertilize, and that vol-atile dynamics underlie the scattered phyloge-netic distribution of SC plant species. A strong
relationship between traits, includingSI, and specia-tion and extinction may result in the unevenpatterns of diversification rates observed amongclades of flowering plants (2, 4), especially whencoupled with time heterogeneity and historicalcontingency. These results provide evidence thatthe evolutionary origin and maintenance of SImay play an important role in shaping the immenseextant diversity of flowering plants (18, 33).
References and Notes1. C. Darwin, F. Darwin, A. C. Seward, More Letters of
Charles Darwin: A Record of His Work in a Series ofHitherto Unpublished Letters ( J. Murray, London, 1903).
2. S. Magallón, M. J. Sanderson, Evolution 55, 1762 (2001).3. S. C. H. Barrett, Philos. Trans. R. Soc. London Ser. B 358,
991 (2003).4. T. J. Davies et al., Proc. Natl. Acad. Sci. U.S.A. 101,
1904 (2004).5. W. P. Maddison, Evolution 60, 1743 (2006).6. E. E. Goldberg, B. Igić, Evolution 62, 2727 (2008).7. C. Goodwillie, S. Kalisz, C. G. Eckert, Annu. Rev. Ecol.
Evol. Syst. 36, 47 (2005).8. B. Igić, J. R. Kohn, Evolution 60, 1098 (2006).9. V. Franklin-Tong, Self-Incompatibility in Flowering
Plants: Evolution, Diversity, and Mechanisms(Springer, Berlin, 2008).
10. E. Porcher, R. Lande, Evolution 59, 46 (2005).11. J. W. Busch, D. J. Schoen, Trends Plant Sci. 13, 128 (2008).12. B. Igić, R. Lande, J. R. Kohn, Int. J. Plant Sci. 169, 93
(2008).13. B. Igić, L. Bohs, J. R. Kohn, Proc. Natl. Acad. Sci. U.S.A.
103, 1359 (2006).14. G. L. Stebbins, Flowering Plants (Belknap Press,
Cambridge, MA, 1974).15. J. E. Steinbachs, K. E. Holsinger, Mol. Biol. Evol. 19,
825 (2002).16. T. R. Ioerger, A. G. Clark, T. H. Kao, Proc. Natl. Acad. Sci.
U.S.A. 87, 9732 (1990).17. B. Igić, L. Bohs, J. R. Kohn, New Phytol. 161, 97 (2004).18. G. C. Williams, Natural Selection: Domains, Levels,
and Challenges (Oxford Univ. Press, New York, 1992).19. Materials, methods, and further results are available as
supporting material on Science Online.20. R. G. Olmstead, L. Bohs, Acta Hortic. 745, 255 (2007).21. R. G. FitzJohn, W. P. Maddison, S. P. Otto, Syst. Biol. 58,
595 (2009).22. W. P. Maddison, P. E. Midford, S. P. Otto, Syst. Biol. 56,
701 (2007).23. R. C. Lewontin, Annu. Rev. Ecol. Syst. 1, 1 (1970).24. S. J. Gould, Science 216, 380 (1982).25. D. Jablonski, Annu. Rev. Ecol. Evol. Syst. 39, 501 (2008).26. D. L. Rabosky, A. R. McCune, Trends Ecol. Evol. 25, 68 (2010).27. D. J. Schoen, J. W. Busch, Int. J. Plant Sci. 169,
119 (2008).28. G. L. Stebbins, Am. Nat. 91, 337 (1957).29. D. J. Schoen, A. H. Brown, Proc. Natl. Acad. Sci. U.S.A.
88, 4494 (1991).30. J. L. Hamrick, M. J. W. Godt, Philos. Trans. R. Soc. London
Ser. B 351, 1291 (1996).31. S. Glémin, E. Bazin, D. Charlesworth, Proc. R. Soc.
London Ser. B 273, 3011 (2006).32. K. Karoly, Am. Nat. 144, 677 (1994).33. M. S. Zavada, T. N. Taylor, Am. Nat. 128, 538 (1986).34. We thank R. FitzJohn, A. Mooers, R. Olmstead, T. Paape,
L. Popović, D. L. Shade, and R. Ree for help anddiscussions. Data are deposited in the Dryad databasewith accession no. 1888. Funded by NSF grant DEB-0919089 to B.I.
Supporting Online Materialwww.sciencemag.org/cgi/content/full/330/6003/493/DC1Materials and MethodsSOM TextFigs. S1 and S2Tables S1 to S4References
1 July 2010; accepted 25 August 201010.1126/science.1194513
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Fig. 2. Further analyses of the posterior rate distributions in Fig. 1. (A) The diversification rate of SI issufficiently higher than that of SC for it to persist deterministically (shown by positive values here) despitefrequent and irreversible loss. (B) The equilibrium frequency of SI is consequently always positive.
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www.sciencemag.org/cgi/content/full/330/6003/493/DC1
Supporting Online Material for
Species Selection Maintains Self-Incompatibility E. E. Goldberg, J. R. Kohn, R. Lande, K. A. Robertson, S. A. Smith, B. Igic∗
*To whom correspondence should be addressed. E-mail: [email protected]
Published 22 October 2010, Science 330, 493 (2010)
DOI: 10.1126/science.1194513
This PDF file includes:
Materials and Methods SOM Text Figs. S1 and S2 Tables S1 to S4 References
Materials and methods
Phylogeny construction
Alignment and tree construction pipeline
The procedure for reconstructing phylogenetic relationships among a subset of Solanaceae
closely followed the one developed and reported in detail by Smith and colleagues (S1, S2).
We implemented this pipeline in Python (v2.5) with the BioPython (v1.48) module (S3) and
using the BioSQL (v1.0.1) database schema (S4). Here, we present the most important aspects
of this procedure.
We found eight loci within Solanaceae with more than 200 taxa represented in GenBank.
Six of these genes are encoded in the chloroplast genome: atpB (ca. 300 entries), matK (520),
ndhF (500), rbcL (220), trnK (210), trnL-trnF (700), and two in the nuclear genome: GBSSI
(790), ITS (910). We removed taxa with identical (duplicated) names and produced a first-
pass multiple alignment using MAFFT (S5), which resulted in a 1084-taxon, 16,405bp (eight-
gene) matrix. Gene-partitioned phylogenetic reconstructions were performed using RAxML
(v7.0.4) (S6). Subsequent analyses were performed on the maximum likelihood (ML) tree found
in a heuristic search and on 100 bootstrap replicates. We manually curated the tree obtained after
the initial pass. The resulting matrix contained 995 ingroup taxa, plus five outgroup species of
Convolvulaceae (Fig. S1).
The resulting trees were then pruned to include only those species contained within the
“x=12” clade, the best-sampled monophyletic group in the family. Cultivars and known hybrid
varieties were removed from the analyses, as were those species for which the self-incompatibility
status is unknown. The final dataset contained 356 species (Fig. S2).
In addition, we present below abbreviated results for the dataset consisting of all 397 species
in the family on the tree and with known character states.
1
Relaxed molecular clock implementation
In order to ultrametricize our phylogenetic trees and obtain node and tip dates proportional to
true time (rather than substitutions per site), we used the semiparametric method developed
by Sanderson (S7). This method accommodates rate variation among lineages by combining a
parametric model with different nucleotide substitution rates on every branch with a nonpara-
metric roughness penalty. The λ parameter for penalized likelihood calculations determines the
contribution of this penalty. It was estimated using a cross-validation procedure implemented
in r8s (v1.71) (S7). We applied 13 values of λ, spaced evenly on a logarithmic scale from 1 to
1000, after randomly pruning the ML tree to 71 taxa (for computational feasibility) 10 times. In
each pruned set, the best estimate was log10 λ = 2.25, which we used for penalized likelihood
rate-smoothing on the ML and bootstrap trees.
Accurate absolute divergence dates are not crucial for our analyses. Nevertheless, we ob-
tained approximate values in order to make the units of the results of our character evolution
analyses meaningful for comparative study. We constrained the age of the focal crown group
(“x=12” clade) to 36 Ma based on the node date obtained by Paape and colleagues (S8). This
dating procedure relies on the use of two key constraints derived from dating and identification
of Solanum- and Physalis-like seeds (S9). Those two dates were used to anchor a normally
distributed age prior (µ = 10.0 Ma, σ = 4.0 Ma; 95% CI = [3.4, 16.6]), along with the date
for stem group age of Solanaceae (divergence from Convolvulaceae; µ = 52 Ma, σ = 5.2 Ma;
95% CI = [43, 60]). The divergence dates we obtained are comparable to others recovered with
different strategies [e.g., (S10, S11)].
Character evolution analyses
Testing for a correlation between character state and net diversification rate has commonly
relied on associations of clade age and number of species, either through the use of sister clade
2
or regression analyses (S12–S14). These methods consider only clades in which most tips
are in the same state and assume that ancestors within the clade had that state. Because the
transition rate from SI to SC is high relative to the family’s age (S15), few non-polymorphic
clades are available, and such tests will have low statistical power (S13, S16). We therefore
employ the recently-developed BiSSE method for estimating from a phylogeny speciation and
extinction rates that depend on character states (S17). We include the correction for incomplete
sampling (S18): the probability of being sampled in the tree is 0.162 for SI species and 0.150
for SC species. By explicitly modeling speciation and extinction associated with the two states
of a binary character, BiSSE allows us to quantify the effects of state-dependent diversification
and state transitions.
Character state encoding
For macroevolutionary models of binary character evolution to be applied to breeding system
evolution, each species must be classified as either SI or SC, and this can be difficult (S19). We
use the same general principles as described elsewhere (S20). The best available data, however
sparse, indicate that the breakdown of SI is so common that no SI species studied in any detail
fails to reveal segregating SC mutants, SC populations, or sister species. Our intention is to
measure the average rate at which an entire lineage, ancestrally SI (see main text and (S20)),
transitions to SC. Therefore, we encode as SI all “polymorphic” taxa that have not entirely
transitioned to SI. This encoding should yield a conservative estimate of the advantage of SI
lineages. The breeding system data were available for 356 species represented on the phylogeny
of “x=12” Solanaceae. Of those, 196 were described in the literature and encoded by us as SC.
Of the remaining species encoded as SI, 116 were unambiguously described as SI, 17 as both
SI and SC, 25 as dioecious, and one each as SI/SC/dioecious and SI/dioecious.
3
Bayesian analysis
We performed a Bayesian analysis of BiSSE on the Solanaceae ML phylogeny. Compared
with maximum likelihood parameter estimation, this approach better handles the potentially-
rough likelihood surfaces and provides a natural means of testing how meaningful parameter
differences are. Although a Bayesian analysis across a posterior set of trees would be more
philosophically consistent, obtaining such a set was not computational feasible due to the large
number of species and sites in the phylogenetic analysis.
We obtained 1,000,000 post-burn-in samples of slice-sampling Markov chain Monte Carlo
(MCMC) on the maximum likelihood tree and 10,000 samples on each of the 100 bootstrap
trees. Priors on each parameter were exponentially distributed and broad, with rate 0.3. We
used the conditional likelihood root state assumption (S18): because the rate of gain of SI was
fixed to zero, this effectively fixes as SI the root and hence the other internal nodes leading to
SI tips. Analyses were conducted with the R package diversitree (S21, S22). Once posterior
distributions of the five model parameters were obtained (Fig. 1A), further analyses (Fig. 1B,
Fig. 2) simply involved computing additional quantities from each MCMC sample. Reported
posterior probabilities are the proportion of MCMC samples for which a statement was true.
Supporting text
Additional character evolution results
Results from maximum likelihood tree
Mean values, standard deviations, and the standard errors of the mean (determined from time
series analysis as implemented in the R package coda (S23)) are reported in Table S1. The
results for λC − λI and µC − µI provide further quantification of our finding that SC lineages
have a higher rate of speciation and an even higher rate of extinction than do self-incompatible
lineages. The results for rI , rC and their difference show not only a higher rate of net diversifi-
4
cation for SI lineages, but in fact negative net diversification for SC lineages. The equilibrium
frequency of SI is only slightly less than the observed frequency and is certainly positive, show-
ing that SI is not bound for deterministic extinction due to its loss through transitions to SC.
Correlations between the five directly estimated parameters are reported in Table S2. The
speciation and extinction rates for each state are very strongly correlated, consistent with the
much tighter estimates of net diversification rates than of speciation and extinction rates sep-
arately (Fig. 1AB, Table S1). The moderate correlations between the transition rate and the
rest of the rates reflects the balance between state change and diversification in explaining the
observed state frequencies.
Results from bootstrap trees
The results reported above include uncertainty from the parameter estimation process but not
uncertainty in the tree topology or branch lengths. Variation in individual parameter estimates
across the bootstrap trees is comparable to uncertainties in estimation on the ML tree (Table S3).
For net diversification rates, however, variation across bootstrap trees is much less (Table S3),
likely because diversification rate is determined largely by the frequency of tip states and the
root age, both of which are constant across the bootstrap set.
Our main results are robust to phylogenetic uncertainty. On 92 out of the 100 bootstrap
trees, µI < λI < λC < µC is true with a posterior probability of at least 0.90. On all 100
bootstrap trees, the following statements are true with posterior probability 0.90: rI > 0.35,
rC < −0.01, rI − rC − qIC > 0.12, pSI > 0.27.
Results with regain of SI allowed
Although we feel we are justified in fixing the rate of SI gain, qCI , to zero in our analyses, we
understand that results without that restriction may be of interest. We therefore also ran the
BiSSE MCMC analysis on the ML tree without the general qCI = 0 constraint, but incorporat-
5
ing information on specific lineages in which reversals were shown not to occur. For the seven-
teen species on our tree in which trans-specific polymorphism has been documented (Solanum
chilense, S. peruvianum, S. carolinense, S. chacoense, Lycium californicum, L. andersonii,
L. parishii, L. ferocissimum, L. cestroides, Physalis cinerascens, P. crassifolia, P. longifolia,
Witheringia solanacea, Nicotiana alata, N. glauca, Iochroma australe, Eriolarynx lorentzii),
every node that is an ancestor of that species was fixed to the SI state by setting its conditional
likelihood of SC to zero in all tree likelihood calculations.
The estimate of qCI is positive but small, and the estimates for other parameters (Table S4)
are similar to those with qCI = 0 (Table S1). Our main conclusions all hold under this anal-
ysis. The ordering of the speciation and extinction rates is the same (the posterior probability
of µI < λI < λC < µC is 0.99). Diversification is greater for SI lineages (rI > rC with pos-
terior probability 1.0). The equilibrium frequency of SI is positive (pSI > 0.30 with posterior
probability 0.90; the pSI computation is somewhat more complicated than the expression given
in the main text when reversals are allowed (S17)). Compared with the results in which qCI is
fixed to zero, the diversification advantage of SI is smaller when regain of SI is allowed but the
equilibrium frequency of SI is slightly larger because the rate of loss of SI is smaller.
Results from whole-family analysis
On the full Solanaceae tree, pruned only to contain species with known SI status, overall sam-
pling intensity is somewhat less than that of the “x=12” clade used in the main analyses: the
sampling proportions are 0.123 for SI and 0.168 for SC. Inclusion in the tree is much less
uniform outside of the “x=12” clade (e.g., Petunia is very well represented but the other deep
genera are not), so we did not use the whole-family in the main analyses.
Nevertheless, it is worthwhile to ask if our results for the clade spanning Solanum and
Nicotiana also hold for what is known of the entire family. We find that the ordering of the
6
speciation and extinction rates is not as clear (on the ML tree, the posterior probability of
µI < λI < λC < µC is only 0.61), but the transition rate qIC is always much less than these
rates, and all of our other conclusions hold. Specifically, with posterior probabilities of at least
0.99, rC < −0.09, rI > 0.26, rI > rC + qIC , and pSI > 0.32.
7
Dinetus truncatusConvolvulus arvensis
Ipomoea purpureaIpomoea batatas
Evolvulus glomeratus
Schizanthus grahamiiSchizanthus hookeri
Schizanthus candidusSchizanthus lacteus
Schizanthus integrifolius
Schizanthus alpestris
Schizanthus laetusSchizanthus porrigens
Schizanthus litoralis
Schizanthus tricolor
Schizanthus parvulus
Schizanthus pinnatus
Tsoala tubiflora
Metternichia principisCoeloneurum ferrugineumEspadaea amoenaGoetzea elegans
Goetzea ekmanii
Henoonia myrtifolia
Duckeodendron cestroides
Vestia lycioides
Vestia foetida
Sessea corymbifloraCestrum megalophyllum
Cestrum strigilatumCestrum acutifolium
Cestrum virgaurea
Cestrum dasyanthum
Cestrum guatemalense
Cestrum pacayense
Cestrum regelii
Cestrum aurantiacum var macrocalyx
Cestrum aurantiacum
Cestrum roseum
Cestrum oblongifolium
Cestrum thyrsoideum
Cestrum miradorense
Cestrum fasciculatum
Cestrum elegans
Cestrum endlicheri
Cestrum laxum
Cestrum fulvescens
Cestrum poasanum
Cestrum sp Montero 213
Cestrum fragileCestrum chiriquianum
Cestrum irazuense
Cestrum luteovirescens
Cestrum nocturnum
Cestrum milciomejiaeCestrum sphaerocarpum
Cestrum violaceumCestrum parqui
Cestrum glanduliferum
Cestrum tuerckheimiiCestrum tomentosum
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Pantacantha ameghinoi
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Physalis coztomatl
Physalis sordida
Physalis glutinosa
Physalis hederifolia
Physalis longifolia
Physalis caudella
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Physalis campanulata
Physalis greenmanii
Physalis hederifolia var puberula
Physalis angustifolia
Physalis walteri
Physalis cinerascens
Physalis curassavica
Physalis mendocina
Physalis fuscomaculata
Physalis aequata
Physalis minimaculata
Margaranthus solanaceus
Physalis lanceifoliaPhysalis acutifoliaPhysalis crassifoliaChamaesaracha coronopus
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Physalis carpenteriLeucophysalis grandifloraLeucophysalis nana
Jaltomata grandiflora
Jaltomata procumbens
Jaltomata auriculata
Jaltomata sinuosa
Salpichroa tristis
Salpichroa origanifolia
Nectouxia formosa
Lycianthes shanesii
Lycianthes biflora
Lycianthes denticulata
Lycianthes lysimachioides
Lycianthes synanthera
Lycianthes sanctaeclarae
Lycianthes pringlei
Lycianthes beckneriana
Lycianthes tricolor
Lycianthes multiflora
Lycianthes furcatistellata
Lycianthes pseudolycioides
Lycianthes glandulosaLycianthes nitida
Lycianthes jalicensis
Lycianthes surotatensisLycianthes lenta
Lycianthes geminiflora
Lycianthes heteroclita
Lycianthes stephanocalyx
Capsicum lanceolatum
Capsicum ciliatum
Capsicum rhom
boideum
Capsicum gem
inifolium
Capsicum lycianthoides
Capsicum parvifolium
Capsicum cam
pylopodium
Capsicum flexuosum
Capsicum
schottianum
Capsicum
hunzikerianum
Capsicum
recurvatum
Capsicum
villosum
Capsicum
pereirae
Capsicum
annuum
Capsicum
tovarii
Capsicum
pubescens
Capsicum
galapagoense
Capsicum
baccatum
Capsicum
coccineum
Capsicum
chacoense
Capsicum
minutiflorum
Capsicum
ceratocalyx
Capsicum
chinense
Capsicum
frutescens
Capsicum
annuum var annuum
Capsicum
cardenasii
Capsicum
eximium
Lycianthes pilifera
Lycianthes lycioides
Lycianthes rantonnei
Lycianthes saltensis
Lycianthes fasciculata
Lycianthes jelskii
Lycianthes acapulcensis
Lycianthes dejecta
Lycianthes peduncularis
Lycianthes rzedowskii
Lycianthes moziniana var margaretiana
Lycianthes ciliolata
Lycianthes acutifolia
Lycianthes inaequilatera
Lycianthes radiata
Lycianthes amatitlanensis
Lycianthes asarifolia
Jaltomata hunzikeri
Jaltomata dentata
Solanum
thelopodium
Sola
num
ule
anu
m
Sola
num
trizygum
Sola
num
phase
olo
ides
Sola
num
evolvu
lifoliu
m
Sola
num
fraxin
ifoliu
m
Sola
num
taenio
trichum
Sola
num
murica
tum S
ola
num
appendicu
latu
m
Sola
num
palu
stre
Sola
num
etu
bero
sum
Sola
num
more
lliform
e
Sola
num
claru
m
Sola
num
circaeifo
lium
Sola
num
polya
deniu
m
Sola
num
pin
natise
ctum
Sola
num
bulb
oca
stanum
Sola
num
ehre
nberg
ii
Sola
num
card
iophyllu
m
Sola
num
jam
esii
Sola
num
stenophyllid
ium
Sola
num
arn
ezi
i
So
lanu
m y
un
ga
sense
So
lanu
m c
ha
coe
nse
So
lanu
m le
pto
phye
s
So
lanu
m o
plo
cense
es
nejir
at m
un
alo
S
Sola
num
infu
ndib
ulif
orm
eS
ola
num
bert
haulti
iS
ola
num
verr
uco
sum
Sola
num
spars
ipilu
mS
ola
num
avi
lesi
i
Sola
num
oka
dae
Sola
num
ugentii
mut
no
dor
cim
mu
nal
oS
ie
nre
v m
un
alo
S
So
lanu
m k
urt
zia
nu
m es
ne
sa
nira
m m
un
alo
S
mu
nis
ob
ma
mu
nal
oS
mu
na
ello
dn
ac
mu
nal
oS
iiv
os
ak
ub
mu
nal
oS
mu
sor
eb
ut m
un
alo
S
elu
aci
ver
b m
un
alo
SS
ola
nu
m lig
nica
ule
So
lanu
m a
cha
cach
en
se
So
lanu
m sa
nto
lalla
em
umi
ssi
xal
m
un
alo
S
So
lanu
m p
am
pa
sen
sem
uil
ofi
na
hp
ar
mu
nal
oS
mu
pra
cy
xo
mu
nal
oS
mui
lof
in
omi
rg
a m
un
alo
S
es
ne
mol
ad
nut
m
un
alo
S
mut
aru
dn
ap
bu
s m
un
alo
Sm
un
aib
mol
oc
mu
nal
oS
mu
cin
oci
gn
ol
mu
nal
oS
mut
aro
mra
mie
cal
oiv
mu
nal
oS
Sola
num
alb
icans
Sola
num
dem
issum
Sola
num
aca
ule
Sola
num
iopeta
lum
Sola
num
doddsii
Sola
num
ala
ndia
e
Sola
num
andre
anum
Sola
num
mosco
panum
Sola
num
hje
rtingii
Sola
num
stolo
nife
rum
Sola
num
inca
mayo
ense
Sola
num
schenckii
Sola
num
guerre
roense
Sola
num
hougasii
Sola
num
spegazzin
ii
Sola
num
com
merso
nii
Sola
num
multiin
terru
ptu
m
Sola
num
acro
scopicu
m
Sola
num
imm
ite
Sola
num
chom
ato
philu
mS
ola
num
pasco
ense
Sola
num
piu
rae
Sola
num
scabrifo
lium
Sola
num
lycopersico
ides
Sola
num
sitiens
Sola
num
habro
chaite
s
Sola
num
pennellii
Sola
num
chm
iele
wskii
Sola
num
neorickii
Sola
num
lycopersicu
m
Sola
num
lycopersicu
m va
r cera
siform
e
Sola
num
cheesm
ania
e
Sola
num
gala
pagense
Sola
num
pim
pin
ellifo
lium
Sola
num
chile
nse
Sola
num
peru
vianum
Sola
num
och
ranth
um
Sola
num
jugla
ndifo
lium
Solanum
pubigerum
Solanum
aligerum
Solanum
nitidum
Solanum
amygdalifolium
Solanum
crispum
Solanum
riojense
Solanum
americanum
Sola
num
ptych
anth
um
Solanum
opacum
Solanum
fiebrigii
Solanum
physalifolium
Solanum
palitans
Solanum
tripartitum
Solanum
ipomoeoides
Solanum
laxum
Solanum
calileguae
Solanum
dulcamara
Solanum
wallacei
Solanum
seaforthianumS
olanum caesium
Solanum
triflorum
Solanum
villosum
Solanum
retroflexum
Solanum
nigrumSolanum
quadrangulare
Solanum
terminale
Solanum
aggregatum
Solanum
symonii
Solanum
linearifolium
Solanum
aviculare
Solanum
laciniatum
Solanum
trisectum
Solanum
herculeum
Solanum
multifidum
Solanum
montanum
Sola
num
allo
phyl
lum
Sola
num
more
llifo
lium
Sola
num
mapir
iense
Sola
num
anom
alu
mS
ola
num
nem
ore
nse
Sola
num
repta
ns
Sola
num
hoehnei
Sola
num
fusi
form
e
Sola
num
melis
saru
m
Sola
num
tobagense
Sola
num
div
ers
ifoliu
m
Sola
num
oxy
phyl
lum
Sola
num
tegore
Sola
num
circi
natu
m
Sola
num
circi
natu
m s
ubsp
circi
natu
m
Sola
num
tenuis
eto
sum
Sola
num
pro
teanth
um
Sola
num
circi
natu
m s
ubsp
ram
osu
m
Sola
num
occ
ultu
m
Sola
num
sib
undoy
ense
Sola
num
endopogon s
ubsp
guia
nensi
s
Sola
num
caja
num
ense
Sola
num
falla
x
Sola
num
calid
um
Sola
num
obliq
uum
Sola
num
rose
um
Sola
num
mate
rnum
Sola
num
beta
ceum
Sola
num
unilo
bum
Sola
num
cyl
indricu
m
Sola
num
gla
uco
phyl
lum
Sola
num
stu
ckert
ii
Sola
num
confu
sum
Sola
num
hib
ern
um
Sola
num
lute
oalb
um
Sola
num
am
ota
pense
Sola
num
pendulu
m
Sola
num
cory
mbifl
oru
m
Sola
num
latif
loru
m
Sola
num
exi
guum
Sola
num
caco
smum
Sola
num
dip
loco
nos
Sola
num
pin
eto
rum
Sola
num
sci
adost
ylis
Sola
num
hav
anense
Sola
num
och
rophy
llum
Sola
num
aphy
odendro
n
Sola
num
capsi
cast
rum
Sol
anum
rov
irosa
num
Sola
num
arg
entin
um
Sola
num
pse
udoca
psi
cum
Sola
num
arb
ore
um
Sol
anum
turn
eroi
des
Sol
anum
ads
cend
ens
Sol
anum
sch
lech
tend
alia
num
Sol
anum
rug
osum
Sol
anum
mau
ritia
num
Sol
anum
cor
dove
nse
Sol
anum
lepi
dotu
m
Sol
anum
abu
tiloi
des
Sol
anum
inel
egan
s
Sol
anum
ref
ract
umS
olan
um b
icor
ne
Sol
anum
wen
dlan
dii
Sol
anum
cla
ndes
tinum
Sol
anum
del
itesc
ens
Sol
anum
am
eric
anum
sub
sp n
odifl
orum
Sol
anum
pol
ygam
um
Solan
um a
ccre
scen
s
Solan
um ro
bust
um
Solan
um s
tagn
ale
Solan
um m
icro
phyllu
m
Solan
um a
grar
ium
Solan
um s
tena
ndru
m
Solan
um c
arol
inen
se
Solanu
m c
onditum
Solan
um c
ompt
um
Solanu
m ja
maice
nse
Solanum
atu
rense
Solanu
m a
dhaerens
Solanum m
ultispinum
Solanum cr
otonoides
Solanum g
lutinosu
m
Solanum cr
initipes
Solanum p
aniculatu
m
Solanum to
rvum
Solanum la
nceolatu
m
Solan
um d
rym
ophi
lum
Solan
um b
aham
ense
Solan
um c
ampe
chie
nse
Solanum sp
Goldblatt
12426
Solanum h
ispidum
Solanum erianthum
Solanum ra
cem
osum
Solanum elaeagnifoliu
m
Solanum tridyn
amum
Solanum hindsianum
Solanum sejunctum
Solanum asymmetriphyllumSolanum cf centrale AMH 1
Solanum centraleSolanum quadriloculatum
Solanum esuriale
Solanum pugiunculiferum
Solanum nummularium
Solanum nemophilum
Solanum cunninghamii
Solanum carduiformeSolanum leopoldense
Solanum cataphractum
Solanum petraeum
Solanum sp Martine 805
Solanum vansittartenseSolanum tudununggaeSolanum aff vansittartense Fryxell 3421
Solanum dioicum
Solanum eremophilum
Solanum ellipticum
Solanum cleistogamum
Solanum aff echinatum Bohs 2727
Solanum echinatumSolanum tetrathecumSolanum orbiculatum
Solanum heteropodiumSolanum oedipus
Solanum melanospermumSolanum clarkiae
Solanum beaugleholei
Solanum phlomoides
Solanum lasiophyllum
Solanum chippendaleiSolanum diversiflorum
Solanum hystrixSolanum hoplopetalum
Solanum petrophilum
Solanum campanulatumSolanum prinophyllum
Solanum stupefactum
Solanum nobileSolanum brownii
Solanum curvicuspeSolanum neoanglicum
Solanum pancheri
Solanum sandwicenseSolanum incompletumSolanum vaccinioides
Solanum stelligerum
Solanum chenopodinum
Solanum cookii
Solanum corifoliumSolanum ferocissimumSolanum parvifolium
Solanum furfuraceumSolanum cinereum
Solanum coacti
liferu
m
Solanum renschii
Solanum giganteum
Solanum thruppii
Solanum aculeastrum
Solanum coagulans
Solanum schimperia
num
Solanum kwebense
Solanum marginatum
Solanum richardii
Solanum incanum
Solanum arundo
Solanum cumingii
Solanum ovigerum
Solanum melongenaSolanum lichtensteinii
Solanum linnaeanum
Solanum sessilistellatumSolanum campylacanthum
Solanum panduriforme
Solanum violaceum
Solanum supinum
Solanum manaense
Solanum macrocarpon
Solanum dasyphyllum
Solanum vespertilio
Solanum lidii
Solanum rigescens
Solanum capense
Solanum tomentosum
Solanum hastifolium
Solanum cyaneopurpureum
Solanum anguivi
Solanum aethiopicum
Solanum virginianum
Solanum myo
xotrichum
Solanum pyraca
nthos
Solanum mahorie
nse
Solanum heinianum
Solanum tolia
raea
Solanum hieronym
i
Solan
um sisym
briifo
lium
Solan
um c
rinitu
m
Solan
um m
itlens
e
Solan
um ly
coca
rpum
Solan
um ro
stra
tum
Solan
um citr
ullifo
lium
Solan
um w
right
ii
Sol
anum
mam
mos
um
Sol
anum
pla
tens
eSol
anum
cap
sico
ides
Sol
anum
ace
rifol
ium
Sol
anum
tenu
ispi
num
Sol
anum
atro
purp
ureu
m
Sol
anum
via
rum
Sol
anum
acu
leat
issi
mum
Sol
anum
myr
iaca
nthu
m
Sol
anum
inca
rcer
atum
Sol
anum
pal
inac
anth
umSol
anum
stra
mon
iifol
ium
var
iner
me
Sol
anum
ses
silif
loru
m
Sol
anum
qui
toen
se
Sol
anum
felin
um
Sol
anum
lasi
ocar
pum
Sol
anum
upo
ro
Sol
anum
repa
ndum
Sol
anum
can
didu
m
Sol
anum
stra
mon
iifol
ium
Sol
anum
ves
tissi
mum
Sol
anum
hyp
orho
dium
Sol
anum
pse
udol
ulo
Solan
um h
irtum
Sol
anum
pec
tinat
um
Sol
anum
hirs
utissim
um
Sol
anum
tequ
ilens
e
0.02 substitutions / site
995 Solanaceae + five outgroup Convolvulaceae taxafrom a sparse eight-gene, 16405-site alignment
Figure S1: Phylogenetic relationships among 995 species of Solanaceae, rooted with five
species of Convolvulaceae.
8
Symonanthus bancroftiiSymonanthus aromaticus
Nicotiana obtusifoliaNicotiana bigelovii
Nicotiana clevelandii
Nicotiana tomentosa
Nicotiana tomentosiformis
Nicotiana setchellii
Nicotiana otophora
Nicotiana linearisNicotiana miersiiNicotiana attenuata
Nicotiana corymbosa
Nicotiana langsdorffii
Nicotiana bonariensis
Nicotiana forgetiana
Nicotiana longiflora
Nicotiana plumbaginifolia
Nicotiana alataNicotiana africana
Nicotiana fragrans
Nicotiana debneyi
Nicotiana simulans
Nicotiana megalosiphon
Nicotiana ingulba
Nicotiana umbratica
Nicotiana exigua
Nicotiana rosulata
Nicotiana goodspeedii
Nicotiana gossei
Nicotiana velutina
Nicotiana amplexicaulis
Nicotiana m
aritima
Nicotiana excelsior
Nicotiana bentham
iana
Nicotiana suaveolens
Nicotiana cavicolaNicotiana rotundifolia
Nicotiana occidentalis
Nicotiana hesperis
Nicotiana sylvestris
Nicotiana nudicaulis
Nicotiana repanda
Nicotiana stocktonii
Nicotiana acaulis
Nicotiana glaucaNicotiana noctiflora
Nicotiana petunioides
Nicotiana cordifolia
Nicotiana solanifoliaNicotiana paniculataNicotiana knightiana
Nicotiana rustica
Nicotiana benavidesii
Nicotiana glutinosaNicotiana undulataNicotiana wigandioides
Lycium tetrand
rumLyci
um a
reni
cola
Lyci
um h
orrid
umLy
cium
fero
ciss
imum
Lyci
um c
iner
eum esnedlevdnarts
muicyLLy
cium
gar
iep
ense
muli
mup
muic
yL
Lycium hirsutum
Lycium villosum
Grabow
skia duplicataLycium
pallidum
Lycium californicum
Lycium m
inimum
Lycium exsertum
Lycium frem
ontii
Lycium and
ersoniiLycium
parishii
Lycium b
erlandieri
Lycium cestroides
Nolana ivaniana
Nolana elegans
Nolana paradoxa
Nolana acum
inataN
olana rupicola
Nolana rostrata
Nolana plicata
Nolana aticoana
Nolana hum
ifusaN
olana laxaN
olana adansonii
Atropa belladonna
Anisodus tanguticus
Hyoscyam
us niger
Hyoscyam
us muticus
Hyoscyam
us albus
Jaborosa integrifolia
Sol
and
ra g
rand
iflor
aD
ysso
chro
ma
virid
iflor
a
Man
dra
gora
off
icin
arum
Bru
gman
sia
aure
aB
rugm
ansi
a sa
ngui
nea
Dat
ura
leic
hhar
dtii
Dat
ura
met
el
Dat
ura
inox
iaD
atur
a st
ram
oniu
m
With
erin
gia
cune
ata
With
erin
gia
cocc
olob
oide
s
Cua
tres
ia ri
paria
Cua
tres
ia e
xigu
iflor
a
Ioch
rom
a cy
aneu
m
Acn
istu
s ar
bore
scen
s
Ioch
rom
a ge
sner
ioid
es
Ioch
rom
a fu
chsi
oide
s
Erio
lary
nx lo
rent
zii
Ioch
rom
a au
stra
le
Dun
alia
bra
chya
cant
ha
Vass
obia
bre
viflo
ra
Dun
alia
sol
anac
ea
With
ania
som
nife
ra
With
ania
coa
gula
ns
Brac
hist
us s
tram
onifo
lius
With
erin
gia
sola
nace
a
With
erin
gia
mei
anth
a
With
erin
gia
mac
rant
ha
With
erin
gia
mex
ican
a
Physa
lis p
ruino
sa
Physa
lis an
gulat
a
Physa
lis p
ubes
cens
Physa
lis p
hilad
elphic
a
Physa
lis vi
scosa
Physa
lis he
terophy
lla
Physa
lis lo
ngifo
lia
Physa
lis ci
nera
scen
s
Physa
lis la
nceif
olia
Phys
alis
cras
sifol
ia
Jalto
mat
a gr
andi
flora
Jalto
mat
a pr
ocum
bens
Jalto
mat
a au
ricul
ata
Jalto
mat
a si
nuos
a
Salpich
roa o
rigan
ifolia
Capsicum la
nceolatum
Capsicum rh
omboideum
Capsicum parvi
folium
Capsicum fle
xuosum
Capsicum sc
hottianum
Capsicum vil
losumCapsicum annuum
Capsicum tovarii
Capsicum pubescens
Capsicum galapagoenseCapsicum baccatum
Capsicum chacoense
Capsicum chinense
Capsicum frutescens
Capsicum cardenasii
Capsicum exim
ium
Lycia
nthes ra
ntonnei
Lycian
thes cilio
lata
Lycian
thes asa
rifolia
Jaltomata hunzikeri
Jaltomata dentata
Solanum trizygumSolanum fraxinifolium
Solanum taeniotrichumSolanum muricatum
Solanum appendiculatum
Solanum palustre
Solanum etuberosum
Solanum morelliforme
Solanum clarum
Solanum polyadenium
Solanum pinnatisectum
Solanum bulbocastanum
Solanum ehrenbergii
Solanum cardiophyllumSolanum jamesii
Solanum stenophyllidium
Solanum chacoense
Solanum leptophyes
Solanum oplocense
Solanum tarijense
Solanum infundibuliform
e
Solanum berthaultii
Solanum verrucosum
Solanum sparsipilum
Solanum m
icrodontum
Solanum vernei
Solanum kurtzianum
Solanum bukasovii
Solanum tuberosum
Solanum santolallae
Solanum laxissim
um
Solanum oxycarpum
Solanum agrim
onifolium
Solanum colom
bianum
Solanum longiconicum
Solanum violaceim
armoratum
Solanum dem
issum
Solanum acauleSolanum iopetalum
Solanum andreanum
Solanum moscopanum
Solanum hjertingii
Solanum stoloniferum
Solanum guerreroense
Solanum hougasii
Solanum spegazzinii
Solanum commersonii
Solanum chomatophilum
Solanum piurae
Solanum lycopersicoidesSolanum sitiens
Solanum habrochaites
Solanum pennellii
Solanum chmielewskiiSolanum neorickii
Solanum lycopersicum var cerasiforme
Solanum cheesmaniae
Solanum galapagenseSolanum pimpinellifolium
Solanum chilenseSolanum peruvianum
Solanum ochranthumSolanum juglandifolium
Solanum crispum
Solanum americanum
Solanum ptychanthumSolanum opacum
Solanum physalifoliumSolanum palitans
Solanum tripartitum
Solanum dulcamaraSolanum wallacei
Solanum seaforthianum
Solanum triflorumSolanum villosumSolanum retroflexum
Solanum nigrum
Solanum terminaleSolanum symoniiSolanum aviculare
Solanum laciniatum
Solanum trisectum
Solanum
allophyllum
Solanum
melissarum
Solanum
tobagense
Solanum
diversifolium
Solanum
oxyphyllum
mutanicric munalo
S Sol
anum
occ
ultu
mS
olan
um s
ibun
doy
ense
Sol
anum
caj
anum
ense
xall
af mu
nalo
S
Solanum
obliquum
Solanum
roseumS
olanum m
aternumS
olanum b
etaceumS
olanum unilobum
Solanum
glaucophyllumS
olanum stuckertii
Solanum
confusumS
olanum hibernum
Solanum
luteoalbum
Solanum
amotapense
Solanum
pendulum
Solanum
corymbiflorum
Solanum
latiflorum
Solanum
exiguum
Solanum
cacosmum
Solanum
diploconosS
olanum pinetorum
Solanum
sciadostylis
Sol
anum
ap
hyod
end
ron
Sol
anum
arg
entin
um
Sol
anum
pse
udoc
apsi
cum
Sol
anum
ad
scen
den
sS
olan
um m
aurit
ianu
m
Sol
anum
cor
dov
ense
Sol
anum
abu
tiloi
des
Sol
anum
wen
dlan
dii
Sol
anum
pol
ygam
um
Sola
num
robu
stum
Sola
num
sta
gnal
eSola
num
car
oline
nse
Solanu
m ja
maic
ense
Solanu
m cr
oton
oides
Solanum
pan
iculat
um
Solanu
m to
rvum
Solan
um d
rym
ophil
um
Solan
um c
ampe
chien
se
Solanum hisp
idum
Solanum
erian
thum
Solanum tri
dynam
um
Solanum hindsia
num
Solanum asymmetriphyllum
Solanum nemophilum
Solanum cunninghamii
Solanum carduiformeSolanum leopoldense
Solanum cataphractumSolanum petraeumSolanum vansittartenseSolanum tudununggae
Solanum dioicumSolanum cleistogamumSolanum echinatum
Solanum melanospermum
Solanum clarkiae
Solanum beaugleholei
Solanum chippendaleiSolanum diversiflorum
Solanum campanulatum
Solanum prinophyllum
Solanum sandwicense
Solanum incompletum
Solanum cinereum
Solanum giganteum
Solanum aculeastrum
Solanum marginatum
Solanum incanum
Solanum melongena
Solanum linnaeanum
Solanum macrocarpon
Solanum dasyphyllum
Solanum vespertilio
Solanum lidiiSolanum tomentosum
Solanum cyaneopurpureum
Solanum anguivi
Solanum aethiopicum
Solanum virginianum
Solanum pyra
canthos
Sola
num
sisy
mbr
iifoliu
m
Solan
um c
rinitu
m
Solan
um ly
coca
rpum
Solan
um ro
stra
tum
Sola
num
citr
ullifo
lium
Sol
anum
mam
mos
umS
olan
um p
late
nse
Sol
anum
cap
sico
ides
Sol
anum
tenu
ispi
num
Sol
anum
atr
opur
pure
um
Sol
anum
via
rum
Sol
anum
acu
leat
issi
mum
Sol
anum
myr
iaca
nthu
m
Sol
anum
pal
inac
anth
um
Sol
anum
ses
silif
loru
m
Sol
anum
qui
toen
se
Sol
anum
felin
umSo
lanu
m la
sioc
arpu
m
Sola
num
repa
ndum
Sol
anum
can
didu
mSo
lanu
m s
tram
oniif
oliu
m
Sola
num
ves
tissi
mum
Sola
num
hyp
orho
dium
Sola
num
pse
udol
ulo
Sola
num
hirt
um
Sola
num
pec
tinat
um
10 million years
356 “x=12” Solanaceae taxa with known breeding system status
Figure S2: Phylogenetic relationships among 356 species of Solanaceae used in the analyses
of character evolution. Branch lengths were obtained with penalized likelihood smoothing,
implemented in r8s (S7), with the crown group age fixed at 36 Ma.
9
mean std dev std errλI 2.933 0.467 0.049λC 5.199 0.738 0.063µI 2.319 0.556 0.059µC 5.433 0.757 0.065qIC 0.555 0.138 0.010λC − λI 2.266 0.899 0.083µC − µI 3.114 1.011 0.095rI 0.613 0.141 0.010rC −0.234 0.075 0.002rI − rC 0.847 0.200 0.012rI − rC − qIC 0.292 0.075 0.002pSI 0.345 0.043 0.002
Table S1: Summary of MCMC results from the ML tree, showing the mean, standard deviation,
and standard error from time-series analysis. The first five quantities are the parameters directly
estimated by the BiSSE analysis.
λI λC µI µC qICλI —λC −0.067 —µI 0.977 −0.142 —µC −0.076 0.995 −0.165 —qIC −0.510 0.352 −0.677 0.414 —
Table S2: Parameter correlations on the ML tree. Correlations between qIC and net diversifica-
tion are 0.984 and −0.719 for rI and rC , respectively.
10
λI λC µI µC qIC rI rCML 0.467 0.738 0.556 0.757 0.138 0.141 0.075BS 0.548 0.812 0.547 0.869 0.124 0.059 0.033
Table S3: Standard deviations of estimated parameters, computed from MCMC on the ML tree
(upper row) and from the median values on the set of bootstrap trees (lower row).
mean std dev std errλI 3.031 0.486 0.013λC 5.108 0.744 0.018µI 2.516 0.563 0.015µC 5.284 0.769 0.018qIC 0.484 0.128 0.002qCI 0.021 0.011 0.000rI − rC 0.690 0.187 0.003pSI 0.355 0.044 0.000
Table S4: Summary of MCMC results from the ML tree when regain of SI is not prohibited.
11
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13