sign in sign up
<<
Home , Actinostrobus, Athrotaxis, Austrocedrus, Callitris, Callitris endlicheri, Callitris macleayana

Supporting Information

Mao et al. 10.1073/pnas.1114319109 SI Text BEAST Analyses. In addition to a BEAST analysis that used uniform Selection of Taxa and Their Phylogenetic Positions. The in- prior distributions for all calibrations (run 1; 144- dataset, tegration of fossil calibrations is the most critical step in molecular calibrations as in Table S4), we performed eight additional dating (1, 2). We only used the fossil taxa with ovulate cones that analyses to explore factors affecting estimates of divergence could be assigned unambiguously to the extant groups (Table S4). time (Fig. S3). The exact phylogenetic position of used to calibrate the First, to test the effect of calibration point P, which is close to molecular clocks was determined using the total-evidence analy- the node and is the only functional hard maximum constraint ses (following refs. 3−5). Cordaixylon iowensis was not included in in BEAST runs using uniform priors, we carried out three runs the analyses because its assignment to the crown Acrogymno- with calibrations A through O (Table S4), and calibration P set to spermae already is supported by previous cladistic analyses (also [306.2, 351.7] (run 2), [306.2, 336.5] (run 3), and [306.2, 321.4] using the total-evidence approach) (6). Two data matrices were (run 4). The age estimates obtained in runs 2, 3, and 4 largely compiled. Matrix A comprised Ginkgo biloba, 12 living repre- overlapped with those from run 1 (Fig. S3). Second, we carried out two runs with different subsets of sentatives from each , and three fossils taxa related fi to Pinaceae and (16 taxa in total; Fig. S5A). In this calibrations using uniform priors. When parsing the log.txt le of matrix, the 105 morphological characters and their states follow run 1 with Tracer 1.4 (15), we noted that the posterior distribution Gernandt et al. (ref. 7 and references therein). Matrix B com- of nodes calibrated with the minimum constraints (calibrations A prised Pinus sylvestris, Sciadopitys verticillata, 39 living taxa, and 17 through O) fell into two groups. One included calibrations C, D, fossil taxa that are closely related to (58 taxa in H, I, M, N, and O. For each node calibrated with these fossils total). In this matrix, the 53 morphological characters and their (Table S4), the posterior distributions of their age estimates significantly violated a normal distribution (hence our name for states follow Farjon (8) and two updates (9-10). Both data ma- “ ” trices include 5,476 molecular characters for all living taxa ex- this subset: VND ). The other group included calibrations A, B, E, F, G, J, K, and L. For each node calibrated with these fossils tracted from the plastid DNA sequence matrix (144-taxon (Table S4), the posterior distributions of their age estimates did dataset), with the fossil taxa coded as having “missing data.” not significantly violate a normal distribution (hence, subset Molecular and morphological characters were concatenated in “NVND”). When comparing between-lineage age estimates de- both matrices, and parsimony analyses were performed using the rived from BEAST runs based on calibration subset VND (plus program TNT 1.1 (11), with heuristic searching based on 5,000 calibration P) (run 5) and subset NVND (plus calibration P) (run random addition sequences and -Bisection-Reconnection 6), we found that the calibration subset NVND (run 6) signifi- swapping (saving 10 per replication). All shortest trees were cantly underestimated lineage ages when compared with the saved and summarized into a strict consensus tree. All characters calibration subset VND (run5) or the calibrations A through P were weighted equally, and the resulting phylogenetic trees were (run 1) (Fig. S3). rooted on Ginkgo biloba (matrix A) (Fig. S5A)oronPinus syl- – Third, we carried out another BEAST run that incorporated vestris (matrix B) (Fig. S5 B I). lognormal priors. Calibrations that may underestimate lineage As shown in Fig. S5A, Matrix A yielded a tree in which the age should not be given lognormal priors, because a lognormal phylogenetic positions of the fossil taxa were well resolved. prior places a rapidly declining probability on older ages (16). Matrix B, however, yielded a tree in which phylogenetic positions Nevertheless, fossils that underestimate lineage ages still may be of more than half of the fossil taxa were unresolved. We then ran useful as hard minimum constraints, as suggested by previous a series of analyses, each of which included a different subset of studies (12, 17, 18). For this reason, uniform priors were retained fossils, and determined that seven fossils (Hughmillerites juddii, for the subset NVND, whereas lognormal priors were applied for ungeri, Austrosequoia wintonensis, sp., the calibration P and the subset VND (run 7) (see Table S4). The prechilensis, polaris, and raven- age estimates obtained in run 7 largely overlapped with those scragensis) are responsible for the collapsing of the tree, likely from runs 1 and 5 (Fig. S3). However, one run (with lognormal because that fewer morphological characters are available for priors; run 7) bias to estimate the node ages younger and another them than for the others included in Matrix B. We therefore run (with uniform priors; run 1) bias to estimate the node ages determined the position of the other 10 fossils by reanalyzing older, so “the truth is likely to be somewhere in between” (19). Matrix B with only these 10 fossils included (Fig. S5I). We fur- Fourth, we also carried out a run that included ther studied the placement of each of the seven problematic americana (calibration Wa) as a hard minimum calibration in fossils by analyzing a version of Matrix B containing only one addition to calibrations A through P (run 8). Integration of this – target fossil alongside all the living taxa (Fig. S5 B H). All data calibration resulted in significantly older age estimates for nodes matrices and resulting trees have been submitted to TreeBASE 1–10 (Fig. S3), demonstrating that the calibration Wa has a po- (study accession no. S12554). tential to overestimate lineage ages. As suggested by the cross- Cross-validation tests of the different fossil calibrations (Fig. S7 validation test and a recent study (14), it is better to exclude the and ref. 12) were performed with the program R8S under Pe- calibration Wa. nalized Likelihood rate smoothing using the 56-taxon dataset. A Finally, we carried out a BEAST run on the 56-taxon matrix maximum constraint was used only for calibration P while the that assumed uniform prior for all calibrations (run 9) (Table S4). remaining 16 calibrations used the minimum constraints (Fig. S7 The ages obtained are slightly younger than these obtained with and Table S4). Only the calibration Wa (Widdringtonia ameri- 144-taxon matrix (Fig. S3). This result is consistent with the ef- cana) (13) resulted in the node ages significantly older than those fects of undersampling observed elsewhere (20). of the other fossil calibrations (Fig. S7). This fossil appears to be wrongly placed in the living Widdringtonia, as suggested Ancestral Area Reconstruction. Ancestral area reconstruction also by Crisp and Cook (14). We therefore excluded the cali- (AAR) under the dispersal--cladogenesis model, as bration Wa from further analyses. implemented in LAGRANGE (21), requires a matrix that defines

Mao et al. www.pnas.org/cgi/content/short/1114319109 1of10 migration probabilities among the six operational geographic extinction is inferred; 10 such events are hypothesized in Fig. S4) areas (see Fig. 2A for their boundaries). Migration probabilities or (ii) inherits a reduced range relative to its parent (one in- among areas were based on geological history, climate history, stance related to is hypothesized in Fig. 2 C–E and and the presence and dissolution of land bridges and island in Fig. S4). Third, cladogenesis events caused by vicariance (in- chains. Geological events considered were the presence of a land dicated by blue arrows on a lineage) are inferred where the an- connection between all operational area before the break-up of cestral range encompassing two or more areas subdivides between Pangea, the separation between Laurasia and Gondwana, the daughter lineages. Fourth, a combination of range expansion and gradual fragmentation of Gondwana and Laurasia, island chains subsequent cladogenesis caused by vicariance is inferred when between North and South America, the collision of Australian one daughter lineage inherits the range of its parent, and the and Asian plates, and the collision of African and Asian plates other inherits a different range (e.g., the separation between (22-26). Migration probabilities range from 0.1 for well-sepa- Athrotaxites berryi and Athrotaxis in Fig. 2 C–E). Note that each of rated areas to 1.0 for contiguous landmasses (Table S6), and the the fossil taxa shown by dashed lines in Fig. 2 and Fig. S4 expe- LAGRANGE online configuration tool (21) was used to devise rienced one extra total extinction event compared with living taxa fl a matrix that re ected different migration probabilities between shown by solid lines. areas at different periods (i.e., time slices) in the past. Based on Our total-evidence analyses fully resolved the phylogenetic fi plate tectonics, we de ned eight area pairs and one area com- position of Athrotaxites berryi and partly resolved the phyloge- bination as ancestral area candidates in AAR analyses: NS, NE, netic positions of Austrohamia minuta, Austrohamia acantho- “ ” SF, NA, AE, FE, SU, NF, and NAE (in which E stands for bractea, and Sewardiodendron laxum (Fig. S5I) but failed for “ ” , north , and northern Arabia; A represents Asia; Hughmillerites juddii (Fig. S5B). We therefore excluded Hugh- “ ” N represents , Caribbean, and Central Amer- millerites juddii from AAR analyses (its inclusion resulted in the ica; “S” represents South America; “F” represents south to “ ” collapse of the Cupressaceae : Fig. S5B). To middle Africa and southern Arabia; and U represents Aus- include Austrohamia minuta, Austrohamia acanthobractea, and tralia, New Guinea, , and ). Because Sewardiodendron laxum in the AARs, we assigned them to three the connectivity between our six operational geographic units possible placement scenarios and performed likelihood AARs changed during the past 275 million years, we decided to develop for each scenario. As shown in Fig. 2 C–E, A. minuta and A. a time-slice model that would reflect changing continental con- acanthobractea always were assumed to be sister to each other. nectivity. To find the best-fitting time-slice model, we compared Scenario 1 (Fig. 2C) assumes that Sewardiodendron diverged models with five time slices (275–160 Ma, 160–125 Ma, 125–70 from Cunninghamioideae (both living and extinct members) Ma, 70–30 Ma, and 30 Ma to the present), six time slices (275– (Fig. 2 and Fig. S4) at 157.2 Ma, and both of them share a most 160 Ma, 160–125 Ma, 125–105 Ma, 105–70 Ma, 70–30 Ma, and recent common ancestor (MRCA) with Austrohamia at 164.2 Ma. 30 Ma to the present), seven time slices (275–160 Ma, 160–125 Ma, 125–105 Ma, 105–70 Ma, 70–45 Ma, 45–30 Ma, and 30 Ma Scenario 2 (Fig. 2D) assumed that Sewardiodendron and Austro- to the present), and eight time slices (275–160 Ma, 160–125 Ma, hamia shared a MRCA at 157.2 Ma and diverged from Cun- 125–105 Ma, 105–70 Ma, 70–45 Ma, 45–30 Ma, 30–5 Ma, and 5 ninghamioideae 164.2 Ma. Scenario 3 (Fig. 2E) assumed that Ma to the present). For each of these four time-slice schemes, we Sewardiodendron and Austrohamia shared a MRCA at 164.2 Ma compiled a separate migration probability matrix and calculated and diverged from the MRCA of all Cupressaceae subfamilies its global maximum likelihood in LAGRANGE. Comparison of except Cunninghamioideae at 211.5 Ma (the intermediate age the resulting global likelihoods suggested that the eight-time-slice between nodes 2 and 3 in Table 1). fi matrix (Table S6) t our data best, and we therefore adopted this fi migration probability matrix for all subsequent AAR analyses. Diversi cation Modeling. Using the TreeSim R package (29) and We performed additional AAR analyses on trees that com- the BEAST highest posterior probability chronogram obtained prised 29 fossils or groups of fossils representing extinct taxa (Fig. for the Cupressaceae (from the 144-taxon dataset) as input, we 2 C–E, Fig. S4, and Table S5) (26, 27), the 122 sequenced living simulated 1,000 trees with the number of tips corresponding to the total number of extant of Cupressaceae (162 species) and taxa of Cupressaceae and four outgroups. For these analyses, fi fossils were placed as extinct sister lineages to those living line- speciation and extinction rates obtained by tting the constant ages with which they showed the closest morphological affinities rate birth-death model to the chronogram. To add the 40 extant as assessed in their original publications and related updates (for species that were not sequenced, we used the sim.missing function detailed placement justifications, see Table S5). The divergence in the CorSiM R package (30) and simulated 1,000 trees under between extinct lineages and their sister lineages (living taxa) was a constant-rate birth-death model, assuming that the missing determined based on the earliest fossil of each extinct lineage speciation events are not distributed randomly over the tree but (always determined as the youngest possible age of the formation probably happened during the past 10 million years. We then or stratum in which a fossil occurred). For the absolute age of applied birth/death likelihood (BDL) analysis (using TreePar) to each geological stratum, we relied on the latest geologic time the 1,000 completed trees to obtain means and SDs for the γ scale (28). statistic, the Akaike information criterion values, and the in- As shown in Fig. 2 and Fig. S4, our AARs inferred four types of ferred rate parameters from the BDL analyses. TreePar also events affecting geographic ranges of either living or extinct calculates the percentage of trees to which a particular model fits lineages. First, instances of dispersal result in range expansion best. Among the five models under comparison (CR-PB, con- (indicated by black arrows on a lineage); such events are common stant-rate birth-death, logistic density dependence, exponential throughout the Cupressaceae tree. Second, local extinction events density dependence, and a two-rate variant of the pure-birth (indicated by a red “X” on a lineage; 11 are hypothesized in Fig. model with a rate shift at a certain time point), the two-rate S4) are inferred when a daughter lineage (i) inherits a range model provided the best fit for all 1,000 trees. The CR-PB different from that of its parent (a range expansion before local provided the second-best fit.

1. Clarke JT, Warnock RC, Donoghue PC (2011) Establishing a time-scale for 4. Peterson KJ, Butterfield NJ (2005) Origin of the Eumetazoa: Testing ecological evolution. New Phytol 192:266–301. predictions of molecular clocks against the Proterozoic fossil record. Proc Natl Acad 2. Hedges SB, Kumar S (2004) Precision of molecular time estimates. Trends Genet 20: Sci USA 102:9547–9552. 242–247. 5. Manos PS, et al. (2007) Phylogeny of extant and fossil Juglandaceae inferred from the 3. Sun G, et al. (2002) Archaefructaceae, a new basal angiosperm family. Science 296:899–904. integration of molecular and morphological data sets. Syst Biol 56:412–430.

Mao et al. www.pnas.org/cgi/content/short/1114319109 2of10 6. Magallon S (2010) Using fossils to break long branches in molecular dating: A comparison 19. Davis CC, Schaefer H (2011) Plant evolution: Pulses of extinction and speciation in of relaxed clocks applied to the origin of angiosperms. Syst Biol 59:384–399. diversity. Curr Biol 21(24):R995–R998. 7. Gernandt DS, et al. (2008) Use of simultaneous analyses to guide fossil-based 20. Linder HP, Hardy CR, Rutschmann F (2005) Taxon sampling effects in molecular clock calibrations of pinaceae phylogeny. Int J Plant Sci 169:1086–1099. dating: An example from the African Restionaceae. Mol Phylogenet Evol 35: 8. Farjon A (2005) A Monograph of Cupressaceae and Sciadopitys (Royal Botanic 569–582. , Kew, UK), pp 47–53, 601−602. 21. Ree RH, Smith SA (2008) Maximum likelihood inference of geographic range 9. Escapa I, Cúneo R, Axsmith B (2008) A new genus of the Cupressaceae (sensu lato) evolution by dispersal, local extinction, and cladogenesis. Syst Biol 57:4–14. from the of : Implications for conifer megasporangiate cone 22. Tiffney BH (1985) The North-Atlantic Land-Bridge: Its importance in tertiary homologies. Rev Palaeobot Palyno 151:110–122. and modern phytogeography of the Northern Hemisphere.2. J Arnold 66: 10. Rothwell GW, Stockey RA, Mapes G, Hilton J (2011) Structure and relationships of the 243–273. Jurassic conifer cone Hughmillerites juddii gen. et comb. nov.: Implications for 23. Scotese CR (2001) Atlas of History (Department of Geology, University of , the origin and evolution of Cupressaceae. Rev Palaeobot Palyno 164:45–59. Arlington, TX). 11. Goloboff PA, Farris JS, Nixon KC (2008) TNT, a free program for phylogenetic analysis. 24. Morley RJ (2003) Interplate dispersal paths for megathermal angiosperms. Perspect Cladistics 24(5):774–786. Plant Ecol Evol Syst 6:5–20. 12. Near TJ, Meylan PA, Shaffer HB (2005) Assessing concordance of fossil calibration points 25. Smith AG, Smith DG, Funnell BM (2004) Atlas of and Mesozoic Coastlines in molecular clock studies: An example using turtles. American Naturalist 165:137–146. (Cambridge University Press, Cambridge, UK). 13. McIver EE (2001) Widdringtonia Endl. (Cupressaceae) from North America. 26. Clayton JW, Soltis PS, Soltis DE (2009) Recent long-distance dispersal overshadows Int J Plant Sci 162:937–961. ancient biogeographical patterns in a pantropical angiosperm family (Simaroubaceae, 14. Crisp MD, Cook LG (2011) Cenozoic account for the low diversity of extant Sapindales). Syst Biol 58:395–410. compared with angiosperms. New Phytol 192:997–1009. 27. Crisp MD, Trewick SA, Cook LG (2011) Hypothesis testing in biogeography. Trends 15. Rambaut A, Drummond AJ (2007) Tracer v1.4. Available at http://beast.bio.ed.ac. Ecol Evol 26:66–72. uk/Tracer. 28. Ogg JG (2010) International Stratigraphic Chart (International Commission on Stratigraphy, 16. Ho SY, Phillips MJ (2009) Accounting for calibration uncertainty in phylogenetic West Lafayette, IN) Available at https://www.seegrid.csiro.au/wiki/pub/CGIModel/ estimation of evolutionary divergence times. Syst Biol 58:367–380. GeologicTime/StratChart2010.jpg. 17. Near TJ, Sanderson MJ (2004) Assessing the quality of molecular divergence time 29. Stadler T (2011) Simulating trees on a fixed number of extant species. Syst Biol 60: estimates by fossil calibrations and fossil-based model selection. Philos Trans R Soc 676–684. Lond B Biol Sci 359:1477–1483. 30. Cusimano N, Stadler T, Renner SS (2012) A new method for handling missing species 18. Near TJ, Bolnick DI, Wainwright PC (2005) Fossil calibrations and molecular divergence in diversification analysis applicable to randomly or non-randomly sampled time estimates in centrarchid fishes (Teleostei: Centrarchidae). Evolution 59:1768–1782. phylogenies. Syst Biol, 10.1093/sysbio/sys031.

Mao et al. www.pnas.org/cgi/content/short/1114319109 3of10 Fig. S1. Maximum likelihood trees based on (A) the 56-taxon dataset (nuclear ribosomal DNA regions: 18S, 26S; mitochondrial DNA regions: coxI, atpA; plastid DNA regions: rbcL, matK, psbB, petB-D, rps4, and trnL-F) and (B) the 144-taxon dataset (plastid DNA regions only: rbcL, matK, psbB, petB-D, rps4, and trnL-F). Strongly supported nodes are marked by asterisks. A black asterisk indicates parsimony bootstrap support (PBS) ≥85% and Bayesian posterior probability (BPP) ≥0.98; a blue asterisk indicates PBS ≥85% but BPP <0.98; an orange asterisk indicates BPP ≥0.98 but PBS <85%.

Mao et al. www.pnas.org/cgi/content/short/1114319109 4of10 29/L ()a Juniperus drupacea Juniperus formosana Hesperocyparis 28 31 30 Callitropsis 24 27 Microbiota 22 26/K 25/J

Chamaecyparis e 10 23/I Fokienia a

e Thuja s 21/H

c u

r muelleri a

e s

p

s 7 20/G i

e Neocallitropsis n

18 r Sect. Sabina u 19/F

p J 16 9 Widdringtonia u 6

15 C 17 8/E Papuacedrus 5 14 13/D Glyptostrobus Tax 4/B 12 11/C Seq 3 Metasequoia Athrotaxis Ath 2/A Tai 29/L 1 Cun Amentotaxus 32 Cephalotaxus Sect. Caryocedrus Sciadopitys Nageia 34 Sect. Juniperus Dacrycarpus e 37 Acmopyle a Phyllocladus e

35 Wollemia d 40 Agathis i

36/M o Araucaria

s

Cathaya Hesperocyparis s

41/P 39/O Picea e

Pinus r 38/N

Keteleeria p Abies 31 Cedrus 28 u Ginkgo 30 C Cycas Callitropsis nootkatensis Xanthocyparis vietnamensis 400 300 200 100 0 (Ma)

e 24 Cupressus sensu stricto a

e

c

Platycladus orientalis a

27 s 22 26/K

25/J Tetraclinis articulata s e

Chamaecyparis formosensis r

Chamaecyparis thyoides p 23/I 10 u Fokienia hodginsii

Thuja standishii C 21/H Thujopsis dolabrata Callitris preissii Callitris muelleri 7 Actinostrobus acuminatus e Actinostrobus pyramidalis a Callitris drummondii e

20/G d Neocallitropsis pancheri i Callitris sulcata o 18 Widdringtonia cedarbergensis r

t

Widdringtonia schwarzii i

Widdringtonia nodiflora l l

6 9 a 16 19/F Diselma archeri

Fitzroya cupressoides C 15 Libocedrus bidwillii 17 Libocedrus plumosa 8/E Pilgerodendron uviferum Austrocedrus chilensis 5 Papuacedrus papuana 14 13/D Tax 4/B Cryptomeria japonica 12 11/C Seq Metasequoia glyptostroboides 3 Ath 2/A Taiwania cryptomerioides Tai 1 Cunninghamia lanceolata Cun 32 Amentotaxus argotaenia 33 Taxus wallichiana (b) Cephalotaxus sinensis Sciadopitys verticillata

Nageia s 34 Podocarpus

Dacrycarpus p 37 Acmopyle Phyllocladus u 35 Agathis o

40 36/M Wollemia r Araucaria Picea g 39/O Cathaya t Pinus 41/P Larix u 38/N Abies Keteleeria O Cedrus Ginkgo Cycas

350 300 250 200 150 100 50 0 (Ma)

Fig. S2. Divergence times for the Cupressaceae based on (A) the 56-taxon dataset and (B) the 144-taxon dataset, with fossil calibration points and key nodes indicated. Light blue bars represent 95% highest posterior density intervals for age estimates. The red line indicates the Cretaceous/Tertiary boundary. Light orange shading represents the breaking up of Pangea into Laurasia and Gondwana.

Mao et al. www.pnas.org/cgi/content/short/1114319109 5of10 Jurassic E Cretaceous L Cretaceous P Eocene O M

1

2

3

4

5

6

Run1: Uniform priors, A to P (P:[306.2, 366.8]) s 7

e Run2: Uniform priors, A to O, P: [306.2, 351.7]

d Run3: Uniform priors, A to O, P: [306.2, 336.5]

o 8 Run4, Uniform priors, A to O, P: [306.2, 321.4]

N Run5,Uniform priors, P, subset VND Run6,Uniform priors, P, subset NVND 9 Run7, Lognormal priors, P, subset VND; uniform priors, subset NVND Run8, Uniform priors, A to P + Wa 10 Run9, Uniform priors, A to P, 56 taxa

34

38

40

41

450 400 350 300 250 200 150 100 50 0 Million years ago (Ma)

Fig. S3. Divergence time estimates for nodes 1–10 (see node descriptions in Table 1), the crown of Conifer clade II (node 34), Pinaceae (node 38), (Node 40), and Acrogymnospermae (Node 41) obtained with different calibration schemes and datasets. Gray bars represent age estimates from the 56-taxon dataset; bars of other colors represent age estimates from the 144-taxon dataset. Pink bars represent age estimates with lognormal priors for a subsetof calibrations; bars of other colors represent age estimates with uniform priors. Gray and dark-blue bars represent age estimates with calibrations A through P (Table S4); light-blue, purple, and green bars represent age estimates with calibrations A through O, with the age ranges for calibration P constrained to [306.2, 351.7], [306.2, 366.5], or [306.2, 321.4] Ma. Yellow bars represent age estimates with calibration P plus calibrations C, D, H, I, M, N, and O (subset VND). Orange Legend continued on following page

Mao et al. www.pnas.org/cgi/content/short/1114319109 6of10 bars represent age estimates with calibration P and calibrations A, B, E, F, G, J, K, and L (subset NVND). Red bars represent age estimation with calibrations A–P and Wa. Pink bars represent age estimate with calibration P and subset VND set as lognormal priors and calibration subset NVND set as uniform priors. Light orange shading represents the breaking-up of Pangea into Laurasia and Gondwana.

0.98 N N N Juniperus N American serrate clade ()15 species 0.93 0.93 A A A Juniperus QTP Clade ()9 species 0.99 N N () 0.45 N Juniperus N American smooth leaf clade 8 species A E N A A A E Juniperus sabina N A 0.20 0.50 A A Juniperus semiglobosa 0.41 A E A Juniperus microsperma 0.98 N A A Juniperus procumbens 0.93 A A N E 0.40 A Juniperus chinensis 0.39 A 0.79 E E Juniperus thurifera E E 0.77 E N E 0.34 E E E Juniperus excelsa A F Juniperus procera E 0.22 E E Juniperus drupacea A E 0.47 N A E N A E Juniperus communis 0.37 A A Juniperus taxifolia 0.39 A A A Juniperus rigida 0.33 A A Juniperus formosana A 0.54 F E E Juniperus oxycedrus E 0.97 E Juniperus deltoides 0.99 S N N Hesperocyparis ()12 species U N N 0.92 0.55 0.66 N Callitropsis nootkatensis A A A Xanthocyparis vietnamensis 0.78 A A A Cupressus QTP Clade (4 species) E 0.89 E E 0.94 A E A Cupressus jiangeensis A 0.89 A A 0.39 A Cupressus chengiana A A Microbiota decussata 0.38 A A 0.92 A Platycladus orientalis 0.84 E E Tetraclinis articulata N E A 0.29 N E N E Tetraclinis N American & European fossils Dispersal resulting in range expansion 0.65 N N Calocedrus decurrens A A N 0.34 A E Calocedrus macrolepis Cladogenesisby vicariance E E Calocedrus European fossils A Chamaecyparis formosensis A A 0.97 Local extinction 0.72 A Chamaecyparis pisifera N N

e

a N N Chamaecyparis lawsoniana

e N 0.65 A A Chamaecyparis obtusa d N A 0.59 A E 0.86 i 0.65 E E Chamaecyparis European fossils o 0.50 A 0.53 s 0.32 N N A Fokienia hodginsii

s N

e N Fokienia N American fossils r N Chamaecyparis N American fossils

p

u A A 0.92

C N A N N Thuja occidentalis N A 0.26 N N N Thuja plicata 0.94 0.56 A A Thuja koraiensis N A E E N A E Thuja European fossils 0.46 N 0.31 N Thuja N American fossils A A Thujopsis dolabrata U U CoreCallitris () 6 species U U Actinostrobus acuminatus N U 0.63 U 0.99 U Actinostrobus pyramidalis S 0.95 U Callitris drummondii U U U Callitris macleayana U Callitris sulcata U U 0.42 U Neocallitropsis pancheri S 0.76 S F F Widdringtonia ()4 species 0.49 U U Diselma archeri S 0.30 S U S S Fitzroya cupressoides S U 0.87 U U Fitzroya Australian fossils e 0.46 U Libocedrus plumosa a S U U 0.99 e 0.89 U Libocedrus bidwillii

d

N 0.52 i S S Pilgerodendron uviferum o S S Austrocedrus chilensis r S 0.47 0.88 t U i U Austrocedrus Australasian fossils

l

l U U Papuacedrus papuana

a 0.76 S S Papuacedrus S Amercian fossils C 0.99 N Taxodium mucronatum N N 0.81 N Taxodium distichum N E E E Taxodium European fossils 0.53 E A Glyptostrobus pensilis N 0.66 N E 0.68 0.55 E Glyptostrobus European fossils

e N 0.66 N Taxodium N American fossils N a Tax 0.17 N Glyptostrobus N American fossils

e E A A Cryptomeria japonica 0.86 c E E Cryptomeria European fossils

a N Sequoia sempervirens 0.62 N 0.92 s 0.87 N N N Sequoiadendron giganteum

s 0.50 N S U Austrosequoia e N N A E Sequoia& Sequoiadendron related fossils r Seq 0.18 A Metasequoia glyptostroboides

p N A A 0.37 N A E Metasequoia N Hemisphere fossils

u 0.90 N 0.31 U U Athrotaxis S S 0.51 C Ath S Athrotaxis S Amercian fossils 0.65 N N Athrotaxites berryi A A Taiwania cryptomerioides 0.40 E E Taiwania European fossils 0.39 A A 0.64 Tai A Taiwania Asian fossils A 0.25 N N Taiwania N American fossils A Cunninghamia lanceolata A 0.64 0.52 A 0.79 N Cunninghamia NAmerican fossils Cun A A Cunninghamia related fossil fromAsia A 0.81 E Cunninghamia related fossil from Europe A 0.38 0.34 A A Sewardiodendron laxum N A N S Austrohamia minuta 0.33 A A Austrohamia acanthobractea A 0.36 N A Amentotaxaceae A 0.21 A 0.30 N A E Taxaceae sensu stricto A Cephalotaxaceae A Sciadopityaceae

250 200 150 100 50 0 (Ma)

Fig. S4. The likelihood-based AAR for living and extinct members of Cupressaceae, which is the basis for Fig. 2C (scenario 1 in SI Text). (Right) The AARs with the highest likelihood are shown as colored boxes at each node. (Left) The six areas used in the analyses and the modeled biogeographic processes. Single-area boxes indicate an ancestor confined to a single geographic area; combined boxes indicate an ancestor with a distribution encompassing two or more areas; two boxes separated by a space indicate the ancestral ranges inherited by each of the daughter lineages arising from the respective ancestor. For nodes with alternative reconstructions (within log2 likelihood units of the maximum), the relative probability of the global likelihood for the optimal reconstruction is given. Extinct lineages known from fossils are indicated by dashed lines.

Mao et al. www.pnas.org/cgi/content/short/1114319109 7of10 Ginkgo biloba Pinus sylvestris Pinus sylvestris Compsostrobus neotericus (f) Sciadopitys verticillata (h) Sciadopitys verticillata Cedrus deodara Cunninghamia lanceolata Cunninghamia lanceolata Abies firma Taiwania cryptomerioides Taiwania cryptomerioides (a) Keteleeria davidiana Athrotaxis cupressoides Athrotaxis cupressoides Larix occidentalis Sequoioideae Cathaya argyrophylla Taxodioideae Taxodioideae Callitroideae Callitroideae Pinus strobus Thujopsis dolabrata Thujopsis dolabrata Pityostrobus bernissartensis Thuja plicata Thuja plicata Podocarpus macrophyllus Thuja polaris Fokienia ravenscragensis Fokienia hodginsii Fokienia hodginsii Araucaria mirabis Chamaecyparis lawsoniana Chamaecyparis lawsoniana Scidopitys verticillata Calocedrus decurrens Calocedrus decurrens Cryptomeria japonica Tetraclinis articulata Tetraclinis articulata Amentotaxus argotaenia Microbiota decussata Microbiota decussata Platycladus orientalis Platycladus orientalis Pinus sylvestris Hesperocyparis bakeri Hesperocyparis bakeri Sciadopitys verticillata Cupressus funebris Cupressus funebris (b) Hughmillerites juddii Xanthocyparis vietnamensis Xanthocyparis vietnamensis Cunninghamia lanceolata Callitropsis nootkatensis Callitropsis nootkatensis Taiwania cryptomerioides Juniperus Juniperus Athrotaxis cupressoides Sequoioideae Taxodioideae Pinus sylvestris Callitroideae Sciadopitys verticillata Cupressoideae (i) Austrohamia minuta Austrohamia acanthobractea Sewardiodendron laxum Pinus sylvestris Cunninghamia lanceolata Sciadopitys verticillata (c) Taiwania cryptomerioides Cunninghamia lanceolata Athrotaxites berryi Taiwania cryptomerioides Athrotaxis cupressoides Athrotaxis ungeri Metasequoia glyptostroboides Athrotaxis cupressoides Metasequoia sp Metasequoia glyptostroboides  Sequoia sempervirens Sequoia sempervirens Sequoiadendron giganteum Sequoiadendron giganteum Cryptomeria japonica Cryptomeria japonica Glyptostrobus pensilis Glyptostrobus pensilis Taxodium distichum Taxodium distichum Papuacedrus papuana Callitroideae Austrocedrus chilensis Cupressoideae Libocedrus plumosa Pilgerodendron uviferum Pinus sylvestris Pinus sylvestris (g) Sciadopitys verticillata Diselma archeri Sciadopitys verticillata (d) Cunninghamia lanceolata Fitzroya cupressoides Cunninghamia lanceolata Taiwania cryptomerioides Fitzroya acutifolia Taiwania cryptomerioides Athrotaxis cupressoides Callitris macleayana Athrotaxis cupressoides Sequoioideae Callitris leaensis Sequoiadendron giganteum Taxodioideae Neocallitropsis pancheri Sequoia semprevirens Papuacedrus papuana Actinostrobus pyramidalis Austrosequoia wintonensis Papuacedrus prechilensis Callitris drummondii Metasequoia glyptostroboides Austrocedrus chilensis Thujopsis dolabrata Taxodium distichum Pilgerodendron uviferum Thuja plicata Glyptostrobus pensilis Libocedrus plumosa Fokienia hodginsii Cryptomeria japonica Widdringtonia nodiflora Chamaecyparis lawsoniana Callitroideae Fitzroya cupressoides Calocedrus decurrens Cupressoideae Diselma archeri Calocedrus suleticensis Callitris macleayana Tetraclinis articulata Neocallitropsis pancheri Tetraclinis salicornioides Pinus sylvestris Actinostrobus pyramidalis Platycladus orientalis Sciadopitys verticillata (e) Callitris drummondii Microbiota decussata Cunninghamia lanceolata Thujopsis dolabrata Cupressus funebris Taiwania cryptomerioides Thuja plicata Hesperocyparis bakeri Athrotaxis cupressoides Fokienia hodginsii Xanthocyparis vietnamensis Metasequoia glyptostroboides Chamaecyparis lawsoniana Callitropsis nootkatensis Sequoia sempervirens Calocedrus decurrens Juniperus virginiana Sequoiadendron giganteum Tetraclinis articulata Juniperus recurva Cryptomeria japonica Platycladus orientalis Juniperus phoenicea Glyptostrobus pensilis Microbiota decussata Juniperus indica Glyptostrobus sp Cupressus funebris Taxodium distichum Xanthocyparis vietnamensis Juniperus pauli Callitroideae Callitropsis nootkatensis Juniperus oxycedrus Cupressoideae Hesperocyparis bakeri Juniperus drupacea Juniperus

Fig. S5. Strict consensus trees reconstructed using a total-evidence approach (SI Text). (A) Plot shows phylogenetic positions of Compsostrobus neotericus, Pityostrobus bernissartensis, and Araucaria mirabilis.(B–H) Plots illustrate phylogenetic positions of Hughmillerites juddii, Athrotaxis ungeri, Austrosequoia wintonensis, Glyptostrobus sp., Thuja polaris, Papuacedrus prechilensis,andFokienia ravenscragensis.(I) Plot shows the phylogenetic positions of the remaining 10 Cupressaceae fossils. Extinct lineages known from fossils are indicated by dashed lines, and their names are highlighted on a gray background.

Mao et al. www.pnas.org/cgi/content/short/1114319109 8of10 Fig. S6. Distributions of fossil (yellow solid circles) and living (green shading or green solid circles) Cupressaceae. (A) Cunninghamioideae. (B) Sequoioideae. (C) Taxodioideae. All three subfamilies underwent range contraction over time. Fossil distribution maps were compiled from the Paleobiology Database (http:// paleodb.org).

Mao et al. www.pnas.org/cgi/content/short/1114319109 9of10 (a) (b)

Dχ SS

Fossil calibration node Fossil calibration node (c) (d) All Calibration Nodes

Dχ S

SS Fossil calibration node removed

Fig. S7. Cross-validation of fossil calibrations A–O and Wa (Table S4) based on the 56-taxon dataset. (A) Histogram of the mean deviation (D) (1) between molecular and fossil age estimates for all nodes, using a single fossil-dated node as a calibration point. (B) Histogram of the SS values (1) for a given fossil calibration node when it was used as the sole calibration point. (C) 2D plot for a given fossil calibration node with SS values (the sum of the squared differences between the molecular and fossil age estimates at all other fossil-dated nodes) (1) on the x axis and the mean deviation on the y axis. (D) Plot illustrating the effect on s (an average squared deviation for the deviation between molecular and fossil age estimates for all fossil calibrations in the analysis) of removing fossil calibration points (1). Open points indicate that the removal of the respective fossil calibration resulted in a significant reduction in the variance of s, based on a one-tailed Fisher’s test (1). A maximum constraint of 366.8 Ma was placed on the older bound of calibration point P based on the arguments provided in Table S4.

1. Near TJ, Meylan PA, Shaffer HB (2005) Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am Nat 165:137–146.

Other Supporting Information Files

Table S1 (DOC) Table S2 (DOC) Table S3 (DOC) Table S4 (DOC) Table S5 (DOC) Table S6 (DOC)

Mao et al. www.pnas.org/cgi/content/short/1114319109 10 of 10