Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae supporting information



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Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae - supporting information


31 Figures

3 Tables




Figure S1: Chronogram calibrated only at the root. Maximum-clade-credibility chronogram obtained in a Bayesian phylogenetic analysis of a concatenated alignment of nuclear ITS and chloroplast matK and ndhF, calibrated only at the root. Branch lengths have been scaled according to time, with nodal ages representing median posterior estimates. Nodes are labelled with posterior probabilities and blue bars represent the 95% credibility intervals of the age estimates.


Figure S2: Chronogram calibrated using fossil pollen. Maximum-clade-credibility chronogram obtained in a Bayesian phylogenetic analysis of a concatenated alignment of nuclear ITS and chloroplast matK and ndhF, calibrated using the most parsimonious placement of fossil pollen data (supporting information Figs. S4-S29). Branch lengths have been scaled according to time, with nodal ages representing median posterior estimates. Nodes are labelled with posterior probabilities and blue bars represent the 95% credibility intervals of the age estimates. Calibrated nodes are labelled with letters A-I (see Table S2).


Figure S3: Chronogram calibrated using macrofossils. Maximum-clade-credibility chronogram obtained in a Bayesian phylogenetic analysis of a concatenated alignment of nuclear ITS and chloroplast matK and ndhF, calibrated using macrofossils. Branch lengths have been scaled according to time, with nodal ages representing median posterior estimates. Nodes are labelled with posterior probabilities and blue bars represent the 95% credibility intervals of the age estimates. Calibrated nodes are labelled with letters A and J-N (see Table S2).


Figure S4. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Cretaceous M. lisamae (Boltenhagen, 1976), as determined by a backbone-constraint analysis.


Figure S5. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Paleocene M. mesonesus (Couper, 1960), as determined by a backbone-constraint analysis.


Figure S6. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Eocene Myrtaceidites mesonesus (Pocknall, 1991), as determined by a backbone-constraint analysis.


Figure S7. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of the fossil Myrtaceidites mesonesus (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.


Figure S8. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Eocene Myrtaceidites parvus (Bratzeva, 1983), as determined by a backbone-constraint analysis.



Figure S9. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Early Eocene Myrtaceidites tenuis (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S10. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Early Eocene Myrtaceidites tenuis (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S11. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Early Eocene Myrtaceidites tenuis (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S12. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Early Eocene Myrtaceidites tenuis (Harris, 1965), as determined by a backbone-constraint analysis.


Figure S13. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Eocene Myrtaceidites eucalyptoides (Alley et al., 1996), as determined by a backbone-constraint analysis.



Figure S14. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Eocene Myrtaceidites eucalyptoides (Alley et al., 1998), as determined by a backbone-constraint analysis.



Figure S15. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Oligocene Myrtaceidites eucalyptoides (Hekel, 1972), as determined by a backbone-constraint analysis.



Figure S16. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Early Oligocene Myrtaceidites eucalyptoides (Macphail and Stone, 2004), as determined by a backbone-constraint analysis.



Figure S17. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an unplaced Eocene Myrtaceidites from the Pilbara (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S18. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an unplaced Late Miocene to early Pliocene Myrtaceidites from Ararat, (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S19. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an unplaced Early Pliocene Myrtaceidites from Grange Burn (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S20. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an unplaced Late Eocene Myrtaceidites from Hatfield (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S21. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an unplaced Early Eocene Myrtaceidites from the Pilbara (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S22. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an unplaced Early Eocene Myrtaceidites from the Pilbara (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.


Figure S23. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Eocene Myrtaceidites verrucosus (Thornhill and Macphail, in review), as determined by a backbone-constraint analysis.



Figure S24. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Eocene Myrtaceidites verrucosus (Alley et al., 1996), as determined by a backbone-constraint analysis.



Figure S25. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Middle Eocene Myrtaceidites verrucosus (Graham, 1985), as determined by a backbone-constraint analysis.



Figure S26. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Late Oligocene Myrtaceidites verrucosus (Pocknall, 1982), as determined by a backbone-constraint analysis.



Figure S27. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of a Middle Eocene Myrtaceidites verrucosus (Romero and Zamaloa, 1985), as determined by a backbone-constraint analysis.


Figure S28. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Oligocene Myrtaceidites oceanicus (Kemp and Harris, 1977), as determined by a backbone-constraint analysis.


Figure S29. Root-only calibrated BEAST chronogram mapped with the most parsimonious (blue), most parsimonious + 1 (red), and most parsimonious + 2 (orange) placements of an Early Eocene Myrtaceidites eugeniioides (Harris, 1965), as determined by a backbone-constraint analysis.


Figure S30. Root only calibrated maximum-clade-credibility chronogram optimized with colpi morphology as observed in light microscopy. Node E represents the placement of Myrtaceidites sp. as the crown of Leptospermeae and Chamelaucieae in Figure 1. Node I represents the placement of M. eugeniioides as a Syzygieae stem calibration in Figure 1.



Figure S31 Root only calibrated maximum-clade-credibility chronogram optimized with extant geographic locality. Nodes F, G, and H represent the placement of M. verrucosus calibrations in Figure 1

Table S1. Taxa and sequences used in the Bayesian phylogenetic analysis

Taxon

GenBank accession

ITS

matK

ndhF

Acca sellowiana (O. Berg) Burret

AM234067.1

AY525128.1

AY498783.1

Acmena divaricata Merr. & L.M.Perry

AY187161.2

DQ088538.1

DQ088463.1

Acmena graveolens (F.M. Bailey) L. S. Sm.

AY187163.2

AF368194.1

AY498759.1

Acmena mackinnoniana B.Hyland

AY187165.2

DQ088543.1

DQ088467.1

Acmena smithii (Poir.) Merr. & L.M.Perry

AM234137.1

AM489974.1

AY498760.1

Acmenosperma claviflorum (Roxb.) Kausel

AY187169.2

DQ088546.1

DQ088470.1

Actinodium cunninghamii Schauer

-

AF489394.2

AY498761.1

Agonis flexuosa (Willd.) Sweet

DQ499115.1

AF184711.2

AY498762.1

Amomyrtus meli (Phil.) D.Legrand & Kausel

AM234069.1

AM489976.1

-

Anetholea anisata (Vickery) Peter G.Wilson

AM234138.1

AF368195.2

DQ088471

Angophora costata Britten

AF058455.1

-

AM235418.1

Angophora hispida (Sm.) Blaxell

-

AF368196.2

AY498763.1

Archirhodomyrtus beckleri (F.Muell.) A.J. Scott

-

AF368197.1

AY498764.1

Arillastrum gummiferum (Brongn. & Gris) Pancher ex Baill.

AF058454

AF368198.2

AY498765.1

Asteromyrtus symphyocarpa (F.Muell.) Craven

EF041509.1

AF184719.1

-

Babingtonia cunninghamii (Schauer) A.R.Bean

-

AF489356.2

EF581215.1

Babingtonia densifolia (Sm.) F.Muell.

-

AF489357.2

EF581216.1

Babingtonia jucunda (S.T.Blake) A.R.Bean

-

EF581198.1

EF581218.1

Babingtonia tozerensis A.R. Bean

-

AF368199.3

AY498767.1

Backhousia citriodora F. Muell.

-

AY525129.1

AY498768.1

Backhousia myrtifolia Hook.

EF026609.1

AF368200.2

AY498769.1

Baeckea frutescens L.

-

AF489365.1

AY498770.1

Baeckea ovalifolia (F.Muell.) F.Muell.

-

EF581206.1

EF581225.1

Beaufortia orbifolia F. Muell.

AF048888.1

AY521530.1

AY498766

Blepharocalyx cruckshanksii (Hook. & Arn.) Nied

AM234070.1

AM489978.1

-

Blepharocalyx salicifolius (Kunth) O.Berg

AM234084.1

AM489979.1

-

Blepharocalyx tweediei (Hook. et Arn.) O. Berg

-

AY521531.1

AY498772.1

Callistemon polandii F.M. Bailey

AF048856.1

AF184705.3

AY498773.

Calothamnus validus S. Moore

-

AF184704.2

AY498774.1

Calyptranthes concinna DC.

AM234103.1

AM489980.1

AY498775.1

Calyptranthes pallens Griseb.

-

AF368201

AY498776.1

Calytrix tetragona Labill.

HM160102/03

AF489396.1

AY498777.1

Campomanesia guazumifolia (Cambess.) O.Berg

AM234076.1

AM489982.1

DQ088473.1

Chamelaucium uncinatum Schauer

EF026605.1

AY259816.1

-

Choricarpia subargentea (C.T. White) L.A.S.Johnson

EF026610.1

AF368202.2

AY498778.1

Cloezia floribunda Brongn. & Gris

AF172767.1

AY521533.1

-

Corymbia variegata (F. Muell.) K.D.Hill & L.A.S.Johnson

AF390462.1

AF368203.2

-

Darwinia fascicularis Rudge

-

AF368204.2

AY498780.1

Decaspermum humile (G. Don) A.J. Scott

AM234128.1

AY521534.1

AY498781.1

Eucalyptopsis papuana C.T.White

AF190354.1

AF368205.2

-

Eucalyptus curtisii Blakely & C.T.White

AF390524.1

AF368206.2

AY498781

Eucalyptus globulus Labill.

AY615678.1

AY521535.1

AY780259

Eugenia uniflora L.

AM234088.1

AF368207.2

DQ088457.1

Euryomyrtus ramosissima (A.Cunn.) Trudgen

-

AF489376.1

AY498824.1

Heteropyxis natalensis Harv.

HM160104/05

AF368208.2

AY498784.1

Hexachlamys edulis (O. Berg) Klaus et Legr.

-

AY525131.1

AY498785.1

Homalocalyx aureus (C.A.Gardner) Craven

HM160106/07

-

AY498785

Homoranthus darwinioides (Maiden & Betche) Cheel

HM160108

-

AY498786.1

Kjellbergiodendron celebicum (Koord.) Merrill

HM160109/10

AF368209.1

AY498788

Kunzea capitata (Sm.) Heynh.

-

AF184721.1

AY498790

Legrandia concinna (Phil.) Kausel

AM234072.1

AF184724.1

-

Leptospermum scoparium J.R.Forst. & G.Forst.

AM234142.1

AY521538.1

-

Leptospermum spectabile Joy Thomps.

-

AY521539.1

AY498791

Leptospermum trinervium (Sm.) Joy Thomps.

-

AF184735.2

AY498792

Lindsayomyrtus racemoides (Greves) Craven

HM160111/12

AF184706.2

AY498793

Lophomyrtus bullata Burret

AM234145.1

AM489992.1

-

Lophostemon confertus (R.Br.) Peter G.Wilson & J.T.Waterh.

AF048897.1

AF184707.2

AY498794

Luma apiculata (DC) Burret

AM234101.1

AM489995.1

AY498795

Lysicarpus angustifolius (Hook.) Druce

-

AF368210.2

AY498796.1

Melaleuca nesophila F.Muell.

AF294591.1

AY525135.1

AY498797

Melaleuca viridiflora Gaertn.

AF294603.1

AF184708.1

AY498798.1

Metrosideros carminea W.R.B.Oliver

AF211498.1

AY521541.1

AY498799

Metrosideros diffusa (G. Forst.) Sm.

AF211500.1

AY521542.1

AY498800

Metrosideros macropus Hook. & Arn.

AF172745.1

AF368212.2

AY498801

Metrosideros nervulosa C.Moore & F.Muell.

AF172747.1

DQ088535.1

DQ088458.1

Micromyrtus ciliata (Sm.) Druce

HM160113/14

AF489400.1

-

Myrceugenia leptospermoides (DC.) Kausel

AM234075.1

AM489999.1

-

Myrciaria vexator McVaugh

-

AY521544.1

AY498804.1

Myrteola nummularia (Lam.) O.Berg

AM234068.1

AM490008.1

-

Myrtus communis L.

AM234149.1

AM490009.1

AF215593.1

Neomyrtus pedunculata (Hook.f.) Allan

AM234144.1

AM490010.1

-

Ochrosperma lineare (C.T.White) Trudgen

-

AF489384.2

EF581229.1

Ochrosperma oligomerum (Radlk.) A.R.Bean

-

AF489385.2

EF581230.1

Osbornia octodonta F.Muell.

EF041844.1

AF368213.2

DQ088459.1

Pericalymma ellipticum (Endl.) Schauer in J.G.C.Lehmann

EF026604.1

AF184740.1

AY498806.1

Pileanthus filifolius Labill.

-

EF581210.1

EF581231

Pilidiostigma papuanum (Lauterb.) A.J. Scott

-

AF368214.1

AY498807.1

Piliocalyx concinnus A.C.Sm.

EF026615.1

DQ088550.1

DQ088476.1

Pimenta racemosa (Mill.) J.W. Moore

AM234082.1

AY521545.

AY498808

Psidium cattleianum Sabine

AM234080

AB354959.1

HM160101

Psiloxylon mauritianum (Hook. f.) Baill.

EF026606.1

AF368215.2

AY498825

Qualea grandiflora Mart. (Vochysiaceae)

-

AF368216.1

AY498829

Rhodamnia argentea Benth.

AM234129.1

AF368217.1

AY498810

Rhodomyrtus macrocarpa Benth.

-

AY525137.1

AY498811

Sphaerantia chartacea Peter G. Wilson & B. Hyland

HM160115/16

AY521547.1

-

Stockwellia quadrifida D.J. Carr, S.G.M.Carr & B.Hyland

AF058452.1

AY525138.1

AY498812

Syncarpia glomulifera (Sm.) Nied.

HM160117/18

AF368220.2

AY498813

Syzygium aromaticum (L.) Merr. & Perry

EF026622.1

-

DQ088485.1

Syzygium australe (Link) B. Hyland

AY187177.2

AF368221.1

-

Syzygium cumini Skeels

FM887016.1

AY525140.1

AY498814.1

Syzygium maire (A.Cunn.) Sykes & Garn.-Jones

AM234136.1

DQ088589.1

DQ088508.1

Syzygium samarangense (Blume) Merr. & L.M. Perry




AY525141.1

AY498815.

Syzygium wilsonii (F.Muell.) B.Hyland

AY187218.2

DQ088618

DQ088530.1

Tepualia stipularis (Hook. & Arn.) Griseb.

AM234071.1

AF368222.2

-

Thaleropia queenslandica (L.S. Sm.) Peter G. Wilson

AY264945.1

AF368223

DQ088460.1

Thryptomene saxicola (Hook.) Schauer

-

AF184709

AY498816

Tristania neriifolia (Sieber ex Sims) R.Br.

EF026608.1

AF368224.2

AY498817.1

Tristaniopsis laurina (Sm.) Peter G. Wilson & J.T. Waterh.

EF041514.1

AF184710.2

AY498818.1

Ugni molinae Turcz.

AM234143.1

AY525142.1

AY498819

Uromyrtus australis A.J. Scott

-

AY527230.1

AY498820.1

Verticordia pennigera Endl.

-

AF489402.2

AY498821.1

Vochysia hondurensis Sprague (Vochysiaceae)

-

AY572446.1

AY498832

Waterhousea floribunda (F. Muell.) B. Hyland

AY187221.2

DQ088620.1

DQ088531.1

Waterhousea hedraiophylla (F. Muell.) B. Hyland

AY187222.2

DQ088621.1

DQ088532.1

Xanthomyrtus papuana Merr. & L.M. Perry

AM234147.1

AF368226.2

-

Xanthostemon chrysanthus (F.Muell.) Benth.

EF041515.1

AF368227.2

EU410135.1

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