Early Photosynthetic Eukaryotes Inhabited Low Salinity Habitats

Early photosynthetic eukaryotes inhabited low salinity habitats

SUPPORTING INFORMATION

Patricia Sánchez-Baracaldo1, John A. Raven2,3, Davide Pisani4, and Andrew H. Knoll5

1School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK; 2Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; 3Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; 4School of Biological Sciences and School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK; 5Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138.

Corresponding author: ([email protected])

Supplementary Figures

Supplementary Figure S1. Genomic tree showing the deep branching relationships for Cyanobacteria. Topology estimated using RaxML (Maximum Likelihood). Bootstrap values are 100 for branches that show no values; values are reported for those that show relatively low values.

Anabaena PCC7122 9 8 Nostoc 0708 Raphidiopsis D9 Nodularia CCY9414 7 2 5 2 Nostoc PCC73102 Nostoc PCC7120 Calothrix PCC6303 Richelia HH01 8 1 Richelia HM01 9 8 Fischerella JSC11 Arthrospira PCC8005 Lyngbya PCC8106 Trichodesmium IMS101 Oscillatoria PCC6506 Crocosphaera WH0003 Cyanothece CCY0110 9 7 Cyanothece PCC8801 6 1 Synechocystis PCC6803 Microcystis NIES843 9 8 Cyanothece PCC7424 Pleurocapsa PCC7327 Leptolyngbya PCC7376 Synechococcus PCC7002 9 1 Prochloron Solomon Prochloron Fiji Lyngbya 3L P marinus MIT9515 P marinus AS9601 P marinus MIT9211 P marinus MIT9303 Synechococcus WH8016 Synechococcus CC9605 Cyanobium PCC7001 Cyanobium PCC6307 Synechococcus CB0101 Synechococcus RCC307 Synechococcus PCC6301 Leptolyngbya PCC7375 Synechococcus PCC7335 Nodosilinea PCC7104 Cyanothece PCC7425 Thermosynechococcus BP1 Acaryochloris MBIC11017 Pseudanabaena PCC6802 Pseudanabaena PCC7429 Pseudanabaena PCC7367 Synechococcus JA-3-3Ab Synechococcus JA-2-3B'a(2-13) Gloeobacter PCC7421

0.2

Supplementary Figure S2. Maximum Likelihood phylogeny of Cyanobacteria and photosynthetic eukaryotes. Bootstrap values are 100 for branches that show no values; values are reported for those that show lower values.

Cyanothece CCY0110 Crocosphaera WH0003 Cyanothece PCC8801 9 1 6 7 Synechocystis PCC6803 6 3 Microcystis NIES843 Cyanothece PCC7424 Pleurocapsa PCC7327 Leptolyngbya PCC7376 8 7 Synechococcus PCC7002 Prochloron Fiji Prochloron Solomon Lyngbya 3L 9 5 Microcoleus PCC7420 Arthrospira PCC8005 Lyngbya PCC8106 Trichodesmium IMS101 Microcoleus FGP2 Oscillatoria PCC6506 Nostoc 0708 Raphidiopsis D9 3 5 Anabaena PCC7122 5 2 Nodularia CCY9414 Nostoc PCC73102 Nostoc PCC7120 Calothrix PCC6303 Richelia HM01 9 1 Richelia HH01 Fischerella JSC11 P marinus MIT9515 9 7 P marinus AS9601 P marinus MIT9211 P marinus MIT9303 Synechococcus CC9605 Synechococcus WH8016 Paulinella Cyanobium PCC6307 Cyanobium PCC7001 8 4 Synechococcus CB0101 Synechococcus RCC307 Synechococcus PCC6301 Synechococcus PCC7335 Leptolyngbya PCC7375 Nodosilinea PCC7104 Cyanothece PCC7425 Thermosynechococcus BP1 Acaryochloris MBIC11017 Spinacia 7 1 Coffea Buus Ranunculus 9 1 Calycanthus 8 7 Illicium Amborella Nymphaea Welwitschia Gnetum Ephedra Cryptomeria 8 4 Pinus Cycas 6 9 Adiantum Angiopteris Psilotum Aneura Ptilidium 9 3 Marchantia 8 8 Syntrichia 7 2 Physcomitrella Anthoceros Chaetosphaeridium Staurastrum Zygnema Chara 7 9 Klebsormidium Volvox Chlamydomonas Dunaliella Scenedesmus Schizomeris Stigeoclonium Floydiella Oedogonium 5 2 Parachlorella 1 7 Pedinomonas 2 4 Bryopsis 2 8 Oocystis 4 8 Coccomya 4 2 4 9 Leptosira Pseudendoclonium Oltmannsiellopsis 4 1 Nephroselmis 8 1 Pycnococcus Ostreococcus Micromonas 9 5 Monomasti Pyramimonas Prasinococcus Prasinoderma Verdigellas 7 7 Chlorokybus Mesostigma Fistulifera Phaeodactylum Synedra 5 8 Thalassiosira 6 6 Odontella Porphyra pur Porphyra yez Gracilaria Cyanidium Cyanidioschyzon Cyanophora Gloeomargarita 9 0 Pseudanabaena PCC7367 Pseudanabaena PCC6802 Pseudanabaena PCC7429 Synechococcus JA-3-3Ab Synechococcus JA-2-3B'a(2-13) Gloeobacter PCC7421

0.2

Supplementary Figure S3. Bayesian phylogeny of Cyanobacteria and photosynthetic eukaryotes. Numbers above branches indicates posterior probability. Branches with no numbers had 100% posterior probability. Convergence statistics: Number of Cycles: 82244; bpcomp maxdiff = 0.219156; Tracecomp effsize was always > 68 except for statalpha where effsize = 29; Tracecomp maxdiff was always < 0.53 except for statalpha that had a maxdiff = 0.93.

Synechocystis PCC6803 Microcystis NIES843 Cyanothece PCC7424 Cyanothece CCY0110 Crocosphaera WH0003 Cyanothece PCC8801 Pleurocapsa PCC7327 Prochloron Solomon Prochloron Fiji 0.99 Synechococcus PCC7002 Leptolyngbya PCC7376 Microcoleus PCC7420 Lyngbya 3L Lyngbya PCC8106 Arthrospira PCC8005 Trichodesmium IMS101 Oscillatoria PCC6506 Microcoleus FGP2 Raphidiopsis D9 Nostoc 0708 0.67 Anabaena PCC7122 Nodularia CCY9414 Nostoc PCC73102 Nostoc PCC7120 Calothrix PCC6303 Richelia HM01 Richelia HH01 Fischerella JSC11 Synechococcus PCC7335 Leptolyngbya PCC7375 Nodosilinea PCC7104 P marinus MIT9515 P marinus AS9601 P marinus MIT9211 P marinus MIT9303 Synechococcus WH8016 Synechococcus CC9605 Paulinella Cyanobium PCC7001 Cyanobium PCC6307 Synechococcus CB0101 Synechococcus RCC307 Synechococcus PCC6301 Spinacia Coffea Buus Ranunculus Calycanthus 0.98 Illicium Amborella Nymphaea Welwitschia Gnetum Ephedra Cryptomeria Pinus contorta Cycas 0.89 Angiopteris Adiantum Psilotum Anthoceros Ptilidium Aneura Marchantia Syntrichia Physcomitrella 0.83 Chaetosphaeridium Zygnema Staurastrum Chara Klebsormidium Stigeoclonium Schizomeris Floydiella Oedogonium Volvox Chlamydomonas Dunaliella Scenedesmus 0.84 Bryopsis 0.99 Pedinomonas Oocystis Pseudendoclonium Oltmannsiellopsis Parachlorella 0.98 0.95 Leptosira Coccomya 0.99 Pycnococcus Nephroselmis Ostreococcus Micromonas Monomasti Pyramimonas 0.71 Prasinoderma Prasinococcus Verdigellas Mesostigma Chlorokybus Cyanophora Phaeodactylum Fistulifera Synedra 0.98 Thalassiosira 0.9 Odontella Porphyra yez Porphyra pur Gracilaria Cyanidium Cyanidioschyzon Gloeomargarita Thermosynechococcus BP1 Cyanothece PCC7425 Acaryochloris MBIC11017 Pseudanabaena PCC7367 Pseudanabaena PCC6802 Pseudanabaena PCC7429 Synechococcus JA-3-3Ab Synechococcus JA-2-3B'a(2-13) Gloeobacter PCC7421

0.3

Supplementary Figure S4. Maximum Likelihood phylogeny including only eukaryotes.

Pycnococcus 28 Nephroselmis Oedogonium 100 Floydiella 94 Schizomeris 100 31 100 Stigeoclonium Scenedesmus 100 Dunaliella 100 Chlamydomonas 100 100 Volvox Pseudendoclonium 97 Oltmannsiellopsis 9 Parachlorella 64 28 Pedinomonas 41 Coccomya 63 Leptosira 5 Bryopsis 14 Oocystis 100 Monomasti 100 Ostreococcus 100 96 Micromonas Pyramimonas 91 Verdigellas 100 Prasinoderma 100 Prasinococcus Klebsormidium Chara 100 Zygnema 100 Staurastrum 100 Chaetosphaeridium Marchantia 100 100 Ptilidium 100 98 Aneura Syntrichia 77 100 Physcomitrella 78 Anthoceros Nymphaea Calycanthus 100 98 Ranunculus 100 99 Spinacia 99 91 100 66 Coffea Buus 88 Illicium 100 Amborella Pinus.contorta Ephedra 100 100 Welwitschia 98 100 100 100 89 Gnetum Cryptomeria Cycas Adiantum 56 100 Angiopteris Psilotum Mesostigma 100 Chlorokybus Cyanophora Cyanidioschyzon 100 Cyanidium Porphyra.pur 100 100 100 Porphyra.yez Gracilaria Phaeodactylum 48 100 100 Fistulifera 100 Synedra Odontella 57 Thalassiosira Paulinella

0.2

Supplementary Figure S5. Maximum Likelihood phylogeny including eukaryotes and Gloeomargarita.

Pyramimonas 95 Ostreococcus 100 100 Micromonas Monomasti Dunaliella 100 Chlamydomonas 100 100 Volvox

100 Scenedesmus Oedogonium 66 100 Floydiella 97 Schizomeris 100 Stigeoclonium 100 Coccomya 66 Leptosira 8 Bryopsis 19 Oocystis 100 51 37 Pedinomonas 34 Parachlorella 10 Pseudendoclonium 100 Oltmannsiellopsis Nephroselmis 25 Pycnococcus 92 Verdigellas 100 Prasinoderma 100 Prasinococcus Klebsormidium Chara Staurastrum 100 100 Zygnema Syntrichia 100 Physcomitrella 98 Aneura 100 100 Ptilidium 69 100 Marchantia Anthoceros Nymphaea 100 Amborella 100 83 Illicium 100 88 Calycanthus 100 99 Ranunculus 99 Buus 100 54 Coffea 99 Spinacia Cycas Welwitschia 100 88 83 100 100 Gnetum 100 Ephedra 100 Cryptomeria 64 Pinus.contorta Psilotum 100 Adiantum 55 Angiopteris Chaetosphaeridium Chlorokybus 100 Mesostigma Cyanidioschyzon 100 Cyanidium 100 Porphyra.pur 100 100 100 Porphyra.yez Gracilaria Fistulifera 50 100 100 Phaeodactylum 100 Synedra Odontella 48 Thalassiosira Cyanophora Gloeomargarita Paulinella

0.2

Supplementary Figure S6. Stochastic mapping analyses of the evolution of habitat. Phylogenetic tree including 119 taxa was estimated in Phylobayes 1.7a (1). A pie chart at each node indicates the Likelihoods for three character states as follows: blue circle = marine; yellow circle = freshwater, and red = brackish. In the analyses shown here, Parachlorella were treated as marine and Pedinomonas as freshwater (Supplementary Table S2).

Gloeobacter PCC7421 Synechococcus JA23Bprimea213 Synechococcus JA33Ab Pseudanabaena PCC7429 Pseudanabaena PCC6802 Pseudanabaena PCC7367 Acaryochloris MBIC11017 Cyanothece PCC7425 Thermosynechococcus BP1 Nodosilinea PCC7104 Leptolyngbya PCC7375 Synechococcus PCC7335 Synechococcus PCC6301 Synechococcus RCC307 Synechococcus CB0101 Cyanobium PCC6307 Cyanobium PCC7001 Paulinella Synechococcus CC9605 Synechococcus WH8016 P marinus MIT9303 P marinus MIT9211 P marinus AS9601 P marinus MIT9515 Fischerella JSC11 Richelia HH01 Richelia HM01 Calothrix PCC6303 Nostoc PCC7120 Nostoc PCC73102 Nodularia CCY9414 Anabaena PCC7122 Nostoc 0708 Raphidiopsis D9 Microcoleus FGP2 Oscillatoria PCC6506 Trichodesmium IMS101 Arthrospira PCC8005 Lyngbya PCC8106 Lyngbya 3L Microcoleus PCC7420 Leptolyngbya PCC7376 Synechococcus PCC7002 Prochloron Fiji Prochloron Solomon Pleurocapsa PCC7327 Cyanothece PCC8801 Crocosphaera WH0003 Cyanothece CCY0110 Cyanothece PCC7424 Microcystis NIES843 Synechocystis PCC6803 Gloeomargarita Cyanidioschyzon Cyanidium Gracilaria Porphyra pur Porphyra yez Odontella Thalassiosira Synedra Fistulifera Phaeodactylum Cyanophora Chlorokybus Mesostigma Verdigellas Prasinococcus Prasinoderma Pyramimonas Monomasti Micromonas Ostreococcus Nephroselmis Pycnococcus Coccomya Leptosira Parachlorella Oltmannsiellopsis Pseudendoclonium Oocystis Pedinomonas Bryopsis Scenedesmus Dunaliella Chlamydomonas Volvox Oedogonium Floydiella Schizomeris Stigeoclonium Klebsormidium Chara Staurastrum Zygnema Chaetosphaeridium Physcomitrella Syntrichia Marchantia Aneura Ptilidium Anthoceros Habitat Psilotum Adiantum Angiopteris Low salinity (freshwater) Cycas Pinus contorta Cryptomeria Marine Ephedra Gnetum Welwitschia Brackish Nymphaea Amborella Illicium Calycanthus Ranunculus Buus Coffea Spinacia

Supplementary Figure S7. Stochastic mapping analyses of the evolution of habitat. Phylogenetic tree including 119 taxa was estimated in Phylobayes 1.7a (1). A pie chart at each node indicates the Likelihoods for three character states as follows: blue circle = marine; yellow circle = freshwater, and red = brackish. In the analyses shown here Parachlorella and Pedinomonas were both treated as freshwater (Supplementary Table S2).

Supplementary Tables

Table S1. Gene composition of genomic dataset.

Gene Description COG category CcsA C-type cytochrome synthesis protein CP; O L14 Ribosomal protein L14 IP; J L20 Ribosomal protein L20 IP; J S11 Ribosomal protein S11 IP; J S12 Ribosomal protein S12 IP; J S19 Ribosomal protein S19 IP; J S2 Ribosomal protein S2 IP; J S3 Ribosomal protein S3 IP; J S4 Ribosomal protein S4 IP; J S7 Ribosomal protein S7 IP; J RpoB RNA polymerase beta and beta prime subunits IP; K RpoC1 RNA polymerase beta' subunit IP; K RpoC2 RNA polymerase beta' chain IP; K AtpA ATP synthase CF1 subunit A Met; C AtpB CF1 beta subunit of ATP synthase Met; C PetB Cytochrome b6 Met; C PetD Cytochrome b6/f complex subunit IV Met; C PsaC Photosystem I subunit VII Met; C RbcL Ribulose 1,5-bisphosphate carboxylase, large Met; G subunit PsaA Photosystem I p700 apoprotein A1 (Met); n.a. PsbA Photosystem II D1 protein (Met); n.a. PsbB CP47 chlorophyll apoprotein of photosystem II (Met); n.a. PsbC Photosystem II CP43 protein (Met); n.a. PsbD Photosystem II protein D2 (Met); n.a. PsbE Cytochrome b559 alpha chain (Met); n.a. Ycf3 Photosystem I assembly protein PC; R COG functional categories (http://www.ncbi.nlm.nih.gov/COG/): CP = Cellular processes IP = Information storage and processing Met = Metabolism PC = Poorly Characterized COG functional sub-categories: C = Energy production and conversion J = Translation, ribosomal structure and biogenesis K = Transcription O = Posttranslational modification, protein turnover, chaperones R = General function prediction only n.a. = not in COG database

Table S2. Character states for the evolution of habitat. Taxa included in this study. Abbreviated taxa names are listed for those analyses shown in Figs 2 and 3. Habitat was coded using multistate discrete character states as follows 0 = freshwater (0-0.5 ppt parts per thousand), 1 = marine (from 30 up to 50 ppt parts per thousand), and 2 = brackish (0.5 – 30 ppt parts per thousand). Character states for the genera Parachlorella, Pedinomonas were treated as marine for analyses shown in Fig. 4; most Parachlorella species are marine, and Pedinomonas have both marine and freshwater.

Taxon name Abbreviated taxa name in Figs. 1 Character and 4. state Acaryochloris marina MBIC11017 Acaryochloris MBIC11017 1 Adiantum capillus veneris Adiantum 0 Amborella trichopoda Amborella 0 Anabaena cylindrica PCC7122 Anabaena PCC7122 0 Aneura mirabilis Aneura 0 Angiopteris evecta Angiopteris 0 Anthoceros formosae Anthoceros 0 Arthrospira sp. PCC8005 Arthrospira PCC8005 1 Bryopsis hypnoides Bryopsis 1 Buus microphylla Buus 0 Calothrix sp. PCC6303 Calothrix PCC6303 0 Calycanthus floridus Calycanthus 0 Chaetosphaeridium globosum Chaetosphaeridium 0 Chara vulgaris Chara 0 Chlamydomonas reinhardtii Chlamydomonas 0 Chlorokybus atmophyticus Chlorokybus 0 Coccomyxa sp. C169 Coccomyxa 0 Coffea arabica Coffea 0 Crocosphaera watsonii WH0003 Crocosphaera WH0003 1 Cryptomeria japonica Cryptomeria 0 Cyanidioschyzon merolae strain 10D Cyanidioschyzon 0 Cyanidium caldarium Cyanidium 0 Cyanobium gracile PCC6307 Cyanobium PCC6307 0 Cyanobium sp. PCC7001 Cyanobium PCC7001 2 Cyanophora paradoxa Cyanophora 0 Cyanothece sp. CCY0110 Cyanothece CCY0110 1 Cyanothece sp. PCC7424 Cyanothece PCC7424 0 Cyanothece sp. PCC7425 Cyanothece PCC7425 0 Cyanothece sp. PCC8801 Cyanothece PCC8801 0 Cycas taitungensis Cycas 0 Dunaliella salina Dunaliella 1 Ephedra equisetina Ephedra 0 Fischerella sp. JSC11 Fischerella JSC11 0 Fistulifera sp. JPCC DA0580 Fistulifera 1 Floydiella terrestris Floydiella 1 Gloeobacter violaceus PCC7421 Gloeobacter PCC7421 0+ Gloeomargarita lithophora Gloeomargarita 0 Gnetum parvifolium Gnetum 0 Gracilaria tenuistipitata Gracilaria 1 Illicium oligandrum Illicium 0 Klebsormidium flaccidum Klebsormidium 0 Leptolyngbya sp. PCC7375 Leptolyngbya PCC7375 1 Leptolyngbya sp. PCC7376 Leptolyngbya PCC7376 1 Leptosira terrestris Leptosira 0 Lyngbya majuscula 3L Lyngbya 3L 1 Lyngbya sp. PCC8106 Lyngbya PCC8106 1 Marchantia polymorpha Marchantia 0 Mesostigma viride Mesostigma 0 Microcoleus vaginatus FGP2 Microcoleus FGP2 0 Microcoleus chthonoplastes PCC7420 Microcoleus PCC7420 1 Microcystis aeruginosa NIES843 Microcystis NIES843 0 Micromonas sp. RCC299 Micromonas 1 Monomasti sp. OKE1 Monomasti 0 Nephroselmis olivacea Nephroselmis 0 Nodosilinea nodulosa PCC7104 Nodosilinea PCC7104 1 Nodularia spumigena CCY9414 Nodularia CCY9414 0 Nostoc azollae 0708 Nostoc 0708 0 Nostoc sp. PCC7120 Nostoc PCC7120 0 Nostoc punctiforme PCC73102 Nostoc PCC73102 0 Nymphaea alba Nymphaea 0 Odontella sinensis Odontella 1 Oedogonium cardiacum Oedogonium 0 Oltmannsiellopsis viridis Oltmannsiellopsis 1 Oocystis solitaria SAG83 80 Oocystis 0 Oscillatoria sp. PCC6506 Oscillatoria PCC6506 0 Ostreococcus tauri Ostreococcus 1 Parachlorella kessleri Parachlorella 1 (0*) Paulinella chromatophora Paulinella 0 Pedinomonas minor Pedinomonas 1 (0*) Phaeodactylum tricornutum Phaeodactylum 1 Pinus contorta Pinus contorta 0 Pleurocapsa sp. PCC7327 Pleurocapsa PCC7327 0 Physcomitrella patens subsp patens Physcomitrella 0 Prasinococcus sp. CCMP1194 Prasinococcus 1 Prasinoderma coloniale Prasinoderma 1 Porphyra purpurea Porphyra pur 1 Porphyra yezoensis Porphyra yez 1 Prochlorococcus marinus str. AS9601 P marinus AS9601 1 Prochlorococcus marinus str. MIT9211 P marinus MIT9211 1 Prochlorococcus marinus str. MIT9303 P marinus MIT9303 1 Prochlorococcus marinus str. MIT9515 P marinus MIT9515 1 Prochloron didemni P2 Fiji Prochloron Fiji 1 Prochloron didemni P3 Solomon Prochloron Solomon 1 Pseudanabaena sp. PCC6802 Pseudanabaena PCC6802 0 Pseudanabaena sp. PCC7367 Pseudanabaena PCC7367 0 Pseudanabaena biceps PCC7429 Pseudanabaena PCC7429 1 Pseudendoclonium akinetum Pseudendoclonium 1 Psilotum nudum Psilotum 0 Ptilidium pulcherrimum Ptilidium 0 Pycnococcus provasolii Pycnococcus 1 Pyramimonas parkeae Pyramimonas 1 Ranunculus macranthus Ranunculus 0 Raphidiopsis brookii D9 Raphidiopsis D9 0 Richelia intracellularis HH01 Richelia HH01 0 Richelia intracellularis HM01 Richelia HM01 0 Scenedesmus obliquus Scenedesmus 0 Schizomeris leibleinii Schizomeris 1 Spinacia oleracea Spinacia 1 Staurastrum punctulatum Staurastrum 0 Stigeoclonium helveticum Stigeoclonium 0 Synechococcus sp. CB0101 Synechococcus CB0101 0 Synechococcus sp. CC9605 Synechococcus CC9605 1 Synechococcus sp. JA-2-3B'a(2-13) Synechococcus JA23Bprimea213 1 Synechococcus sp. JA-3-3Ab Synechococcus JA33Ab 1 Synechococcus elongatus PCC6301 Synechococcus PCC6301 1 Synechococcus sp. PCC7002 Synechococcus PCC7002 2 Synechococcus sp. PCC7335 Synechococcus PCC7335 0 Synechococcus sp. RCC307 Synechococcus RCC307 0 Synechococcus sp. WH8016 Synechococcus WH8016 1 Synechocystis sp. PCC6803 Synechocystis PCC6803 0 Synedra acus Synedra 0 Syntrichia ruralis Syntrichia 1 Thalassiosira oceanica CCMP1005 Thalassiosira 0 Thermosynechococcus elongatus BP1 Thermosynechococcus BP1 0 Trichodesmium erythraeum IMS101 Trichodesmium IMS101 0 Verdigellas peltata Verdigellas 1 Volvox carteri nagariensis UTE2908 Volvox 0 Welwitschia mirabilis Welwitschia 0 Zygnema circumcarinatum Zygnema 0

+An epilithic or endolithic freshwater cyanobacterium * A freshwater species

Table S3. Posterior age estimates in Myr using a Bayesian approach.

Node Clade UGAM CIR Log normal

1 Gloeomargarita + 2,084 (2,278–1,906) 2,166 (2,334–2,015) 2,159 (2,360–1,998) Archaeplastida

2 Archaeplastida 1,828 (2,028–1,656) 1,813 (1,962–1,642) 1,731 (1,894–1,575)

3 Cyanophora 1,828 (2,028–1,656) 1,813 (1,962–1,642) 1,731 (1,894–1,575)

4 Rhodophyta 1,132 (1,335–973) 993 (1,091–864) 968 (1,061–824)

5 Chlorophyta 1,091 (1,348–897) 1087 (1,295–914) 1,001 (1,165–838)

6 Streptophyta 890 (1,209–651) 982 (1,177–832) 939 (1,102–802)

7 Palmophyllophyceae 890 (1,008–404) 878 (1,088–714) 797 (990–651)

8 Prasinophytes 673 (1,008–459) 900 (1,080–744) 822 (1,014–679)

9 Paulinella + Marine 731 (86–415) 419 (575–298) 364 (506–247) SynPro

Node ID corresponds to those shown in Fig. 1. Age estimates are given for analyses under UGAM, CIR and log normal clock models for the topology generated by Maximum Likelihood. The CAT-GTR replacement model was implemented and the root was set with a maximum age of 2.7 Bya (2) and a minimum age of 2.32 Bya (3).

Table S4. Posterior age estimates in Myr using a Bayesian approach.

Node Clade UGAM CIR Log normal

1 Gloeomargarita + 2,164 (2,396–1,940) 2,195 (2,390–2,022) 2,169 (2,351–1,990) Archaeplastida

2 Archaeplastida 1,947 (2,180–1,723) 1,969 (2,157–1,797) 1,946 (2,118–1,779)

3 Cyanophora 1,737 (1,986–1,455) 1,808 (1,984–1,656) 1,781 (1,940–1,624)

4 Rhodophyta 1,172 (1,362–920) 1,063 (1,179–944) 1,065 (1,202–949)

5 Chlorophyta 1,111 (1,362–920) 1,065 (1,231–943) 1,042 (1,179–904)

6 Streptophyta 743 (1,202–664) 1,005 (1,151–881) 985 (1,123–851)

7 Palmophyllophyceae 702. (1,053–464) 883 (1,065–739) 841 (1,004–670)

8 Prasinophytes 755 (1,034–491) 883 (1,044–744) 839 (984–688)

9 Paulinella + Marine 654 (928–449) 413 (576–310) 339 (457–228) SynPro

References

1. Lartillot N, Rodrigue N, Stubbs D, & Richer J (2013) PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment. Syst Biol 62(4):611-615. 2. Crowe SA, et al. (2013) Atmospheric oxygenation three billion years ago. Nature 501(7468):535-+. 3. Bekker A, et al. (2004) Dating the rise of atmospheric oxygen. Nature 427(6970):117- 120.