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Origin of marine planktonic cyanobacteria 5  

Supplementary Information 6  

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Patricia Sánchez-Baracaldo1 10  

1School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK 11  

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and requests for materials should be addressed to (p.sánchez-baracaldo@bristol.ac.uk) 13  

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Materials and Methods 23  

Bayesian divergence time estimation 24   25  MCMCtree: For each gene, branch lengths were estimated in BASEML1 and CODEML1. For 26  nucleotides, I tested three of models of nucleotide evolution (HKY85, GTR) and found that age 27  estimates are congruent across models of evolution (Table 1). For proteins, I tested two of models 28  of protein evolution (LG and REV) with age estimates being congruent between both models 29  (Table 1). I used 1 billion years per unit time for all analyses. The substitution rate was calculated 30  independently for each gene in BASEML1 for nucleotides and in CODEML1 for proteins 31  (Supplementary Table S1) and an average of all substitution rates was used depending on the 32  analyses. For proteins and nucleotides each gene was treated (Table 1) as separate loci for which 33  the same substitution model is used, but different parameters were assigned and estimated for 34  each partition. The gamma prior used to describe how variable rates are across branches was 35  specified as follows G (α and β); the priors used were for proteins G (1, 10.6) and G (1, 12.5) for 36  

nucleotides. The mean and standard deviation was specified as m =α/β. The gamma priors for the 37  substitution model parameters κ (transition/transversion rate ratio) and α (gamma shape parameter 38  for variable rates among sites) were all specified by gamma distributions. Respective means and 39  standard deviations were (6, 2) for κ and (1, 1) for α. For all analyses, I used fixed values for the 40  birth-death process λ = µ = 1 and ρ = 0. Test runs were performed to determine the number of 41  iterations, the burn-in and the sample frequency. All analyses were performed twice to ensure 42  convergence of the MCMC, however only one analysis is reported. For all age calibrations, both 43  minimum and maximum bounds were soft and specified by uniform distributions between the 44  maximum/minimum time constraints with 2.5% tail probabilities above/below these limits allowing 45  for molecular data to correct for conflicting fossil information1. Priors on divergence times were 46  assessed by running chains without data to examine prior intervals in relation to expected 47  divergence times. To check whether analyses had converged I used Tracer v1.62. 48   49  Phylobayes: Additional molecular clock analyses were performed in Phylobayes 3.3b3 using the 50  same data sets described above. I implemented the Uncorrelated Gamma Multipliers (UGM) 51  model4 as this model seems to fit better cyanobacteria data sets based on Bayes Factors as 52  previously shown5. Because the large data sets analyzed both proteins (6,187 sites) and 53  nucleotides (4,555 sites), I implemented the CAT-GT replacement model as recommended in the 54  manual3. I used a birth-death prior on divergence times. I also ran two independent experiments 55  with permissive gamma distributed root priors that allowed a 95% credibility interval of the root 56  node to range between 2,320-2,700 Mya and 2,320-3,000 Mya. I treated all calibration points as 57  soft to allow for 2.5 % on each side for an upper and lower bound. 58  

  3  

Supplementary Table S1: Proteins and RNA used to estimate substitution rates and age 59  

divergences. 60  

61  Gene abbreviation and name Length of

alignment Substitution rate per billion years

Protein sequences AtpA, ATP Synthase CF1 Alpha Chain 518 0.085614 AtpB, ATP Synthase F1 Subcomplex Subunit Beta 484 0.068306 AtpH, ATP Synthase CF0 C Chain 82 0.074095 L1 Ribosomal Protein Translation (RplA), 242 0.113598 L4 Ribosomal Protein Translation (RplD) 219 0.163141 L5 Ribosomal Protein Translation (RplE) 182 0.100793 NdhH, NADH Dehydrogenase Subunit 7 395 0.079125 PetB, Cytochrome b6 222 0.055031 PetD, Cytochrome b6-f Complex Subunit IV 161 0.097252 PsaA, Photosystem I p700 Apoprotein A1 857 0.090560 PsbE, Cytochrome b559 Alpha Chain 82 0.160873 RbcL, Ribulose Bisphosphate Carboxylase-Oxygenase 483 0.059598 S10 Ribosomal Protein Translation (RpsJ) 105 0.038472 S13 Ribosomal Protein Translation (RpsM) 117 0.130683 S19 Ribosomal Protein Translation (RpsS) 96 0.077682 SecY, Pre-protein Translocase 123 0.132346 TufA, Elongation Factor Tu 411 0.057311 Ycf3, Photosystem I Assembly Protein 201 0.139499

Nucleotide sequences LSU, Large Subunit Ribosomal RNA 3002 0.077336 SSU, Small Subunit Ribosomal RNA 1540 0.081187  62   63  

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Supplementary Table S2. Character states for evolution of morphology, cell diameter and habitat. 73  

Major Clades and Taxa Morphology Cell Diameter Habitat Macrocyanobacteria Anabaena cylindrica PCC7122 1 2 0 Anabaena sp. 90 1 3 0 Anabaena sp. PCC7108 1 2 0 Anabaena variabilis ATCC29413 1 3 0 Arthrospira maxima CS328 1 3 1 Arthrospira platensis str. Paraca 1 3 1 Arthrospira sp. PCC8005 1 3 1 Calothrix sp. PCC6303 1 3 0 Calothrix sp. PCC7103 1 3 0 Calothrix sp. PCC7507 1 3 0 Chamaesiphon minutus PCC6605 1 1 0 Chroococcidiopsis thermalis PCC7203 0 3 0 Crinalium epipsammum PCC9333 1 2 1 Crocosphaera watsonii WH0003 0 2 1 Crocosphaera watsonii WH8501 0 2 1 Cyanobacterium aponinum PCC10605 1 1 1 Cyanobacterium stanieri PCC7202 1 1 1 Cyanobacterium UCYNA 0 1 1 Cyanobacterium UCYNA2 0 1 1 Cyanothece sp. ATCC51142 0 2 1 Cyanothece sp. ATCC51472 0 2 1 Cyanothece sp. CCY0110 0 2 1 Cyanothece sp. PCC7424 0 2 0 Cyanothece sp. PCC7822 0 2 0 Cyanothece sp. PCC8801 0 2 0 Cyanothece sp. PCC8802 0 2 0 Cylindrospermopsis raciborskii CS505 1 2 0 Cylindrospermum stagnale PCC7417 1 3 0 Dactylococcopsis salina PCC8305 1 3 1 Fischerella muscicola PCC7414 1 3 0 Fischerella muscicola SAG14271 1 3 0 Fischerella sp. JSC11 1 3 0 Fischerella sp. PCC9339 1 3 0 Fischerella thermalis PCC7521 1 3 0 Geitlerinema sp. PCC7105 1 1 0 Geitlerinema sp. PCC7407 1 0 0 Geminocystis herdmanii PCC6308 1 2 0 Gloeocapsa sp. PCC7428 0 2 1 Halothece sp. PCC7418 1 3 1 Leptolyngbya boryana PCC6306 1 1 0 Leptolyngbya sp. PCC7376 1 0 1 Lyngbya majuscula 3L 1 3 1 Lyngbya sp. PCC8106 1 ? 1 Mastigocladopsis repens PCC10914 1 2 0 Microchaete sp. PCC7126 1 3 0 Microcoleus chthonoplastes PCC7420 1 2 1 Microcoleus sp. PCC7113 1 2 0 Microcoleus vaginatus FGP2 1 ? 0 Microcystis aeruginosa NIES843 0 2 0 Microcystis aeruginosa PCC9443 0 2 0

  5  

Microcystis aeruginosa PCC9806 0 2 0 Nodularia spumigena CCY9414 1 3 1 North Pacific Trichodesmium 1 3 1 Nostoc azollae 0708 1 3 0 Nostoc punctiforme PCC73102 1 3 0 Nostoc sp. PCC7107 1 3 0 Nostoc sp. PCC7120 1 2 0 Nostoc sp. PCC7524 1 3 0 Oscillatoria acuminata PCC6304 1 2 0 Oscillatoria formosa PCC6407 1 2 0 Oscillatoria nigro viridis PCC7112 1 3 0 Oscillatoria sp. PCC10802 1 ? 0 Oscillatoria sp. PCC6506 1 2 0 Oscillatoriales cyanobacterium JSC12 1 1 0 Pleurocapsa sp. PCC7319 1 3 1 Pleurocapsa sp. PCC7327 1 3 0 Prochloron didemni P1 Palau 0 3 1 Prochloron didemni P2 Fiji 0 3 1 Prochloron didemni P3 Solomon 0 3 1 Prochloron didemni P4 Papua New Guinea 0 3 1 Raphidiopsis brookii D9 1 ? 0 Richelia intracellularis HH01 1 3 1 Richelia intracellularis HM01 1 3 1 Rivularia sp. PCC7116 1 2 1 Spirulina subsalsa PCC9445 1 2 1 Stanieria cyanosphaera PCC7437 0 3 0 Synechococcus sp. PCC 0 0 1 Synechocystis sp. PCC6803 0 1 0 Synechocystis sp. PCC7509 0 2 0 Trichodesmium erythraeum IMS101 1 3 1 Xenococcus sp. PCC7305 0 3 1 Microcyanobacteria Cyanobium gracile PCC6307 0 0 0 Cyanobium sp. PCC7001 0 0 1 Cyanothece sp. PCC7425 0 2 0 Leptolyngbya sp. PCC6406 1 0 0 Leptolyngbya sp. PCC7375 1 0 1 Nodosilinea nodulosa PCC7104 1 0 0 Prochlorococcus marinus str. NATL2A 0 0 1 Prochlorococcus marinus str.AS9601 0 0 1 Prochlorococcus marinus str.MIT9202 0 0 1 Prochlorococcus marinus str.MIT9211 0 0 1 Prochlorococcus marinus str.MIT9215 0 0 1 Prochlorococcus marinus str.MIT9301 0 0 1 Prochlorococcus marinus str.MIT9303 0 0 1 Prochlorococcus marinus str.MIT9312 0 0 1 Prochlorococcus marinus str.MIT9313 0 0 1 Prochlorococcus marinus str.MIT9515 0 0 1 Prochlorococcus marinus str.NATL1A 0 0 1 Prochlorococcus marinus subsp. marinus str. CCMP1375 0 0 1

Prochlorococcus marinus subsp. pastoris str. CCMP1986 0 0 1

Prochlorothrix hollandica PCC9006 0 0 0

  6  

Synechococcus elongatus PCC6301 0 0 0 Synechococcus elongatus PCC7942 0 0 0 Synechococcus sp. BL107 0 0 1 Synechococcus sp. CB0101 0 0 1 Synechococcus sp. CB0205 0 0 1 Synechococcus sp. CC9311 0 0 1 Synechococcus sp. CC9605 0 0 1 Synechococcus sp. CC9902 0 0 1 Synechococcus sp. PCC7335 0 1 1 Synechococcus sp. RCC307 0 0 1 Synechococcus sp. RS9916 0 0 1 Synechococcus sp. RS9917 0 0 1 Synechococcus sp. WH5701 0 0 1 Synechococcus sp. WH7803 0 0 1 Synechococcus sp. WH7805 0 0 1 Synechococcus sp. WH8016 0 0 1 Synechococcus sp. WH8102 0 0 1 Synechococcus sp. WH8109 0 0 1 Basal lineages Acaryochloris marina MBIC11017 0 1 1 Acaryochloris sp. CCMEE5410 0 0 1 Gloeobacter violaceus PCC7421 0 0 0 Pseudanabaena biceps PCC7429 1 1 0 Pseudanabaena sp. PCC6802 1 1 0 Pseudanabaena sp. PCC7367 1 0 1 Synechococcus sp. JA23Bprimea213 0 0 0 Synechococcus sp. JA33Ab 0 0 0 Synechococcus sp. PCC6312 0 0 0 Synechococcus sp. PCC7336 0 0 1 Synechococcus sp. PCC7502 0 0 0 Thermosynechococcus elongatus BP1 0 0 0 74  

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Supplementary Figures 84  

Supplementary Figure S1. Genomic tree of cyanobacteria estimated using RaxML (Maximum 85  Likelihood). Bootstrap values are 100 for branches that show no values; values are reported for 86  those that show relatively low values. A total of 131 genomes were analyzed based on 135 87  proteins and two ribosomal RNAs (SSU and LSU). Bar represents the scale of the branch lengths. 88   89  

90   91   92   93   94   95   96   97   98  

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Supplementary Figure S2. Evolution of morphology. 99   100  

101   102   103   104   105   106   107   108   109   110  

Synechococcus sp. PCC7336Synechococcus sp. JA23Bprimea213Synechococcus sp. JA33AbPseudanabaena biceps PCC7429Synechococcus sp. PCC7502Pseudanabaena sp. PCC6802Pseudanabaena sp. PCC7367Geitlerinema sp. PCC7105Oscillatoria acuminata PCC6304

Oscillatoria sp. PCC10802Oscillatoria sp. PCC6506Oscillatoria formosa PCC6407

Microcoleus vaginatus FGP2Oscillatoria nigro viridis PCC7112Trichodesmium North Pacific

Trichodesmium erythraeum IMS101Lyngbya sp. PCC8106Arthrospira maxima CS328Arthrospira sp. PCC8005Arthrospira platensis str. ParacaChroococcidiopsis thermalis PCC7203Synechocystis sp. PCC7509Gloeocapsa sp. PCC7428Nostoc sp. PCC7107Nostoc sp. PCC7524Nostoc sp. PCC7120Anabaena variabilis ATCC29413

Calothrix sp. PCC7507Microchaete sp. PCC7126Cylindrospermum stagnale PCC7417Nostoc azollae 0708

Raphidiopsis brookii D9Cylindrospermopsis raciborskii CS505Anabaena sp. 90Anabaena cylindrica PCC7122Anabaena sp. PCC7108Nodularia spumigena CCY9414Nostoc punctiforme PCC73102Rivularia sp. PCC7116Calothrix sp. PCC7103Calothrix sp. PCC6303Richelia intracellularis HM01Richelia intracellularis HH01Fischerella muscicola SAG14271Fischerella sp. PCC9339Fischerella thermalis PCC7521Fischerella muscicola PCC7414Fischerella sp. JSC11Mastigocladopsis repens PCC10914Crinalium epipsammum PCC9333Chamaesiphon minutus PCC6605Microcoleus sp. PCC7113Microcoleus chthonoplastes PCC7420Lyngbya majuscula 3LStanieria cyanosphaera PCC7437Xenococcus sp. PCC7305Pleurocapsa sp. PCC7319Geminocystis herdmanii PCC6308Cyanobacterium aponinum PCC10605Cyanobacterium stanieri PCC7202Synechococcus sp. PCC7002Leptolyngbya sp. PCC7376Cyanothece sp. CCY0110Cyanothece sp. ATCC51472Cyanothece sp. ATCC51142Crocosphaera watsonii WH0003Crocosphaera watsonii WH8501Cyanobacterium UCYNACyanobacterium UCYNA2

Cyanothece sp. PCC8802Cyanothece sp. PCC8801Microcystis aeruginosa PCC9806Microcystis aeruginosa PCC9443Microcystis aeruginosa NIES843Synechocystis sp. PCC6803Cyanothece sp. PCC7424Cyanothece sp. PCC7822Pleurocapsa sp. PCC7327Prochloron didemni P2 FijiProchloron didemni P3 SolomonProchloron didemni P1 PalauProchloron didemni P4 Papua New GuineaSpirulina subsalsa PCC9445Halothece sp. PCC7418Dactylococcopsis salina PCC8305Oscillatoriales cyanobacterium JSC12Leptolyngbya boryana PCC6306Geitlerinema sp. PCC7407Synechococcus elongatus PCC6301Synechococcus elongatus PCC7942Synechococcus sp. RCC307Cyanobium gracile PCC6307Synechococcus sp. WH5701Cyanobium sp. PCC7001Synechococcus sp. CB0101Synechococcus sp. CB0205P marinus str. MIT9211

P marinus subsp. marinus str. CCMP1375P marinus str. NATL2AP marinus str. NATL1A

P marinus subsp. pastoris str. CCMP1986P marinus str. MIT9515P marinus str. MIT9312P marinus str. AS9601P marinus str. MIT9301P marinus str. MIT9202P marinus str. MIT9215P marinus str. MIT9303P marinus str. MIT9313

Synechococcus sp. BL107Synechococcus sp. CC9902Synechococcus sp. WH8102Synechococcus sp. CC9605Synechococcus sp. WH8109Synechococcus sp. WH7803Synechococcus sp. WH7805Synechococcus sp. WH8016Synechococcus sp. CC9311Synechococcus sp. RS9917Synechococcus sp. RS9916Prochlorothrix hollandica PCC9006Nodosilinea nodulosa PCC7104

Leptolyngbya sp. PCC6406Synechococcus sp. PCC7335Leptolyngbya sp. PCC7375Cyanothece sp. PCC7425Synechococcus sp. PCC6312Thermosynechococcus elongatus BP1Acaryochloris sp. CCMEE5410Acaryochloris marina MBIC11017Gloeobacter violaceus PCC7421

= 0 (unicellular)

= 1 (filamentous)

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Supplementary Figure S3. Evolution of cell diameter. 111   112  

113   114   115   116   117   118   119   120   121   122   123  

Synechococcus sp. PCC7336Synechococcus sp. JA23Bprimea213Synechococcus sp. JA33AbPseudanabaena biceps PCC7429Synechococcus sp. PCC7502Pseudanabaena sp. PCC6802Pseudanabaena sp. PCC7367Geitlerinema sp. PCC7105Oscillatoria acuminata PCC6304Oscillatoria sp. PCC10802Oscillatoria sp. PCC6506Oscillatoria formosa PCC6407Microcoleus vaginatus FGP2Oscillatoria nigro viridis PCC7112Trichodesmium North PacificTrichodesmium erythraeum IMS101Lyngbya sp. PCC8106Arthrospira maxima CS328Arthrospira sp. PCC8005Arthrospira platensis str. ParacaChroococcidiopsis thermalis PCC7203Synechocystis sp. PCC7509Gloeocapsa sp. PCC7428Nostoc sp. PCC7107Nostoc sp. PCC7524Nostoc sp. PCC7120Anabaena variabilis ATCC29413Calothrix sp. PCC7507Microchaete sp. PCC7126Cylindrospermum stagnale PCC7417Nostoc azollae 0708Raphidiopsis brookii D9Cylindrospermopsis raciborskii CS505Anabaena sp. 90Anabaena cylindrica PCC7122Anabaena sp. PCC7108Nodularia spumigena CCY9414Nostoc punctiforme PCC73102Rivularia sp. PCC7116Calothrix sp. PCC7103Calothrix sp. PCC6303Richelia intracellularis HM01Richelia intracellularis HH01Fischerella muscicola SAG14271Fischerella sp. PCC9339Fischerella thermalis PCC7521Fischerella muscicola PCC7414Fischerella sp. JSC11Mastigocladopsis repens PCC10914Crinalium epipsammum PCC9333Chamaesiphon minutus PCC6605Microcoleus sp. PCC7113Microcoleus chthonoplastes PCC7420Lyngbya majuscula 3LStanieria cyanosphaera PCC7437Xenococcus sp. PCC7305Pleurocapsa sp. PCC7319Geminocystis herdmanii PCC6308Cyanobacterium aponinum PCC10605Cyanobacterium stanieri PCC7202Synechococcus sp. PCC7002Leptolyngbya sp. PCC7376Cyanothece sp. CCY0110Cyanothece sp. ATCC51472Cyanothece sp. ATCC51142Crocosphaera watsonii WH0003Crocosphaera watsonii WH8501Cyanobacterium UCYNACyanobacterium UCYNA2Cyanothece sp. PCC8802Cyanothece sp. PCC8801Microcystis aeruginosa PCC9806Microcystis aeruginosa PCC9443Microcystis aeruginosa NIES843Synechocystis sp. PCC6803Cyanothece sp. PCC7424Cyanothece sp. PCC7822Pleurocapsa sp. PCC7327Prochloron didemni P2 FijiProchloron didemni P3 SolomonProchloron didemni P1 PalauProchloron didemni P4 Papua New GuineaSpirulina subsalsa PCC9445Halothece sp. PCC7418Dactylococcopsis salina PCC8305Oscillatoriales cyanobacterium JSC12Leptolyngbya boryana PCC6306Geitlerinema sp. PCC7407Synechococcus elongatus PCC6301Synechococcus elongatus PCC7942Synechococcus sp. RCC307Cyanobium gracile PCC6307Synechococcus sp. WH5701Cyanobium sp. PCC7001Synechococcus sp. CB0101Synechococcus sp. CB0205P marinus str. MIT9211P marinus subsp. marinus str. CCMP1375P marinus str. NATL2AP marinus str. NATL1AP marinus subsp. pastoris str. CCMP1986P marinus str. MIT9515P marinus str. MIT9312P marinus str. AS9601P marinus str. MIT9301P marinus str. MIT9202P marinus str. MIT9215P marinus str. MIT9303P marinus str. MIT9313Synechococcus sp. BL107Synechococcus sp. CC9902Synechococcus sp. WH8102Synechococcus sp. CC9605Synechococcus sp. WH8109Synechococcus sp. WH7803Synechococcus sp. WH7805Synechococcus sp. WH8016Synechococcus sp. CC9311Synechococcus sp. RS9917Synechococcus sp. RS9916Prochlorothrix hollandica PCC9006Nodosilinea nodulosa PCC7104Leptolyngbya sp. PCC6406Synechococcus sp. PCC7335Leptolyngbya sp. PCC7375Cyanothece sp. PCC7425Synechococcus sp. PCC6312Thermosynechococcus elongatus BP1Acaryochloris sp. CCMEE5410Acaryochloris marina MBIC11017Gloeobacter violaceus PCC7421

= 0 (< 2 µm)

= 1 (2-3 µm)

= 2 (3-5 µm)

= 3 (>5 µm)

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Supplementary Figure S4. Evolution of habitat. 124   125  

126    127   128   129   130   131   132   133   134   135   136  

Synechococcus sp. PCC7336Synechococcus sp. JA23Bprimea213Synechococcus sp. JA33AbPseudanabaena biceps PCC7429Synechococcus sp. PCC7502Pseudanabaena sp. PCC6802Pseudanabaena sp. PCC7367Geitlerinema sp. PCC7105Oscillatoria acuminata PCC6304

Oscillatoria sp. PCC10802Oscillatoria sp. PCC6506Oscillatoria formosa PCC6407

Microcoleus vaginatus FGP2Oscillatoria nigro viridis PCC7112Trichodesmium North Pacific

Trichodesmium erythraeum IMS101Lyngbya sp. PCC8106Arthrospira maxima CS328Arthrospira sp. PCC8005Arthrospira platensis str. ParacaChroococcidiopsis thermalis PCC7203Synechocystis sp. PCC7509Gloeocapsa sp. PCC7428Nostoc sp. PCC7107Nostoc sp. PCC7524Nostoc sp. PCC7120Anabaena variabilis ATCC29413

Calothrix sp. PCC7507Microchaete sp. PCC7126Cylindrospermum stagnale PCC7417Nostoc azollae 0708

Raphidiopsis brookii D9Cylindrospermopsis raciborskii CS505Anabaena sp. 90Anabaena cylindrica PCC7122Anabaena sp. PCC7108Nodularia spumigena CCY9414Nostoc punctiforme PCC73102Rivularia sp. PCC7116Calothrix sp. PCC7103Calothrix sp. PCC6303Richelia intracellularis HM01Richelia intracellularis HH01Fischerella muscicola SAG14271

Fischerella sp. PCC9339Fischerella thermalis PCC7521Fischerella muscicola PCC7414

Fischerella sp. JSC11Mastigocladopsis repens PCC10914Crinalium epipsammum PCC9333Chamaesiphon minutus PCC6605Microcoleus sp. PCC7113Microcoleus chthonoplastes PCC7420Lyngbya majuscula 3LStanieria cyanosphaera PCC7437Xenococcus sp. PCC7305Pleurocapsa sp. PCC7319Geminocystis herdmanii PCC6308Cyanobacterium aponinum PCC10605Cyanobacterium stanieri PCC7202Synechococcus sp. PCC7002Leptolyngbya sp. PCC7376Cyanothece sp. CCY0110Cyanothece sp. ATCC51472Cyanothece sp. ATCC51142Crocosphaera watsonii WH0003Crocosphaera watsonii WH8501Cyanobacterium UCYNACyanobacterium UCYNA2

Cyanothece sp. PCC8802Cyanothece sp. PCC8801Microcystis aeruginosa PCC9806Microcystis aeruginosa PCC9443Microcystis aeruginosa NIES843Synechocystis sp. PCC6803Cyanothece sp. PCC7424Cyanothece sp. PCC7822Pleurocapsa sp. PCC7327Prochloron didemni P2 FijiProchloron didemni P3 SolomonProchloron didemni P1 Palau

Prochloron didemni P4 Papua New GuineaSpirulina subsalsa PCC9445Halothece sp. PCC7418Dactylococcopsis salina PCC8305Oscillatoriales cyanobacterium JSC12Leptolyngbya boryana PCC6306Geitlerinema sp. PCC7407Synechococcus elongatus PCC6301Synechococcus elongatus PCC7942Synechococcus sp. RCC307Cyanobium gracile PCC6307Synechococcus sp. WH5701Cyanobium sp. PCC7001Synechococcus sp. CB0101Synechococcus sp. CB0205P marinus str. MIT9211

P marinus subsp. marinus str. CCMP1375P marinus str. NATL2AP marinus str. NATL1A

P marinus subsp. pastoris str. CCMP1986P marinus str. MIT9515P marinus str. MIT9312P marinus str. AS9601P marinus str. MIT9301P marinus str. MIT9202P marinus str. MIT9215P marinus str. MIT9303P marinus str. MIT9313

Synechococcus sp. BL107Synechococcus sp. CC9902Synechococcus sp. WH8102Synechococcus sp. CC9605Synechococcus sp. WH8109Synechococcus sp. WH7803Synechococcus sp. WH7805Synechococcus sp. WH8016Synechococcus sp. CC9311Synechococcus sp. RS9917Synechococcus sp. RS9916Prochlorothrix hollandica PCC9006Nodosilinea nodulosa PCC7104

Leptolyngbya sp. PCC6406Synechococcus sp. PCC7335Leptolyngbya sp. PCC7375Cyanothece sp. PCC7425Synechococcus sp. PCC6312Thermosynechococcus elongatus BP1Acaryochloris sp. CCMEE5410Acaryochloris marina MBIC11017Gloeobacter violaceus PCC7421

= 0 (freshwater)

= 1 (brackish or

marine)

  11  

References 137   138  1 Yang, Z. PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 139  

1586–1591 (2007). 140  2 Rambaut, A. Suchard, M. A, Xie, D. & Drummond. Tracer v1. 6. Edinburgh: University of 141  

Edinburgh. Available from http://beast.bio.ed.ac.uk/Tracer. (2014). (Accessed: 6th August 142  2015) 143  

3 Lartillot N., Lepage T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for 144  phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288. 145  

4 Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed Phylogenetics and 146  Dating with Confidence. Plos Biol. 4, e88 (2006). 147  

5 Sánchez-Baracaldo, P., Ridgwell, A. & Raven, J. A. A Neoproterozoic transition in the 148  marine nitrogen cycle. Curr. Biol. 24, 652-657, doi:10.1016/j.cub.2014.01.041 (2014). 149  

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