Project 2525: J. C. Uyeda, L. J. Harmon, C. E. Blank. 2016. A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics Through Deep Geologic Time. PLOS ONE. 11 (9):e0162539. (In Press)
Specimen: Fischerella muscicola pcc73103 (unvouchered)

Abstract

Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record---phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth’s history have shaped---and been shaped by---evolution in Cyanobacteria. We identify a robust core cyanobacterial phylogeny and a smaller set of taxa that exhibit long-branch attraction artifacts. We estimated the age of nodes and reconstruct the ancestral character states of 43 phenotypic characters. We find high levels of phylogenetic signal for nearly all traits, indicating the phylogeny carries substantial predictive power. The earliest cyanobacterial lineages likely lived in freshwater habitats, had small cell diameters, were benthic or sessile, and possibly epilithic/endolithic with a sheath. We jointly analyzed a subset of 25 binary traits to determine whether rates of trait evolution have shifted over time in conjunction with major geologic events. Phylogenetic comparative analysis reveal an overriding signal of decreasing rates of trait evolution through time. Furthermore, the data suggest two major rate shifts in trait evolution associated with bursts of evolutionary innovation. The first rate shift occurs in the aftermath of the Great Oxidation Event and “Snowball Earth” glaciations and is associated with decrease in the evolutionary rates around 1.8-1.6 Ga. This rate shift seems to indicate the end of a major diversification of cyanobacterial phenotypes--particularly related to traits associated with filamentous morphology, heterocysts and motility in freshwater ecosystems. Another burst appears around the time of the Neoproterozoic Oxidation Event in the Neoproterozoic, and is associated with the acquisition of traits involved in planktonic growth in marine habitats. Our results demonstrate how uniting genomic and phenotypic datasets in extant bacterial species can shed light on billion-year old events in Earth’s history.


Read the article »

Article DOI: http://dx.doi.org/10.1371/journal.pone.0162539

Project DOI: 10.7934/P2525, http://dx.doi.org/10.7934/P2525
This project containsMatrices
  • 1 Media
  • 1 Matrix
  • 268 Taxa
  • 1 Specimen
  • 44 Characters
Total size of project's media files: 1 MB

Download Project SDD File
Total scored cells: 5672
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 44
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 103
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:44/0
Currently Viewing:
MorphoBank Project 2525

    This research
    supported by



    Members

    member name taxa specimens media media
    notes
    chars character
    comms
       
    notes  media
    labels
    cell scorings
    (scored, NPA, "-")
    cell
    comms
        
    notes  medialabels
    rules
    Josef Uyeda
    Project Administrator
    Last logged in 09/06/16
    2681114400005672
    (5672, 0, 0)
    00000
    Carrine Blank
    Full membership
    Last logged in Never
    0000000000
    (0, 0, 0)
    00000


    Taxonomic Overview for Matrix 'M24191' (134 Taxa)

    taxon unscored
    cells
    scored
    cells
    no cell
    support
    NPA
    cells
    "-" cellscell images labels on
    cell images
    member
    access
    [1] Acaryochloris.marina.MBIC11017
    Last Modified in 09/05/16
    0444400002
    [2] Acaryochloris.sp.CCMEE5410
    Last Modified in 09/05/16
    0454400002
    [3] Anabaena.cylindrica.PCC7122
    Last Modified in 09/05/16
    0454400002
    [4] Anabaena.sp.PCC7108
    Last Modified in 09/05/16
    0484400002
    [5] Anabaena.variabilis.ATCC29413
    Last Modified in 09/05/16
    0474400002
    [6] Arthrospira.maxima.CS.328
    Last Modified in 09/05/16
    0454400002
    [7] Arthrospira.platensis.str.Paraca
    Last Modified in 09/05/16
    10343400002
    [8] Arthrospira.sp.PCC8005
    Last Modified in 09/05/16
    0454400002
    [9] Calothrix.sp.PCC6303
    Last Modified in 09/05/16
    0454400002
    [10] Calothrix.sp.PCC7103
    Last Modified in 09/05/16
    0454400002
    [11] Calothrix.sp.PCC7507
    Last Modified in 09/05/16
    0464400002
    [12] Chamaesiphon.minutus.PCC6605
    Last Modified in 09/05/16
    0454400002
    [13] Chlorogloeopsis.fritschii.PCC6912
    Last Modified in 09/05/16
    0464400002
    [14] Chlorogloeopsis.sp.PCC9212
    Last Modified in 09/05/16
    0464400002
    [15] Chroococcidiopsis.thermalis.PCC7203
    Last Modified in 09/05/16
    0474400002
    [16] Crinalium.epipsammum.PCC9333
    Last Modified in 09/05/16
    0444400002
    [17] Crocosphaera.watsonii.WH0003
    Last Modified in 09/05/16
    0444400002
    [18] Crocosphaera.watsonii.WH8501
    Last Modified in 09/05/16
    0444400002
    [19] Cyanobacterium.aponinum.PCC10605
    Last Modified in 09/05/16
    4434000002
    [20] Cyanobacterium.stanieri.PCC7202
    Last Modified in 09/05/16
    0474400002
    [21] Cyanobacterium.UCYN.A
    Last Modified in 09/05/16
    6383800002
    [22] Cyanobium.gracile.PCC6307
    Last Modified in 09/05/16
    0444400002
    [23] Cyanobium.sp.PCC7001
    Last Modified in 09/05/16
    10373400002
    [24] Cyanothece.sp.ATCC51142
    Last Modified in 09/05/16
    0444400002
    [25] Cyanothece.sp.ATCC51472
    Last Modified in 09/05/16
    0444400002
    [26] Cyanothece.sp.CCY0110
    Last Modified in 09/05/16
    4404000002
    [27] Cyanothece.sp.PCC7424
    Last Modified in 09/05/16
    0444400002
    [28] Cyanothece.sp.PCC7425
    Last Modified in 09/05/16
    0444400002
    [29] Cyanothece.sp.PCC7822
    Last Modified in 09/05/16
    0444400002
    [30] Cyanothece.sp.PCC8801
    Last Modified in 09/05/16
    0444400002
    [31] Cyanothece.sp.PCC8802
    Last Modified in 09/05/16
    0444400002
    [32] Cylindrospermopsis.raciborskii.CS.505
    Last Modified in 09/05/16
    0444400002
    [33] Cylindrospermum.stagnale.PCC7417
    Last Modified in 09/05/16
    0444400002
    [34] Dactylococcopsis.salina.PCC8305
    Last Modified in 09/05/16
    0444400002
    [35] Fischerella.muscicola.PCC73103
    Last Modified in 09/05/16
    0474400002
    [36] Fischerella.muscicola.PCC7414
    Last Modified in 09/05/16
    0474400002
    [37] Fischerella.sp.JSC.11
    Last Modified in 09/05/16
    1464300002
    [38] Fischerella.sp.PCC9339
    Last Modified in 09/05/16
    0474400002
    [39] Fischerella.thermalis.PCC7521
    Last Modified in 09/05/16
    0474400002
    [40] Geitlerinema.sp.PCC7105
    Last Modified in 09/05/16
    0454400002
    [41] Geitlerinema.sp.PCC7407
    Last Modified in 09/05/16
    0484400002
    [42] Geminocystis.herdmanii.PCC6308
    Last Modified in 09/05/16
    0444400002
    [43] Gloeobacter.violaceus.PCC7421
    Last Modified in 09/05/16
    0444400002
    [44] Gloeocapsa.sp.PCC73106
    Last Modified in 09/05/16
    0454400002
    [45] Gloeocapsa.sp.PCC7428
    Last Modified in 09/05/16
    0484400002
    [46] Halothece.sp.PCC7418
    Last Modified in 09/05/16
    4414000002
    [47] Leptolyngbya.sp.PCC6406
    Last Modified in 09/05/16
    0464400002
    [48] Leptolyngbya.sp.PCC7375
    Last Modified in 09/05/16
    5413900002
    [49] Leptolyngbya.sp.PCC7376
    Last Modified in 09/05/16
    4424000002
    [50] Lyngbya.sp.PCC8106
    Last Modified in 09/05/16
    0464400002
    [51] Mastigocladopsis.repens.PCC10914
    Last Modified in 09/05/16
    0444400002
    [52] Microchaete.sp.PCC7126
    Last Modified in 09/05/16
    0464400002
    [53] Microcoleus.chthonoplastes.PCC7420
    Last Modified in 09/05/16
    0464400002
    [54] Microcoleus.sp.PCC7113
    Last Modified in 09/05/16
    0464400002
    [55] Microcoleus.vaginatus.FGP.2
    Last Modified in 09/05/16
    0464400002
    [56] Microcystis.aeruginosa.NIES.843
    Last Modified in 09/05/16
    0444400002
    [57] Microcystis.aeruginosa.PCC7806
    Last Modified in 09/05/16
    0444400002
    [58] Microcystis.aeruginosa.PCC7941
    Last Modified in 09/05/16
    3414100002
    [59] Microcystis.aeruginosa.PCC9432
    Last Modified in 09/05/16
    3414100002
    [60] Microcystis.aeruginosa.PCC9443
    Last Modified in 09/05/16
    3414100002
    [61] Microcystis.aeruginosa.PCC9701
    Last Modified in 09/05/16
    3414100002
    [62] Microcystis.aeruginosa.PCC9717
    Last Modified in 09/05/16
    3414100002
    [63] Microcystis.aeruginosa.PCC9806
    Last Modified in 09/05/16
    3414100002
    [64] Microcystis.aeruginosa.PCC9807
    Last Modified in 09/05/16
    3414100002
    [65] Microcystis.aeruginosa.PCC9808
    Last Modified in 09/05/16
    3414100002
    [66] Microcystis.aeruginosa.PCC9809
    Last Modified in 09/05/16
    3414100002
    [67] Microcystis.sp.T1.4
    Last Modified in 09/05/16
    3414100002
    [68] Moorea.producta.3L
    Last Modified in 09/05/16
    0454400002
    [69] Nodosilinea.nodulosa.PCC7104
    Last Modified in 09/05/16
    0494400002
    [70] Nodularia.spumigena.CCY9414
    Last Modified in 09/05/16
    0444400002
    [71] Nostoc.azollae.0708
    Last Modified in 09/05/16
    1444300002
    [72] Nostoc.punctiforme.PCC73102
    Last Modified in 09/05/16
    0464400002
    [73] Nostoc.sp.PCC7107
    Last Modified in 09/05/16
    0464400002
    [74] Nostoc.sp.PCC7120
    Last Modified in 09/05/16
    0464400002
    [75] Nostoc.sp.PCC7524
    Last Modified in 09/05/16
    0464400002
    [76] Oscillatoria.acuminata.PCC6304
    Last Modified in 09/05/16
    1454300002
    [77] Oscillatoria.formosa.PCC6407
    Last Modified in 09/05/16
    1454300002
    [78] Oscillatoria.nigro.viridis.PCC7112
    Last Modified in 09/05/16
    1454300002
    [79] Oscillatoria.sp.PCC10802
    Last Modified in 09/05/16
    2444200002
    [80] Oscillatoria.sp.PCC6506
    Last Modified in 09/05/16
    0464400002
    [81] Oscillatoriales.cyanobacterium.JSC.12
    Last Modified in 09/05/16
    11333300002
    [82] Pleurocapsa.sp.PCC7319
    Last Modified in 09/05/16
    0474400002
    [83] Pleurocapsa.sp.PCC7327
    Last Modified in 09/05/16
    1454300002
    [84] Prochlorococcus.marinus.str.AS9601
    Last Modified in 09/05/16
    0444400002
    [85] Prochlorococcus.marinus.str.MIT9202
    Last Modified in 09/05/16
    0444400002
    [86] Prochlorococcus.marinus.str.MIT9211
    Last Modified in 09/05/16
    0444400002
    [87] Prochlorococcus.marinus.str.MIT9215
    Last Modified in 09/05/16
    0444400002
    [88] Prochlorococcus.marinus.str.MIT9301
    Last Modified in 09/05/16
    0444400002
    [89] Prochlorococcus.marinus.str.MIT9303
    Last Modified in 09/05/16
    0444400002
    [90] Prochlorococcus.marinus.str.MIT9312
    Last Modified in 09/05/16
    0444400002
    [91] Prochlorococcus.marinus.str.MIT9313
    Last Modified in 09/05/16
    0444400002
    [92] Prochlorococcus.marinus.str.MIT9515
    Last Modified in 09/05/16
    0444400002
    [93] Prochlorococcus.marinus.str.NATL1A
    Last Modified in 09/05/16
    0444400002
    [94] Prochlorococcus.marinus.str.NATL2A
    Last Modified in 09/05/16
    0444400002
    [95] Prochlorococcus.marinus.subsp.marinus.str.CCMP1375
    Last Modified in 09/05/16
    0444400002
    [96] Prochlorococcus.marinus.subsp.pastoris.str.CCMP1986
    Last Modified in 09/05/16
    0444400002
    [97] Prochloron.didemni
    Last Modified in 09/05/16
    4404000002
    [98] Prochlorothrix.hollandica.PCC9006
    Last Modified in 09/05/16
    0444400002
    [99] Pseudanabaena.biceps.PCC7429
    Last Modified in 09/05/16
    10363400002
    [100] Pseudanabaena.sp.PCC6802
    Last Modified in 09/05/16
    10363400002
    [101] Pseudanabaena.sp.PCC7367
    Last Modified in 09/05/16
    0454400002
    [102] Raphidiopsis.brookii.D9
    Last Modified in 09/05/16
    0444400002
    [103] Rivularia.sp.PCC7116
    Last Modified in 09/05/16
    0464400002
    [104] Spirulina.sp.PCC9445
    Last Modified in 09/05/16
    0444400002
    [105] Stanieria.cyanosphaera.PCC7437
    Last Modified in 09/05/16
    0444400002
    [106] Synechococcus.elongatus.PCC6301
    Last Modified in 09/05/16
    11333300002
    [107] Synechococcus.elongatus.PCC7942
    Last Modified in 09/05/16
    15292900002
    [108] Synechococcus.sp.BL107
    Last Modified in 09/05/16
    8363600002
    [109] Synechococcus.sp.CB0101
    Last Modified in 09/05/16
    5423900002
    [110] Synechococcus.sp.CB0205
    Last Modified in 09/05/16
    5423900002
    [111] Synechococcus.sp.CC9311
    Last Modified in 09/05/16
    8363600002
    [112] Synechococcus.sp.CC9605
    Last Modified in 09/05/16
    8363600002
    [113] Synechococcus.sp.CC9902
    Last Modified in 09/05/16
    8363600002
    [114] Synechococcus.sp.JA.2.3Bprime.a.2.13
    Last Modified in 09/05/16
    7373700002
    [115] Synechococcus.sp.JA.3.3Ab
    Last Modified in 09/05/16
    7373700002
    [116] Synechococcus.sp.PCC6312
    Last Modified in 09/05/16
    11333300002
    [117] Synechococcus.sp.PCC7002
    Last Modified in 09/05/16
    11363300002
    [118] Synechococcus.sp.PCC7335
    Last Modified in 09/05/16
    11333300002
    [119] Synechococcus.sp.PCC7336
    Last Modified in 09/05/16
    18262600002
    [120] Synechococcus.sp.PCC7502
    Last Modified in 09/05/16
    11333300002
    [121] Synechococcus.sp.RCC307
    Last Modified in 09/05/16
    8363600002
    [122] Synechococcus.sp.RS9916
    Last Modified in 09/05/16
    8363600002
    [123] Synechococcus.sp.RS9917
    Last Modified in 09/05/16
    8393600002
    [124] Synechococcus.sp.WH5701
    Last Modified in 09/05/16
    5423900002
    [125] Synechococcus.sp.WH7803
    Last Modified in 09/05/16
    5393900002
    [126] Synechococcus.sp.WH7805
    Last Modified in 09/05/16
    5393900002
    [127] Synechococcus.sp.WH8016
    Last Modified in 09/05/16
    19252500002
    [128] Synechococcus.sp.WH8102
    Last Modified in 09/05/16
    5393900002
    [129] Synechococcus.sp.WH8109
    Last Modified in 09/05/16
    8363600002
    [130] Synechocystis.sp.PCC6803
    Last Modified in 09/05/16
    0484400002
    [131] Synechocystis.sp.PCC7509
    Last Modified in 09/05/16
    0454400002
    [132] Thermosynechococcus.elongatus.BP.1
    Last Modified in 09/05/16
    15332900002
    [133] Trichodesmium.erythraeum.IMS101
    Last Modified in 09/05/16
    10343400002
    [134] Xenococcus.sp.PCC7305
    Last Modified in 09/05/16
    0454400002


    Project views

    type number of views Individual items viewed (where applicable)
    Total project views8940
    Project overview1576
    Media views1833Media search (1542 views); M430669 (291 views);
    Matrix views921Matrix landing page (826 views); cyanobacteria trait matrix (95 views);
    Bibliography337
    Taxon list3501
    Specimen list772




    Project downloads

    type number of downloads Individual items downloaded (where applicable)
    Total downloads from project129
    Project downloads110
    Matrix downloads19cyanobacteria trait matrix (19 downloads);