Project 3763: W. J. Baker, V. Savolainen, C. B. Asmussen-Lange, M. W. Chase, J. Dransfield, F. Forest, M. M. Harley, N. W. Uhl, M. Wilkinson. 2009. Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches. Systematic Biology. 58 (2):240-256.
Specimen: Asterogyne (unvouchered)
View: external

Abstract

Supertree and supermatrix methods have great potential in the quest to build the tree of life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here, we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid restriction fragment length polymorphism data, and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of matrix representation with parsimony (MRP) analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap-weighted matrix elements performed most effectively in this case, generating trees with the greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Nonindependence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations, with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semistrict consensus, enumerating shared clades and compatible clades. The semistrict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate 2 composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit, and complimentary mechanisms for synthesizing disjointed phylogenetic evidence while emphasizing the need for further refinement of supertree methods.


Read the article »

Article DOI: 10.1093/sysbio/syp021

Project DOI: 10.7934/P3763, http://dx.doi.org/10.7934/P3763
This project containsMatrices
  • 1 Media
  • 1 Matrix
  • 3 Documents
  • 205 Taxa
  • 1 Specimen
  • 105 Characters
Total size of project's media files: 471.39k

Download Project SDD File
Total scored cells: 19034
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 105
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 262
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:105/0
Currently Viewing:
MorphoBank Project 3763

    Authors' Institutions

    • Natural History Museum, London

    • Copenhagen University

    • Cornell University

    • Imperial College London

    • Royal Botanic Gardens Kew



    Members

    member name taxa specimens media chars character
    media
    labels
    cell scorings
    (scored, NPA, "-")
    cell
    medialabels
    rules
    MorphoBank Curator
    Project Administrator
    Last logged in 06/30/20
    205111050019034
    (17242, 0, 1792)
    000
    William Baker
    Full membership
    Last logged in Never
    0000000
    (0, 0, 0)
    000


    Taxonomic Overview for Matrix 'M26786' (205 Taxa)

    taxon unscored
    cells
    scored
    cells
    no cell
    support
    NPA
    cells
    "-" cellscell images labels on
    cell images
    member
    access
    [1] Acanthophoenix
    Last Modified in 06/30/20
    6939306002
    [2] Acoelorraphe
    Last Modified in 06/30/20
    28686017002
    [3] Acrocomia
    Last Modified in 06/30/20
    2989805002
    [4] Actinokentia
    Last Modified in 06/30/20
    9909006002
    [5] Actinorhytis
    Last Modified in 06/30/20
    4959506002
    [6] Adonidia
    Last Modified in 06/30/20
    7929206002
    [7] Aiphanes
    Last Modified in 06/30/20
    3969606002
    [8] Allagoptera
    Last Modified in 06/30/20
    48989012002
    [9] Alloschmidia
    Last Modified in 06/30/20
    7929206002
    [10] Alsmithia
    Last Modified in 06/30/20
    5949406002
    [11] Ammandra
    Last Modified in 06/30/20
    78080018002
    [12] Aphandra
    Last Modified in 06/30/20
    68282017002
    [13] Archontophoenix
    Last Modified in 06/30/20
    6939306002
    [14] Areca
    Last Modified in 06/30/20
    4939308002
    [15] Arenga
    Last Modified in 06/30/20
    48888013002
    [16] Asterogyne
    Last Modified in 06/30/20
    4949407002
    [17] Astrocaryum
    Last Modified in 06/30/20
    5929208002
    [18] Attalea
    Last Modified in 06/30/20
    16848405002
    [19] Bactris
    Last Modified in 06/30/20
    8909007002
    [20] Balaka
    Last Modified in 06/30/20
    11888806002
    [21] Barcella
    Last Modified in 06/30/20
    9919105002
    [22] Basselinia
    Last Modified in 06/30/20
    7919107002
    [23] Beccariophoenix
    Last Modified in 06/30/20
    7929206002
    [24] Bentinckia
    Last Modified in 06/30/20
    3969606002
    [25] Bismarckia
    Last Modified in 06/30/20
    2979706002
    [26] Borassodendron
    Last Modified in 06/30/20
    39090012002
    [27] Borassus
    Last Modified in 06/30/20
    2969607002
    [28] Brahea
    Last Modified in 06/30/20
    48484017002
    [29] Brassiophoenix
    Last Modified in 06/30/20
    6939306002
    [30] Brongniartikentia
    Last Modified in 06/30/20
    21787806002
    [31] Burretiokentia
    Last Modified in 06/30/20
    6929207002
    [32] Butia
    Last Modified in 06/30/20
    3979705002
    [33] Calamus
    Last Modified in 06/30/20
    7919107002
    [34] Calospatha
    Last Modified in 06/30/20
    3959507002
    [35] Calyptrocalyx
    Last Modified in 06/30/20
    78585013002
    [36] Calyptrogyne
    Last Modified in 06/30/20
    58787013002
    [37] Calyptronoma
    Last Modified in 06/30/20
    3969606002
    [38] Campecarpus
    Last Modified in 06/30/20
    10888807002
    [39] Carpentaria
    Last Modified in 06/30/20
    7929206002
    [40] Carpoxylon
    Last Modified in 06/30/20
    13868606002
    [41] Caryota
    Last Modified in 06/30/20
    5939307002
    [42] Ceratolobus
    Last Modified in 06/30/20
    5939307002
    [43] Ceroxylon
    Last Modified in 06/30/20
    3949408002
    [44] Chamaedorea
    Last Modified in 06/30/20
    11888806002
    [45] Chamaerops
    Last Modified in 06/30/20
    29292011002
    [46] Chambeyronia
    Last Modified in 06/30/20
    5939307002
    [47] Chelyocarpus
    Last Modified in 06/30/20
    58282018002
    [48] Chuniophoenix
    Last Modified in 06/30/20
    38585017002
    [49] Clinosperma
    Last Modified in 06/30/20
    12878706002
    [50] Clinostigma
    Last Modified in 06/30/20
    12878706002
    [51] Coccothrinax
    Last Modified in 06/30/20
    27979024002
    [52] Cocos
    Last Modified in 06/30/20
    2989805002
    [53] Colpothrinax
    Last Modified in 06/30/20
    58383017002
    [54] Copernicia
    Last Modified in 06/30/20
    28686017002
    [55] Corypha
    Last Modified in 06/30/20
    28686017002
    [56] Cryosophila
    Last Modified in 06/30/20
    68181018002
    [57] Cyphokentia
    Last Modified in 06/30/20
    11888806002
    [58] Cyphophoenix
    Last Modified in 06/30/20
    10888807002
    [59] Cyphosperma
    Last Modified in 06/30/20
    8909007002
    [60] Cyrtostachys
    Last Modified in 06/30/20
    3969606002
    [61] Daemonorops
    Last Modified in 06/30/20
    2959508002
    [62] Deckenia
    Last Modified in 06/30/20
    3959507002
    [63] Desmoncus
    Last Modified in 06/30/20
    29707006002
    [64] Dictyocaryum
    Last Modified in 06/30/20
    6939306002
    [65] Dictyosperma
    Last Modified in 06/30/20
    2979706002
    [66] Dransfieldia
    Last Modified in 06/30/20
    11888806002
    [67] Drymophloeus
    Last Modified in 06/30/20
    9909006002
    [68] Dypsis
    Last Modified in 06/30/20
    3969606002
    [69] Elaeis
    Last Modified in 06/30/20
    2989805002
    [70] Eleiodoxa
    Last Modified in 06/30/20
    6909009002
    [71] Eremospatha
    Last Modified in 06/30/20
    166969020002
    [72] Eugeissona
    Last Modified in 06/30/20
    68888011002
    [73] Euterpe
    Last Modified in 06/30/20
    2949409002
    [74] Gastrococos
    Last Modified in 06/30/20
    3959507002
    [75] Gaussia
    Last Modified in 06/30/20
    2979706002
    [76] Geonoma
    Last Modified in 06/30/20
    8919106002
    [77] Guihaia
    Last Modified in 06/30/20
    4929209002
    [78] Hedyscepe
    Last Modified in 06/30/20
    9909006002
    [79] Hemithrinax
    Last Modified in 06/30/20
    97272024002
    [80] Heterospathe
    Last Modified in 06/30/20
    2979706002
    [81] Howea
    Last Modified in 06/30/20
    48887014002
    [82] Hydriastele
    Last Modified in 06/30/20
    7909008002
    [83] Hyophorbe
    Last Modified in 06/30/20
    2979706002
    [84] Hyospathe
    Last Modified in 06/30/20
    17808008002
    [85] Hyphaene
    Last Modified in 06/30/20
    3959507002
    [86] Iguanura
    Last Modified in 06/30/20
    6939306002
    [87] Iriartea
    Last Modified in 06/30/20
    3959507002
    [88] Iriartella
    Last Modified in 06/30/20
    11878707002
    [89] Itaya
    Last Modified in 06/30/20
    68080019002
    [90] Johannesteijsmannia
    Last Modified in 06/30/20
    28686017002
    [91] Juania
    Last Modified in 06/30/20
    6919108002
    [92] Jubaea
    Last Modified in 06/30/20
    2979706002
    [93] Jubaeopsis
    Last Modified in 06/30/20
    8929205002
    [94] Kentiopsis
    Last Modified in 06/30/20
    8919106002
    [95] Kerriodoxa
    Last Modified in 06/30/20
    49090011002
    [96] Korthalsia
    Last Modified in 06/30/20
    58585015002
    [97] Laccospadix
    Last Modified in 06/30/20
    78585013002
    [98] Laccosperma
    Last Modified in 06/30/20
    68181018002
    [99] Latania
    Last Modified in 06/30/20
    2989805002
    [100] Lavoixia
    Last Modified in 06/30/20
    8919106002
    [101] Lemurophoenix
    Last Modified in 06/30/20
    11888806002
    [102] Leopoldinia
    Last Modified in 06/30/20
    5949406002
    [103] Lepidocaryum
    Last Modified in 06/30/20
    2979706002
    [104] Lepidorrhachis
    Last Modified in 06/30/20
    11888806002
    [105] Leucothrinax
    Last Modified in 06/30/20
    57676024002
    [106] Licuala
    Last Modified in 06/30/20
    68282017002
    [107] Linospadix
    Last Modified in 06/30/20
    68686013002
    [108] Livistona
    Last Modified in 06/30/20
    28585018002
    [109] Lodoicea
    Last Modified in 06/30/20
    5929208002
    [110] Loxococcus
    Last Modified in 06/30/20
    9909006002
    [111] Lytocaryum
    Last Modified in 06/30/20
    4959506002
    [112] Manicaria
    Last Modified in 06/30/20
    3959507002
    [113] Marojejya
    Last Modified in 06/30/20
    3969606002
    [114] Masoala
    Last Modified in 06/30/20
    10898906002
    [115] Mauritia
    Last Modified in 06/30/20
    6919108002
    [116] Mauritiella
    Last Modified in 06/30/20
    2969607002
    [117] Maxburretia
    Last Modified in 06/30/20
    6919108002
    [118] Medemia
    Last Modified in 06/30/20
    8919106002
    [119] Metroxylon
    Last Modified in 06/30/20
    68888011002
    [120] Moratia
    Last Modified in 06/30/20
    8919106002
    [121] Myrialepis
    Last Modified in 06/30/20
    4949407002
    [122] Nannorrhops
    Last Modified in 06/30/20
    28686017002
    [123] Nenga
    Last Modified in 06/30/20
    5919109002
    [124] Neonicholsonia
    Last Modified in 06/30/20
    48484017002
    [125] Neoveitchia
    Last Modified in 06/30/20
    7939206002
    [126] Nephrosperma
    Last Modified in 06/30/20
    3969606002
    [127] Normanbya
    Last Modified in 06/30/20
    7929206002
    [128] Nypa
    Last Modified in 06/30/20
    28888015002
    [129] Oenocarpus
    Last Modified in 06/30/20
    2949409002
    [130] Oncocalamus
    Last Modified in 06/30/20
    7929206002
    [131] Oncosperma
    Last Modified in 06/30/20
    5949406002
    [132] Orania
    Last Modified in 06/30/20
    13838309002
    [133] Oraniopsis
    Last Modified in 06/30/20
    68989010002
    [134] Parajubaea
    Last Modified in 06/30/20
    12888805002
    [135] Pelagodoxa
    Last Modified in 06/30/20
    2979706002
    [136] Phoenicophorium
    Last Modified in 06/30/20
    2969607002
    [137] Phoenix
    Last Modified in 06/30/20
    39292010002
    [138] Pholidocarpus
    Last Modified in 06/30/20
    38484018002
    [139] Pholidostachys
    Last Modified in 06/30/20
    48888013002
    [140] Physokentia
    Last Modified in 06/30/20
    8909007002
    [141] Phytelephas
    Last Modified in 06/30/20
    38585017002
    [142] Pigafetta
    Last Modified in 06/30/20
    5919109002
    [143] Pinanga
    Last Modified in 06/30/20
    157878012002
    [144] Plectocomia
    Last Modified in 06/30/20
    6919108002
    [145] Plectocomiopsis
    Last Modified in 06/30/20
    3959507002
    [146] Podococcus
    Last Modified in 06/30/20
    78685013002
    [147] Pogonotium
    Last Modified in 06/30/20
    6919108002
    [148] Polyandrococos
    Last Modified in 06/30/20
    38989013002
    [149] Ponapea
    Last Modified in 06/30/20
    9909006002
    [150] Prestoea
    Last Modified in 06/30/20
    18818106002
    [151] Pritchardia
    Last Modified in 06/30/20
    68282017002
    [152] Pritchardiopsis
    Last Modified in 06/30/20
    78181017002
    [153] Pseudophoenix
    Last Modified in 06/30/20
    28686017002
    [154] Ptychococcus
    Last Modified in 06/30/20
    4959506002
    [155] Ptychosperma
    Last Modified in 06/30/20
    2979706002
    [156] Raphia
    Last Modified in 06/30/20
    3959507002
    [157] Ravenea
    Last Modified in 06/30/20
    4929209002
    [158] Reinhardtia
    Last Modified in 06/30/20
    7919107002
    [159] Retispatha
    Last Modified in 06/30/20
    6929207002
    [160] Rhapidophyllum
    Last Modified in 06/30/20
    3979606002
    [161] Rhapis
    Last Modified in 06/30/20
    2949409002
    [162] Rhopaloblaste
    Last Modified in 06/30/20
    3969606002
    [163] Rhopalostylis
    Last Modified in 06/30/20
    4959506002
    [164] Roscheria
    Last Modified in 06/30/20
    6939306002
    [165] Roystonea
    Last Modified in 06/30/20
    2979706002
    [166] Sabal
    Last Modified in 06/30/20
    38585017002
    [167] Salacca
    Last Modified in 06/30/20
    5929208002
    [168] Satakentia
    Last Modified in 06/30/20
    6939306002
    [169] Satranala
    Last Modified in 06/30/20
    29707006002
    [170] Schippia
    Last Modified in 06/30/20
    38484018002
    [171] Sclerosperma
    Last Modified in 06/30/20
    38787015002
    [172] Serenoa
    Last Modified in 06/30/20
    28686017002
    [173] Socratea
    Last Modified in 06/30/20
    3959507002
    [174] Solfia
    Last Modified in 06/30/20
    9909006002
    [175] Sommieria
    Last Modified in 06/30/20
    5949406002
    [176] Syagrus
    Last Modified in 06/30/20
    4969605002
    [177] Synechanthus
    Last Modified in 06/30/20
    8898908002
    [178] Tectiphiala
    Last Modified in 06/30/20
    8909007002
    [179] Thrinax
    Last Modified in 06/30/20
    27979024002
    [180] Trachycarpus
    Last Modified in 06/30/20
    2969607002
    [181] Trithrinax
    Last Modified in 06/30/20
    78080018002
    [182] Veillonia
    Last Modified in 06/30/20
    9909006002
    [183] Veitchia
    Last Modified in 06/30/20
    4959506002
    [184] Verschaffeltia
    Last Modified in 06/30/20
    3969606002
    [185] Voanioala
    Last Modified in 06/30/20
    12898805002
    [186] Wallichia
    Last Modified in 06/30/20
    4939308002
    [187] Washingtonia
    Last Modified in 06/30/20
    38585017002
    [188] Welfia
    Last Modified in 06/30/20
    4949407002
    [189] Wendlandiella
    Last Modified in 06/30/20
    8898908002
    [190] Wettinia
    Last Modified in 06/30/20
    88180017002
    [191] Wodyetia
    Last Modified in 06/30/20
    7919107002
    [192] Zombia
    Last Modified in 06/30/20
    37777025002
    [193] Anigozanthos
    Last Modified in 06/30/20
    1050000002
    [194] Calectasia
    Last Modified in 06/30/20
    1050000002
    [195] Catopsis
    Last Modified in 06/30/20
    1050000002
    [196] Costus
    Last Modified in 06/30/20
    1050000002
    [197] Dasypogon
    Last Modified in 06/30/20
    1050000002
    [198] Fargesia
    Last Modified in 06/30/20
    1050000002
    [199] Hanguana
    Last Modified in 06/30/20
    1050000002
    [200] Kingia
    Last Modified in 06/30/20
    1050000002
    [201] Musa
    Last Modified in 06/30/20
    1050000002
    [202] Tradescantia
    Last Modified in 06/30/20
    1050000002
    [203] Typha
    Last Modified in 06/30/20
    1050000002
    [204] Vriesia
    Last Modified in 06/30/20
    1050000002
    [205] Zea
    Last Modified in 06/30/20
    1050000002


    Project views

    type number of views Individual items viewed (where applicable)
    Total project views1050
    Project overview95
    Bibliography39
    Matrix views72Matrix landing page (58 views); Morphological matrix from Baker et al 2009 (prepared by MorphoBank curators from original submission) (14 views);
    Media views195Media search (165 views); M692403 (30 views);
    Views for media list55
    Documents list50
    Specimen list83
    Taxon list461




    Project downloads

    type number of downloads Individual items downloaded (where applicable)
    Total downloads from project20
    Project downloads19
    Matrix downloads1Morphological matrix from Baker et al 2009 (prepared by MorphoBank curators from original submission) (1 download);