Project 4111: J. Rasplus, L. J. Rodriguez, L. Sauné, Y. Peng, A. Bain, F. Kjellberg, R. D. Harrison, R. A. Pereira, R. Ubaidillah, C. Tollon‐Cordet, M. Gautier, J. Rossi, A. Cruaud. 2021. Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae). Cladistics. 37 (4):402-422.
Specimen: Ficus carica (unvouchered)
View: leaves and fruit

Abstract

Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction-site-associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase phylogenetic information for higher-level relationships, we targeted conserved regions and assembled paired reads into long loci to enable the retrieval of homologous loci in outgroup genomes. We compared morphological and molecular results to highlight discrepancies and reveal possible inference bias. For the first time, we recovered a monophyletic subgenus Urostigma (stranglers) and a clade with all gynodioecious Ficus. However, we show, with a new approach based on iterative principal component analysis, that it is not (and will probably never be) possible to homogenize evolutionary rates and GC content for all taxa before phylogenetic inference. Four competing positions for the root of the molecular tree are possible. The placement of section Pharmacosycea as sister to other fig trees is not supported by morphological data and considered a result of a long-branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides Ficus into monoecious versus gynodioecious species appears most plausible. It seems most likely that the ancestor of fig trees was a freestanding tree and active pollination is inferred as the ancestral state, contrary to previous hypotheses. However, ambiguity remains on the ancestral breeding system. Despite morphological plasticity, we advocate restoring a central role to morphology in our understanding of the evolution of Ficus, as it can help detect systematic errors that appear more pronounced with larger molecular datasets.


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Article DOI: 10.1111/cla.12443

Project DOI: 10.7934/P4111, http://dx.doi.org/10.7934/P4111
This project containsMatrices
  • 1 Media
  • 1 Matrix
  • 1 Document
  • 74 Taxa
  • 1 Specimen
  • 102 Characters
Total size of project's media files: 121.16k

Download Project SDD File
Total scored cells: 7752
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 102
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 226
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:102/0
Currently Viewing:
MorphoBank Project 4111
  • Creation Date:
    28 October 2021
  • Publication Date:
    28 October 2021
  • Project views: 227

    Authors' Institutions

    • Bogor Zoological Museum Kebun Raya Bogor, Bogor

    • Chinese Academy of Sciences

    • Universite de Montpellier

    • Universidade de Sao Paulo (USP, University of Sao Paulo)

    • University of the Philippines-Diliman

    • Xishuangbanna Tropical Botanical Garden

    • National Sun Yat-sen University

    • World Agroforestry



    Members

    member name taxa specimens media chars character
    media
    labels
    cell scorings
    (scored, NPA, "-")
    cell
    medialabels
    rules
    MorphoBank Curator
    Project Administrator
    7411102007752
    (7225, 0, 527)
    000
    Jean-Yves Rasplus
    Full membership
    0000000
    (0, 0, 0)
    000


    Taxonomic Overview for Matrix 'M27696' (74 Taxa)

    taxon unscored
    cells
    scored
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    "-" cellscell images labels on
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    [1] Ficus brunneoaurata
    Last Modified in 10/28/21
    099950700none
    [2] Ficus fulva
    Last Modified in 10/28/21
    095940800none
    [3] Ficus hirta
    Last Modified in 10/28/21
    0100950700none
    [4] Ficus padana
    Last Modified in 10/28/21
    095940800none
    [5] Ficus carica
    Last Modified in 10/28/21
    098950700none
    [6] Ficus austrocaledonica
    Last Modified in 10/28/21
    098960600none
    [7] Ficus callosa
    Last Modified in 10/28/21
    0101960600none
    [8] Ficus gigantifolia
    Last Modified in 10/28/21
    0101970500none
    [9] Ficus magnoliifolia
    Last Modified in 10/28/21
    0101970500none
    [10] Ficus nervosa
    Last Modified in 10/28/21
    099970500none
    [11] Ficus racemigera
    Last Modified in 10/28/21
    197950600none
    [12] Ficus carchiana
    Last Modified in 10/28/21
    096960600none
    [13] Ficus crassivenosa
    Last Modified in 10/28/21
    096960600none
    [14] Ficus gigantosyce
    Last Modified in 10/28/21
    098960600none
    [15] Ficus insipida
    Last Modified in 10/28/21
    098960600none
    [16] Ficus maxima
    Last Modified in 10/28/21
    096950700none
    [17] Ficus torresiana
    Last Modified in 10/28/21
    097950700none
    [18] Ficus subulata
    Last Modified in 10/28/21
    0103950700none
    [19] Ficus virgata
    Last Modified in 10/28/21
    0103970500none
    [20] Ficus elmeri
    Last Modified in 10/28/21
    097950700none
    [21] Ficus exasperata
    Last Modified in 10/28/21
    098960600none
    [22] Ficus subincisa
    Last Modified in 10/28/21
    098950700none
    [23] Ficus deltoidea
    Last Modified in 10/28/21
    095940800none
    [24] Ficus formosana
    Last Modified in 10/28/21
    098940800none
    [25] Ficus ischnopoda
    Last Modified in 10/28/21
    098940800none
    [26] Ficus oleifolia
    Last Modified in 10/28/21
    098940800none
    [27] Ficus pedunculosa
    Last Modified in 10/28/21
    097940800none
    [28] Ficus vaccinioides
    Last Modified in 10/28/21
    096940800none
    [29] Ficus adenosperma
    Last Modified in 10/28/21
    0102970500none
    [30] Ficus minahassae
    Last Modified in 10/28/21
    098970500none
    [31] Ficus rivularis
    Last Modified in 10/28/21
    096940800none
    [32] Ficus semicordata
    Last Modified in 10/28/21
    099970500none
    [33] Ficus variegata
    Last Modified in 10/28/21
    0104980400none
    [34] Ficus pritchardii
    Last Modified in 10/28/21
    0100970500none
    [35] Ficus hispida
    Last Modified in 10/28/21
    099970500none
    [36] Ficus septica
    Last Modified in 10/28/21
    099960600none
    [37] Ficus racemosa
    Last Modified in 10/28/21
    0102980400none
    [38] Ficus sycomorus
    Last Modified in 10/28/21
    0103980400none
    [39] Ficus aurantiacea
    Last Modified in 10/28/21
    0100960600none
    [40] Ficus ruginervia
    Last Modified in 10/28/21
    0100960600none
    [41] Ficus pumila
    Last Modified in 10/28/21
    097950700none
    [42] Ficus sagittata
    Last Modified in 10/28/21
    098950700none
    [43] Ficus villosa
    Last Modified in 10/28/21
    099950700none
    [44] Ficus trichocarpa
    Last Modified in 10/28/21
    099940800none
    [45] Ficus aurea
    Last Modified in 10/28/21
    0101970500none
    [46] Ficus citrifolia
    Last Modified in 10/28/21
    0100970500none
    [47] Ficus nymphaeifolia
    Last Modified in 10/28/21
    098970500none
    [48] Ficus obtusifolia
    Last Modified in 10/28/21
    099970500none
    [49] Ficus schultesi
    Last Modified in 10/28/21
    099970500none
    [50] Ficus cordatula
    Last Modified in 10/28/21
    099960600none
    [51] Ficus elastica
    Last Modified in 10/28/21
    097950700none
    [52] Ficus forstenii
    Last Modified in 10/28/21
    098950700none
    [53] Ficus glaberrima
    Last Modified in 10/28/21
    099960600none
    [54] Ficus microcarpa
    Last Modified in 10/28/21
    0102970500none
    [55] Ficus cyathistipula
    Last Modified in 10/28/21
    099960600none
    [56] Ficus laurifolia
    Last Modified in 10/28/21
    0106980400none
    [57] Ficus saussureana
    Last Modified in 10/28/21
    0100960600none
    [58] Ficus lyrata
    Last Modified in 10/28/21
    099970500none
    [59] Ficus natalensis
    Last Modified in 10/28/21
    099960600none
    [60] Ficus ottonifolia
    Last Modified in 10/28/21
    0102980400none
    [61] Ficus glandifera
    Last Modified in 10/28/21
    095950700none
    [62] Ficus macrophylla
    Last Modified in 10/28/21
    095950700none
    [63] Ficus obliqua
    Last Modified in 10/28/21
    095950700none
    [64] Ficus rubiginosa
    Last Modified in 10/28/21
    095950700none
    [65] Ficus watkinsiana
    Last Modified in 10/28/21
    096950700none
    [66] Ficus caulocarpa
    Last Modified in 10/28/21
    0100970500none
    [67] Ficus prolixa
    Last Modified in 10/28/21
    098960600none
    [68] Ficus religiosa
    Last Modified in 10/28/21
    097960600none
    [69] Ficus salicifolia
    Last Modified in 10/28/21
    0100970500none
    [70] Ficus saxophila
    Last Modified in 10/28/21
    097960600none
    [71] Antiaris
    Last Modified in 10/28/21
    0868102100none
    [72] Morus
    Last Modified in 10/28/21
    0757502700none
    [73] Artocarpus
    Last Modified in 10/28/21
    0807702500none
    [74] Sparattosyce
    Last Modified in 10/28/21
    0787802400none


    Project views

    type number of views Individual items viewed (where applicable)
    Total project views227
    Project overview30
    Matrix views25Matrix landing page (25 views);
    Media views51Media search (44 views); M824216 (7 views);
    Documents list24
    Bibliography11
    Views for media list15
    Specimen list30
    Taxon list41




    Project downloads

    type number of downloads Individual items downloaded (where applicable)
    Total downloads from project5
    Project downloads5