Project 2216: Rosa Fernández, Gregory D. Edgecombe, Gonzalo Giribet. 2016. Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction. Systematic Biology. 65 (5):871-889.
Specimen: Theatops spinicaudus (mcz/iz:46873)
View: Anterior dorsal

Abstract

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.


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Article DOI: 10.1093/sysbio/syw041

Project DOI: 10.7934/P2216, http://dx.doi.org/10.7934/P2216
This project containsMatrices
  • 1 Media
  • 1 Matrix
  • 61 Taxa
  • 1 Specimen
  • 232 Characters
Total size of project's media files: 1 MB

Download Project SDD File
Total scored cells: 10027
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 232
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 528
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:227/5
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MorphoBank Project 2216

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    Gonzalo Giribet
    Project Administrator
    Last logged in 10/03/17
    61000232000010027
    (7448, 0, 2579)
    05000
    Greg Edgecombe
    Full membership
    Last logged in 10/03/17
    0111000000
    (0, 0, 0)
    00000


    Taxonomic Overview for Matrix 'M23457' (61 Taxa)

    taxon unscored
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    [1] Peripatopsis capensis
    Last Modified in 07/19/15
    6037370135002
    [2] Anoplodactylus insignis
    Last Modified in 10/03/17
    954141096002
    [3] Limulus polyphemus
    Last Modified in 10/03/17
    1105858064002
    [4] Liphistius malayanus
    Last Modified in 07/19/15
    1155555062002
    [5] Damon variegatus
    Last Modified in 07/19/15
    1165454062002
    [6] Mastigoproctus giganteus
    Last Modified in 07/19/15
    1125656064002
    [7] Centruroides vittatus
    Last Modified in 07/19/15
    1165454062002
    [8] Proscorpius osborni
    Last Modified in 07/19/15
    1722323037002
    [9] Metasiro americanus
    Last Modified in 07/19/15
    1204949063002
    [10] Calanus finmarchicus
    Last Modified in 10/03/17
    1415151040002
    [11] Daphnia pulex
    Last Modified in 10/03/17
    1415151040002
    [12] Rehbachiella kinnekullensis
    Last Modified in 07/19/15
    1852828019002
    [13] Apis mellifera
    Last Modified in 10/03/17
    1356363034002
    [14] Drosophila melanogaster
    Last Modified in 10/03/17
    1266161045002
    [15] Hanseniella sp.
    Last Modified in 07/19/15
    47116116069002
    [16] Scutigerella sp.
    Last Modified in 07/19/15
    42121121069002
    [17] Eudigraphis taiwanensis
    Last Modified in 07/19/15
    43130130059002
    [18] Glomeris marginata
    Last Modified in 10/03/17
    36138138058002
    [19] Cyliosoma sp.
    Last Modified in 07/19/15
    44130130058002
    [20] Glomeridesmus sp.
    Last Modified in 07/19/15
    55117117060002
    [21] Cowiedesmus eroticopodus
    Last Modified in 07/19/15
    1932828011002
    [22] Archidesmus macnicoli
    Last Modified in 07/19/15
    1514545036002
    [23] Petaserpes sp.
    Last Modified in 07/19/15
    68115115049002
    [24] Brachycybe lecontii
    Last Modified in 07/19/15
    59119119054002
    [25] Pseudopolydesmus sp.
    Last Modified in 07/19/15
    38133133061002
    [26] Prostemmiulus sp.
    Last Modified in 07/19/15
    61120120051002
    [27] Abacion magnum
    Last Modified in 07/19/15
    65117117050002
    [28] Cleidogona sp.
    Last Modified in 07/19/15
    63119119050002
    [29] Gaspestria genselorum
    Last Modified in 07/19/15
    1783131023002
    [30] Narceus americanus
    Last Modified in 07/19/15
    39136136057002
    [31] Cambala annulata
    Last Modified in 07/19/15
    69116116047002
    [32] Cylindroiulus sp.
    Last Modified in 07/19/15
    41134134057002
    [33] Crussolum spp.
    Last Modified in 07/19/15
    212202000002
    [34] Scutigerina weberi
    Last Modified in 07/19/15
    27177177028002
    [35] Sphendononema guildingii
    Last Modified in 10/03/17
    27177177028002
    [36] Scutigera coleoptrata
    Last Modified in 07/19/15
    0198198034002
    [37] Lithobius forficatus
    Last Modified in 07/19/15
    0202202030002
    [38] Eupolybothrus cavernicolus
    Last Modified in 07/19/15
    18184184030002
    [39] Anopsobius giribeti
    Last Modified in 07/19/15
    18184184030002
    [40] Paralamyctes validus
    Last Modified in 07/19/15
    21182182029002
    [41] Devonobius delta
    Last Modified in 07/19/15
    1427373017002
    [42] Craterostigmus tasmanianus
    Last Modified in 07/19/15
    12188188032002
    [43] Craterostigmus crabilli
    Last Modified in 07/19/15
    43161161028002
    [44] Mazoscolopendra richardsoni
    Last Modified in 07/19/15
    171535308002
    [45] Scolopendropsis bahiensis
    Last Modified in 07/19/15
    26178177029002
    [46] Akymnopellis chilensis
    Last Modified in 07/19/15
    23179179030002
    [47] Rhysida longipes
    Last Modified in 07/19/15
    13187187032002
    [48] Alipes grandidieri
    Last Modified in 07/19/15
    20180180032002
    [49] Cryptops hortensis
    Last Modified in 10/03/17
    8192191032002
    [50] Theatops spinicaudus
    Last Modified in 10/03/17
    17183183032002
    [51] Scolopocryptops sexspinosus
    Last Modified in 07/19/15
    17182181033002
    [52] Newportia adisi
    Last Modified in 07/19/15
    17183183032002
    [53] Mecistocephalus guildingii
    Last Modified in 07/19/15
    12184184036002
    [54] Tygarrup javanicus
    Last Modified in 07/19/15
    27169169036002
    [55] Notiphilides grandis
    Last Modified in 07/19/15
    24174174034002
    [56] Himantarium gabrielis
    Last Modified in 07/19/15
    15186186031002
    [57] Stenotaenia linearis
    Last Modified in 07/19/15
    16180180036002
    [58] Henia brevis
    Last Modified in 07/19/15
    32169168032002
    [59] Strigamia maritima
    Last Modified in 07/19/15
    3193192036002
    [60] Hydroschendyla submarina
    Last Modified in 07/19/15
    23176176033002
    [61] Kachinophilus pereirai
    Last Modified in 07/19/15
    107108108017002


    Project views

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    Project overview926
    Matrix views345Matrix landing page (314 views); Myriapod tree of Life (31 views);
    Taxon list2247
    Media views951Media search (702 views); M462274 (249 views);
    Specimen list432
    Views for media list282
    Bibliography194




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