Project 689: T. H. Oakley, J. M. Wolfe, A. R. Lindgren, A. K. Zaharoff. 2012. Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement and Pancrustacean Phylogeny. Molecular Biology and Evolution.
Specimen: Puriana sp (SBMNH/Sample 169:Voucher 198)
View: lateral

Abstract

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. Yet many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often under-sampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome, nuclear genome and rDNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Brachiopoda+Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. Yet, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a ‘total evidence’ philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.


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Project DOI: 10.7934/P689, http://dx.doi.org/10.7934/P689
This project containsMatrices
  • 31 Media
  • 2 Matrices
  • 109 Taxa
  • 4 Specimens
  • 183 Characters
Total size of project's media files: 51 MB

Download Project SDD File
Total scored cells: 21204
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 366
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 451
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:366/0
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MorphoBank Project 689

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    member name taxa specimens media media
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    Jo Wolfe
    Project Administrator
    Last logged in 09/13/12
    1094312036603660021204
    (16921, 0, 4283)
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    Bryan Juarez
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    Todd Oakley
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    Taxonomic Overview for Matrix 'M1593' (76 Taxa)

    taxon unscored
    cells
    scored
    cells
    no cell
    support
    NPA
    cells
    "-" cellscell images labels on
    cell images
    member
    access
    [1] Acanthocyclops vernalis
    Last Modified in 12/05/13
    778585021003
    [2] Acyrthosiphon pisum
    Last Modified in 12/05/13
    649896021003
    [3] Apis mellifera
    Last Modified in 12/05/13
    59102102022003
    [4] Argulus sp
    Last Modified in 12/05/13
    699492020003
    [5] Armadillidium vulgare
    Last Modified in 12/05/13
    44121117018003
    [6] Armillifer armillatus
    Last Modified in 12/05/13
    444946090003
    [7] Artemia franciscana
    Last Modified in 12/05/13
    38127126018003
    [8] Actinoseta jonesi
    Last Modified in 12/05/13
    739090020003
    [9] Artemia salina
    Last Modified in 12/05/13
    38127125018003
    [10] Bombyx mori
    Last Modified in 12/05/13
    58103102022003
    [11] † Bredocaris admirabilis
    Last Modified in 12/05/13
    1096363011003
    [12] Calanus finmarchicus
    Last Modified in 12/05/13
    52106106025003
    [13] Caligus rogercresseyi
    Last Modified in 12/05/13
    748888021003
    [14] Chthamalus fragilis
    Last Modified in 12/05/13
    837877022003
    [15] † Cinerocaris magnifica
    Last Modified in 12/05/13
    111646308003
    [16] † Colymbosathon ecplecticos
    Last Modified in 12/05/13
    937461016003
    [17] Conchoecia sp
    Last Modified in 12/05/13
    679087026003
    [18] Ctenolepisma lineata
    Last Modified in 12/05/13
    35131131017003
    [19] Cypridopsis vidua
    Last Modified in 12/05/13
    569795030003
    [20] Cytherelloidea californica
    Last Modified in 12/05/13
    679089026003
    [21] Daphnia pulex
    Last Modified in 12/05/13
    60104100019003
    [22] Darwinula sp
    Last Modified in 12/05/13
    669187026003
    [23] Derocheilocaris typicus
    Last Modified in 12/05/13
    877372023003
    [24] Drosophila melanogaster
    Last Modified in 12/05/13
    26128128029003
    [25] Ephemerella inconstans
    Last Modified in 12/05/13
    63103103017003
    [26] Eumesocampa frigilis
    Last Modified in 12/05/13
    46105105032003
    [27] Euphilomedes morini
    Last Modified in 12/05/13
    769190016003
    [28] Eurytemora affinis
    Last Modified in 12/05/13
    52106104025003
    [29] Harbansus paucichelatus
    Last Modified in 12/05/13
    719189021003
    [30] Heterocypris sp
    Last Modified in 12/05/13
    669188026003
    [31] Hutchinsoniella macracantha
    Last Modified in 12/05/13
    36122119025003
    [32] † Klausmuelleria salopensis
    Last Modified in 12/05/13
    967171016003
    [33] † Kunmingella sp
    Last Modified in 12/05/13
    1095554019003
    [34] † Kunyangella cheni
    Last Modified in 12/05/13
    1402928014003
    [35] Lepas anserifera
    Last Modified in 12/05/13
    728280029003
    [36] Lepeophtheirus salmonis
    Last Modified in 12/05/13
    729090021003
    [37] † Lepidocaris rhyniensis
    Last Modified in 12/05/13
    927670015003
    [38] Lernaeocera branchialis
    Last Modified in 12/05/13
    817878024003
    [39] Libinia emarginata
    Last Modified in 12/05/13
    789086015003
    [40] Limnadia lenticularis
    Last Modified in 12/05/13
    769087017003
    [41] Limulus polyphemus
    Last Modified in 12/05/13
    30114111039003
    [42] Loxothylacus texanus
    Last Modified in 12/05/13
    493737097003
    [43] Lynceus sp
    Last Modified in 12/05/13
    749189018003
    [44] Machiloides banksi
    Last Modified in 12/05/13
    55106106022003
    [45] Manawa staceyi
    Last Modified in 12/05/13
    689085025003
    [46] Mesocyclops edax
    Last Modified in 12/05/13
    798383021003
    [47] Metajapyx subterraneus
    Last Modified in 12/05/13
    579595031003
    [48] † Nahecaris stuertzi
    Last Modified in 12/05/13
    106696608003
    [49] † Nasunaris flata
    Last Modified in 12/05/13
    1105853015003
    [50] Nebalia hessleri
    Last Modified in 12/05/13
    52118116013003
    [51] Neogonodactylus oerstedii
    Last Modified in 12/05/13
    44124123015003
    [52] Neonesidea sp
    Last Modified in 12/05/13
    708785026003
    [53] † Nymphatelina gravida
    Last Modified in 12/05/13
    986961016003
    [54] Orchesella imitari
    Last Modified in 12/05/13
    42119118022003
    [55] † Pattersoncypris micropapillosa
    Last Modified in 12/05/13
    1046357016003
    [56] Pedetontus saltator
    Last Modified in 12/05/13
    41120120022003
    [57] Periplaneta americana
    Last Modified in 12/05/13
    45121118017003
    [58] Propontocypris sp1
    Last Modified in 12/05/13
    708784026003
    [59] Puriana sp
    Last Modified in 12/05/13
    669187026003
    [60] † Rehbachiella kinnekullensis
    Last Modified in 12/05/13
    1007370010003
    [61] Rutiderma apex
    Last Modified in 12/05/13
    768686021003
    [62] Sandersiella sp
    Last Modified in 12/05/13
    44115114024003
    [63] Scutigera coleoptrata
    Last Modified in 12/05/13
    39116116028003
    [64] Semibalanus balanoides
    Last Modified in 12/05/13
    609693027003
    [65] Skogsbergia lerneri
    Last Modified in 12/05/13
    679594021003
    [66] Speleonectes tulumensis
    Last Modified in 12/05/13
    55101100027003
    [67] Streptocephalus seali
    Last Modified in 12/05/13
    57108108018003
    [68] Terrestricythere pratensis
    Last Modified in 12/05/13
    718685026003
    [69] Tomocerus sp
    Last Modified in 12/05/13
    46115115022003
    [70] † Triadocypris spitzbergensis
    Last Modified in 12/05/13
    1086054015003
    [71] Tribolium castaneum
    Last Modified in 12/05/13
    639898022003
    [72] Triops longicaudatus
    Last Modified in 12/05/13
    42123123018003
    [73] Vargula tsujii
    Last Modified in 12/05/13
    6110199021003
    [74] † Vestrogothia sp
    Last Modified in 12/05/13
    947373016003
    [75] † Waptia fieldensis
    Last Modified in 12/05/13
    1185552010003
    [76] † Yicaris dianensis
    Last Modified in 12/05/13
    977271014003


    Taxonomic Overview for Matrix 'M1597' (109 Taxa)

    taxon unscored
    cells
    scored
    cells
    no cell
    support
    NPA
    cells
    "-" cellscell images labels on
    cell images
    member
    access
    [1] Limulus polyphemus
    Last Modified in 12/05/13
    30114110039003
    [2] Scutigera coleoptrata
    Last Modified in 12/05/13
    39116115028003
    [3] † Bredocaris admirabilis
    Last Modified in 12/05/13
    1096357011003
    [4] † Cinerocaris magnifica
    Last Modified in 12/05/13
    111646108003
    [5] † Colymbosathon ecplecticos
    Last Modified in 12/05/13
    937452016003
    [6] † Klausmuelleria salopensis
    Last Modified in 12/05/13
    967171016003
    [7] † Kunmingella sp
    Last Modified in 12/05/13
    1095552019003
    [8] † Kunyangella cheni
    Last Modified in 12/05/13
    1402928014003
    [9] † Lepidocaris rhyniensis
    Last Modified in 12/05/13
    927669015003
    [10] † Nahecaris stuertzi
    Last Modified in 12/05/13
    106696508003
    [11] † Nasunaris flata
    Last Modified in 12/05/13
    1105850015003
    [12] † Nymphatelina gravida
    Last Modified in 12/05/13
    986950016003
    [13] † Pattersoncypris micropapillosa
    Last Modified in 12/05/13
    1046352016003
    [14] † Rehbachiella kinnekullensis
    Last Modified in 12/05/13
    1007367010003
    [15] † Triadocypris spitzbergensis
    Last Modified in 12/05/13
    1086049015003
    [16] † Vestrogothia sp
    Last Modified in 12/05/13
    947372016003
    [17] † Waptia fieldensis
    Last Modified in 12/05/13
    1185550010003
    [18] † Yicaris dianensis
    Last Modified in 12/05/13
    977266014003
    [19] Artemia franciscana
    Last Modified in 12/05/13
    38127124018003
    [20] Artemia salina
    Last Modified in 12/05/13
    38127125018003
    [21] Daphnia pulex
    Last Modified in 12/05/13
    6010496019003
    [22] Limnadia lenticularis
    Last Modified in 12/05/13
    769087017003
    [23] Lynceus sp
    Last Modified in 12/05/13
    749187018003
    [24] Streptocephalus seali
    Last Modified in 12/05/13
    57108106018003
    [25] Triops longicaudatus
    Last Modified in 12/05/13
    42123123018003
    [26] Argulus sp
    Last Modified in 12/05/13
    699491020003
    [27] Hutchinsoniella macracantha
    Last Modified in 12/05/13
    36122115025003
    [28] Sandersiella sp
    Last Modified in 12/05/13
    44115113024003
    [29] Acanthocyclops vernalis
    Last Modified in 12/05/13
    778584021003
    [30] Calanus finmarchicus
    Last Modified in 12/05/13
    52106105025003
    [31] Caligus rogercresseyi
    Last Modified in 12/05/13
    748888021003
    [32] Eurytemora affinis
    Last Modified in 12/05/13
    52106102025003
    [33] Lepeophtheirus salmonis
    Last Modified in 12/05/13
    729088021003
    [34] Lernaeocera branchialis
    Last Modified in 12/05/13
    817877024003
    [35] Mesocyclops edax
    Last Modified in 12/05/13
    798383021003
    [36] Acyrthosiphon pisum
    Last Modified in 12/05/13
    649896021003
    [37] Apis mellifera
    Last Modified in 12/05/13
    59102102022003
    [38] Bombyx mori
    Last Modified in 12/05/13
    58103100022003
    [39] Ctenolepisma lineata
    Last Modified in 12/05/13
    35131130017003
    [40] Drosophila melanogaster
    Last Modified in 12/05/13
    26128127029003
    [41] Ephemerella inconstans
    Last Modified in 12/05/13
    63103103017003
    [42] Eumesocampa frigilis
    Last Modified in 12/05/13
    46105103032003
    [43] Machiloides banksi
    Last Modified in 12/05/13
    55106106022003
    [44] Metajapyx subterraneus
    Last Modified in 12/05/13
    579595031003
    [45] Orchesella imitari
    Last Modified in 12/05/13
    42119117022003
    [46] Pedetontus saltator
    Last Modified in 12/05/13
    41120120022003
    [47] Periplaneta americana
    Last Modified in 12/05/13
    45121118017003
    [48] Tomocerus sp
    Last Modified in 12/05/13
    46115115022003
    [49] Tribolium castaneum
    Last Modified in 12/05/13
    639898022003
    [50] Armadillidium vulgare
    Last Modified in 12/05/13
    44121109018003
    [51] Libinia emarginata
    Last Modified in 12/05/13
    789083015003
    [52] Nebalia hessleri
    Last Modified in 12/05/13
    52118113013003
    [53] Neogonodactylus oerstedii
    Last Modified in 12/05/13
    44124120015003
    [54] Derocheilocaris typicus
    Last Modified in 12/05/13
    877370023003
    [55] Actinoseta jonesi
    Last Modified in 12/05/13
    739090020003
    [56] Conchoecia sp
    Last Modified in 12/05/13
    679086026003
    [57] Conchoecissa sp
    Last Modified in 12/05/13
    679090026003
    [58] Euphilomedes morini
    Last Modified in 12/05/13
    769186016003
    [59] Eusarsiella sp
    Last Modified in 12/05/13
    769191016003
    [60] Harbansus paucichelatus
    Last Modified in 12/05/13
    719187021003
    [61] Polycope japonica
    Last Modified in 12/05/13
    679090026003
    [62] Polycope sp
    Last Modified in 12/05/13
    679090026003
    [63] Rutiderma apex
    Last Modified in 12/05/13
    768685021003
    [64] Skogsbergia lerneri
    Last Modified in 12/05/13
    679592021003
    [65] Vargula hilgendorfii
    Last Modified in 12/05/13
    61101101021003
    [66] Vargula tsujii
    Last Modified in 12/05/13
    6110198021003
    [67] Aurila disparata
    Last Modified in 12/05/13
    669191026003
    [68] Bythoceratina hanejiensis
    Last Modified in 12/05/13
    669191026003
    [69] Candona holzkampfi
    Last Modified in 12/05/13
    669191026003
    [70] Cypridopsis japonica
    Last Modified in 12/05/13
    569797030003
    [71] Cypridopsis sp
    Last Modified in 12/05/13
    569797030003
    [72] Cypridopsis vidua
    Last Modified in 12/05/13
    569790030003
    [73] Cythere lutea
    Last Modified in 12/05/13
    669191026003
    [74] Cytherelloidea californica
    Last Modified in 12/05/13
    679083026003
    [75] Cytherelloidea sp
    Last Modified in 12/05/13
    679090026003
    [76] Cytheropteron subuchioi
    Last Modified in 12/05/13
    669191026003
    [77] Darwinula sp
    Last Modified in 12/05/13
    669185026003
    [78] Darwinula stevensoni
    Last Modified in 12/05/13
    669191026003
    [79] Heterocypris sp
    Last Modified in 12/05/13
    669186026003
    [80] Ilyocypris japonica
    Last Modified in 12/05/13
    669191026003
    [81] Ilyocypris sp
    Last Modified in 12/05/13
    669191026003
    [82] Ishizakiella miurensis
    Last Modified in 12/05/13
    669191026003
    [83] Kotoracythere inconspicua
    Last Modified in 12/05/13
    669191026003
    [84] Limnocythere sp
    Last Modified in 12/05/13
    669191026003
    [85] Loxocorniculum mutsuense
    Last Modified in 12/05/13
    669191026003
    [86] Macrocypris sp
    Last Modified in 12/05/13
    708787026003
    [87] Manawa staceyi
    Last Modified in 12/05/13
    689085025003
    [88] Neomonoceratina microreticulata
    Last Modified in 12/05/13
    669191026003
    [89] Neonesidea oligodentata
    Last Modified in 12/05/13
    708787026003
    [90] Neonesidea sp
    Last Modified in 12/05/13
    708783026003
    [91] Paradoxostoma setoense
    Last Modified in 12/05/13
    669191026003
    [92] Paradoxostoma sp
    Last Modified in 12/05/13
    669191026003
    [93] Parakrithella pseudadonta
    Last Modified in 12/05/13
    669191026003
    [94] Perissocytheridea japonica
    Last Modified in 12/05/13
    669191026003
    [95] Pontocypris mytiloides
    Last Modified in 12/05/13
    708787026003
    [96] Pontocythere subjaponica
    Last Modified in 12/05/13
    669191026003
    [97] Propontocypris sp1
    Last Modified in 12/05/13
    708783026003
    [98] Propontocypris sp2
    Last Modified in 12/05/13
    708787026003
    [99] Puriana sp
    Last Modified in 12/05/13
    669185026003
    [100] Terrestricythere pratensis
    Last Modified in 12/05/13
    718682026003
    [101] Vestalenula sp
    Last Modified in 12/05/13
    669191026003
    [102] Xestoleberis hanaii
    Last Modified in 12/05/13
    669191026003
    [103] Xestoleberis sp
    Last Modified in 12/05/13
    669191026003
    [104] Armillifer armillatus
    Last Modified in 12/05/13
    444946090003
    [105] Speleonectes tulumensis
    Last Modified in 12/05/13
    5510197027003
    [106] Chthamalus fragilis
    Last Modified in 12/05/13
    837875022003
    [107] Lepas anserifera
    Last Modified in 12/05/13
    728280029003
    [108] Loxothylacus texanus
    Last Modified in 12/05/13
    493737097003
    [109] Semibalanus balanoides
    Last Modified in 12/05/13
    609691027003


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