, Volume 796, Issue 1, pp 39–58 | Cite as

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

  • Scott Mills
  • J. Arturo Alcántara-Rodríguez
  • Jorge Ciros-Pérez
  • Africa Gómez
  • Atsushi Hagiwara
  • Kayla Hinson Galindo
  • Christian D. Jersabek
  • Reza Malekzadeh-Viayeh
  • Francesca Leasi
  • Jae-Seong Lee
  • David B. Mark Welch
  • Spiros Papakostas
  • Simone Riss
  • Hendrik Segers
  • Manuel Serra
  • Russell Shiel
  • Radoslav Smolak
  • Terry W. Snell
  • Claus-Peter Stelzer
  • Cuong Q. Tang
  • Robert L. Wallace
  • Diego FontanetoEmail author
  • Elizabeth J. Walsh


Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).


Biodiversity COI Cryptic species Evolution ITS1 Phylogenetic comparative methods Zooplankton 



We acknowledge support from the staff of the Department of Biological Sciences at the University of Texas at El Paso, especially B. Smith, T. Valenzuela, L. and L. Hamden. Two anonymous reviewers provided useful comments to improve an earlier draft of the manuscript. Funding was provided by UTEP’s Office of Research and Sponsored Projects, College of Science, Department of Biological Sciences, NSF DEB 1257068 (E. J. Walsh) and NSF DEB 1257116 (R. L. Wallace).

Supplementary material

10750_2016_2725_MOESM1_ESM.jpg (391 kb)
Supplementary Figure S1. ITS1 from BEAST (JPEG 392 kb)
10750_2016_2725_MOESM2_ESM.jpg (436 kb)
Supplementary Figure S2. ITS1 from PhyML (JPEG 436 kb)
10750_2016_2725_MOESM3_ESM.jpg (1.7 mb)
Supplementary Figure S3. COI from BEAST (JPEG 1704 kb)
10750_2016_2725_MOESM4_ESM.jpg (1.7 mb)
Supplementary Figure S4. COI from PhyML (JPEG 1710 kb)
10750_2016_2725_MOESM5_ESM.jpg (436 kb)
Supplementary Figure S5. RAxML on combined alignment (JPEG 437 kb)
10750_2016_2725_MOESM6_ESM.txt (102 kb)
Supplementary File S1. List of all 1273 isolates with accession numbers for COI and ITS1. For each isolate, the identification of unique sequences, and the attribution to the 15 species is reported. [GenBank accessions to be disclosed later] (TXT 103 kb)
10750_2016_2725_MOESM7_ESM.docx (95 kb)
Supplementary material 7 (DOCX 96 kb)
10750_2016_2725_MOESM8_ESM.txt (0 kb)
Supplementary File S3. Phylogeny of the 14 species with COI and ITS1 in newick format (TXT 1 kb)


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Scott Mills
    • 1
  • J. Arturo Alcántara-Rodríguez
    • 2
  • Jorge Ciros-Pérez
    • 2
  • Africa Gómez
    • 3
  • Atsushi Hagiwara
    • 4
  • Kayla Hinson Galindo
    • 5
  • Christian D. Jersabek
    • 6
  • Reza Malekzadeh-Viayeh
    • 7
  • Francesca Leasi
    • 8
  • Jae-Seong Lee
    • 9
  • David B. Mark Welch
    • 10
  • Spiros Papakostas
    • 11
  • Simone Riss
    • 12
  • Hendrik Segers
    • 13
  • Manuel Serra
    • 14
  • Russell Shiel
    • 15
  • Radoslav Smolak
    • 16
  • Terry W. Snell
    • 17
  • Claus-Peter Stelzer
    • 12
  • Cuong Q. Tang
    • 18
  • Robert L. Wallace
    • 19
  • Diego Fontaneto
    • 20
    Email author
  • Elizabeth J. Walsh
    • 5
  1. 1.James Cook UniversityTownsvilleAustralia
  2. 2.Proyecto de Investigación en Limnología Tropical, FES IztacalaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
  3. 3.School of Biological, Biomedical and Environmental SciencesUniversity of HullHullUK
  4. 4.Graduate School of Fisheries and Environmental SciencesNagasaki UniversityNagasakiJapan
  5. 5.Department of Biological SciencesUniversity of Texas at El PasoEl PasoUSA
  6. 6.Department of Organismal BiologyUniversity of SalzburgSalzburgAustria
  7. 7.Artemia and Aquatic Research InstituteUrmia UniversityUrmiaIran
  8. 8.Department of Invertebrate ZoologySmithsonian National Museum of Natural HistoryWashingtonUSA
  9. 9.Department of Biological Science, College of ScienceSungkyunkwan UniversitySuwonSouth Korea
  10. 10.Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleUSA
  11. 11.Division of Genetics and Physiology, Department of BiologyUniversity of TurkuTurkuFinland
  12. 12.Research Institute for LimnologyUniversity of InnsbruckMondseeAustria
  13. 13.OD NatureRoyal Belgian Institute of Natural SciencesBrusselsBelgium
  14. 14.Institut Cavanilles de Biodiversitat i Biologia EvolutivaUniversitat de ValènciaValenciaSpain
  15. 15.Biological SciencesUniversity of AdelaideAdelaideAustralia
  16. 16.Department of Ecology, Faculty of Humanities and Natural SciencesPresov UniversityPresovSlovakia
  17. 17.School of BiologyGeorgia Institute of TechnologyAtlantaUSA
  18. 18.Department of Life SciencesThe Natural History MuseumLondonUK
  19. 19.Department of BiologyRipon CollegeRiponUSA
  20. 20.Institute of Ecosystem StudyNational Research Council of ItalyVerbania PallanzaItaly

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