Data Descriptor

Tree of Sex: A database of sexual systems

  • Scientific Data 1, Article number: 140015 (2014)
  • doi:10.1038/sdata.2014.15
  • Download Citation
Received:
Accepted:
Published online:

Abstract

The vast majority of eukaryotic organisms reproduce sexually, yet the nature of the sexual system and the mechanism of sex determination often vary remarkably, even among closely related species. Some species of animals and plants change sex across their lifespan, some contain hermaphrodites as well as males and females, some determine sex with highly differentiated chromosomes, while others determine sex according to their environment. Testing evolutionary hypotheses regarding the causes and consequences of this diversity requires interspecific data placed in a phylogenetic context. Such comparative studies have been hampered by the lack of accessible data listing sexual systems and sex determination mechanisms across the eukaryotic tree of life. Here, we describe a database developed to facilitate access to sexual system and sex chromosome information, with data on sexual systems from 11,038 plant, 705 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian, and 11,556 invertebrate species.

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    & Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis. Genetics 197, 561–572 (2014).

  2. 2.

    & An Atlas of Mammalian Chromosomes Vol. 1 (Springer, 1967).

  3. 3.

    & An Atlas of Mammalian Chromosomes Vol. 2 (Springer, 1968).

  4. 4.

    & An Atlas of Mammalian Chromosomes Vol. 3 (Springer, 1969).

  5. 5.

    & An Atlas of Mammalian Chromosomes Vol. 4 (Springer, 1970).

  6. 6.

    & An Atlas of Mammalian Chromosomes Vol. 5 (Springer, 1971).

  7. 7.

    & An Atlas of Mammalian Chromosomes Vol. 6 (Springer, 1972).

  8. 8.

    & An Atlas of Mammalian Chromosomes Vol. 7 (Springer, 1973).

  9. 9.

    & An Atlas of Mammalian Chromosomes Vol. 8 (Springer, 1974).

  10. 10.

    & An Atlas of Mammalian Chromosomes Vol. 9 (Springer, 1975).

  11. 11.

    Fish Karyotypes (Springer, 2011).

  12. 12.

    & Chromorep: a reptile chromosomes database, (2005).

  13. 13.

    & Female meiosis drives karyotype evolution in mammals. Genetics 159, 1179–1189 (2001).

  14. 14.

    & Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture 208, 191–364 (2002).

  15. 15.

    , & ScaleNet () (2001).

  16. 16.

    & Dioecy and its correlates in the flowering plants. Am. J. Bot. 82, 596–606 (1995).

  17. 17.

    & Polyploidy and the evolution of gender dimorphism in plants. Science 289, 2335–2338 (2000).

  18. 18.

    , & Sex chromosomes in land plants. Ann. Rev. Plant Biol. 62, 485–514 (2011).

  19. 19.

    , et al. GenBank. Nucleic Acids Res. 41, D36–D42 (2013).

  20. 20.

    The Plant List, v1.1 () (2013).

  21. 21.

    USDA, NRCS. The PLANTS Database () (National Plant Data Team, 2014).

  22. 22.

    & Pollination and mating systems of Apodanthaceae and the distribution of reproductive traits in parasitic angiosperms. Am. J. Bot. 100, 1083–1094 (2013).

  23. 23.

    et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).

  24. 24.

    et al. Data from: Three keys to the radiation of angiosperms into freezing environments, (Dryad Digital Repository, 2014b).

  25. 25.

    , & TraitDB: a web application for storing and searching trait data () (2014).

  26. 26.

    R Development Core Team. R: A Language and Environment for Statistical Computing () (R foundation for Statistical Computing, 2005).

  27. 27.

    , & . APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).

  28. 28.

    Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution 3, 1084–1092 (2012).

  29. 29.

    GraPhlAn, v0.9 () (2012).

Download references

Data Citations

  1. 1.

    The Tree of Sex Consortium, Dryad http://dx.doi.org/10.5061/dryad.v1908 (2014)

  2. 2.

    The Tree of Sex Consortium, TreeOfSex in NESCent TraitDB http://purl.org/nescent/treeofsex (2014)

Acknowledgements

We would like to thank the following people for assistance with data collection: Gilad Berman, Marcus Campbell, Anna Johnson, Carlos Larrea, Angelica Lillico-Ouachour, Jason Rae, Nishant Singh, Kohta Yoshida, and Christie Ziegler. We thank Karen Cranston, Mercedes Gosby, Sandra Hall, and Daniel Leehr for developing TraitDB to allow user-designed queries of the database. We are grateful to the following experts in particular taxonomic groups who helped refine the database and/or provide additional data: Rafael Torres Colin, Chris Davies, Bryan Drew, Vladimir Gokhman, Favio Gonzalez, Claes Gustafsson, Peter Heenan, Norbert Holstein, Zhu Hua, Boris Igic, José Luis León de la Luz, Pedro Lorite, Timothy J. Motley, Roy Norton, Rafael Navajas Pérez, Susanne Renner, Jerzy Rzedowski, Stacey Smith, Valerie Souza, Robert Soreng, Daniel Thomas, Henk van der Werff, Amy Zanne. The database development was sponsored by NESCent as part of ‘The Tree of Sex’ working group (NSF EF-0905606). Funding was also provided by European Research Council Grant 260233 to J.M., National Science Foundation DEB-1020523 and -1241006 to T.-L.A., DEB-1120279 to E.E.G., and MCB-1244355 to N.V., NESCent visiting fellowship to H.B., Marie Curie Reintegration Grant CIG-293878 to I.M., MEXT Grant-in-Aid for Scientific Research on Innovative Areas (23113007) to J.K., Natural Environment Research Council grant to L.R., and Natural Sciences and Engineering Research Council Discovery grants to S.P.O. and J.C.V.

Author information

Affiliations

  1. Department Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA

    • Tia-Lynn Ashman
  2. Department of Integrative Biology, University of California, Berkeley, CA 94720, USA

    • Doris Bachtrog
  3. Department of Biology, University of Texas, Arlington, TX 76019, USA

    • Heath Blackmon
  4. Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA

    • Emma E Goldberg
  5. Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA

    • Matthew W Hahn
  6. Department of Integrative Biology, University of Texas, Austin, TX 78712, USA

    • Mark Kirkpatrick
  7. National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan

    • Jun Kitano
  8. Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK

    • Judith E Mank
  9. Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel-Aviv, 69978, Israel

    • Itay Mayrose
  10. Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA

    • Ray Ming
  11. Department of Zoology, University of British Columbia, Vancouver, BC V6J 3S7, Canada

    • Sarah P Otto
  12. Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

    • Catherine L Peichel
  13. Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA

    • Matthew W Pennell
  14. Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland

    • Nicolas Perrin
  15. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK

    • Laura Ross
  16. Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA

    • Nicole Valenzuela
  17. Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, USA

    • Jana C Vamosi

Consortia

  1. The Tree of Sex Consortium

Authors

    Contributions

    Working group organizers: D.B., J.E.M., C.L.P. Vertebrate data collectors: J.K., M.K., J.E.M., C.L.P. (fish); N.V. (non-avian reptiles); N.P. (amphibians); J.K. (mammals); J.M. (birds). Invertebrate data collectors: D.B., H.B., M.H., L.R. Plant data collectors: T.-L.A., E.E.G., I.M., R.M., S.P.O., J.C.V. To process and organize the databases, E.E.G., I.M., and S.P.O. wrote custom scripts. S.P.O., C.L.P., H.B., M.W.P., and J.C.V. contributed to the writing of the data descriptor. All authors contributed to the development of the ontology and edited the manuscript. All authors are members of The Tree of Sex Consortium.

    Competing interests

    The authors declare no competing financial interests.

    Corresponding author

    Correspondence to Sarah P Otto.

    Creative Commons BYThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0 Metadata associated with this Data Descriptor is available at http://www.nature.com/sdata/ and is released under the CC0 waiver to maximize reuse.