A database of amphibian karyotypes

  • Riddhi D. Perkins
  • Julio Rincones Gamboa
  • Michelle M Jonika
  • Johnathan Lo
  • Amy Shum
  • Richard H. Adams
  • Heath BlackmonEmail author
Original Article


One of the first characteristics that we learn about the genome of many species is the number of chromosomes it is divided among. Despite this, many questions regarding the evolution of chromosome number remain unanswered. Testing hypotheses of chromosome number evolution using comparative approaches requires trait data to be readily accessible and associated with currently accepted taxonomy. The lack of accessible karyotype data that can be linked to phylogenies has limited the application of comparative approaches that could help us understand the evolution of genome structure. Furthermore, for taxonomists, the significance of new karyotype data can only be determined with reference to records for other species. Here, we describe a curated database ( developed to facilitate access to chromosome number and sex chromosome system data for amphibians. The open web interface for this database allows users to generate customized exploratory plots and tables of selected clades, as well as downloading CSV files for offline analyses.


Amphibian Chromosome number Cytogenetic Cytotaxonomy Sex chromosome 



for the Latin conformis or conferre


for the Latin affinis


Authors’ contributions

HB and RHA conceived of the database and developed the ontology used. HB and RP both contributed to writing the manuscript, and collection of records. Research towards name resolution was performed by all authors and all authors edited the manuscript.

Compliance with ethical standards

Competing interests

The authors declare no conflict of interest.


  1. Blackmon H, Demuth JP (2015) Genomic origins of insect sex chromosomes. Curr Opin Insect Sci 7:45–50CrossRefGoogle Scholar
  2. Blackmon H, Hardy NB, Ross L (2015) The evolutionary dynamics of haplodiploidy: genome architecture and haploid viability. Evolution 69:2971–2978CrossRefPubMedPubMedCentralGoogle Scholar
  3. Blackmon H, Justison J, Mayrose I, Goldberg EE (2019) Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 73:511–523CrossRefPubMedPubMedCentralGoogle Scholar
  4. Chang, W., Cheng, J., Allaire, J., Xie, Y. & Mcpherson, J. 2018. Shiny: web application framework for R version 1.1.0Google Scholar
  5. Charlesworth D, Charlesworth B (1980) Sex differences in fitness and selection for centric fusions between sex-chromosomes and autosomes. Genet Res 35:205–214CrossRefPubMedGoogle Scholar
  6. Fitzjohn RG (2012) Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol Evol 3:1084–1092CrossRefGoogle Scholar
  7. Flemming, W. 1882. Zellsubstanz, kern und zelltheilung, VogelGoogle Scholar
  8. Freyman WA, Höhna S (2017) Cladogenetic and anagenetic models of chromosome number evolution: A Bayesian model averaging approach. Syst Biol 67:195–215CrossRefGoogle Scholar
  9. Frost DR (2018) Amphibian species of the world: an online reference. Version 6. 11 July 2018. American Museum of Natural HistoryGoogle Scholar
  10. Green DM, Sessions SK (1991) Amphibian cytogenetics and evolution. Academic Press, San DiegoGoogle Scholar
  11. Gregory TR (2001) The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cell Mol Dis 27:830–843CrossRefGoogle Scholar
  12. Hillis DM (1991) The phylogeny of amphibians: current knowledge and the role of cytogenetics. Amphibian Cytogenet Evol:7–31Google Scholar
  13. Kezer J (1964) Meiosis in salamander spermatocytes. The meehanics of inheritance. Found Mod Genetics Series 100Google Scholar
  14. King M (1990) Animal cytogenetics: Amphibia. Gebruder Borntraeger, BerlinGoogle Scholar
  15. Kitano J, Ross JA, Mori S, Kume M, Jones FC, Chan YF, Absher DM, Grimwood J, Schmutz J, Myers RM (2009) A role for a neo-sex chromosome in stickleback speciation. Nature 461:1079–1083CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lande R (1985) The fixation of chromosomal rearrangements in a subdivided population with local extinction and colonization. Heredity 54:323–332CrossRefPubMedGoogle Scholar
  17. Liedtke HC, Gower DJ, Wilkinson M, Gomez-Mestre I (2018) Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. In: Nature Ecology & EvolutionGoogle Scholar
  18. Mohlhenrich ER, Mueller RL (2016) Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 70:2865–2878CrossRefPubMedGoogle Scholar
  19. Morescalchi A (1973) Amphibia. In: Cytotaxonomy and vertebrate evolution, pp 233–347Google Scholar
  20. Paradis E, Blomberg S, Bolker B, Brown J, Claude J, Cuong HS, Desper R, Didier G (2018) Package ‘ape’. In: Analyses of phylogenetics and evolution, version, vol 2, pp 4–1Google Scholar
  21. Pennell MW, Kirkpatrick M, Otto SP, Vamosi JC, Peichel CL, Valenzuela N, Kitano J (2015) Y fuse? Sex chromosome fusions in fishes and reptiles. PLoS Genet 11:e1005237CrossRefPubMedPubMedCentralGoogle Scholar
  22. Rees JA, Cranston K (2017) Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data JGoogle Scholar
  23. Revell LJ (2012) Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 3:217–223CrossRefGoogle Scholar
  24. Ross L, Blackmon H, Lorite P, Gokhman V, Hardy N (2015) Recombination, chromosome number and eusociality in the hymenoptera. J Evol Biol 28:105–116CrossRefPubMedPubMedCentralGoogle Scholar
  25. Roth G, Blanke J, Wake DB (1994) Cell size predicts morphological complexity in the brains of frogs and salamanders. Proc Natl Acad Sci 91:4796–4800CrossRefPubMedGoogle Scholar
  26. Schmid M, Bogart J, Hedges S (2010) The chromosomes of terraranan frogs. Insights into vertebrate cytogenetics. Cytogenet Genome Res 130:1–568CrossRefPubMedGoogle Scholar
  27. Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538:336–343CrossRefPubMedPubMedCentralGoogle Scholar
  28. Sherman PW (1979) Insect chromosome numbers and Eusociality. Am Nat 113:925–935CrossRefGoogle Scholar
  29. Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL (2011) LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol 4:168–183CrossRefPubMedPubMedCentralGoogle Scholar
  30. Sved JA, Chen Y, Shearman D, Frommer M, Gilchrist AS, Sherwin WB (2016) Extraordinary conservation of entire chromosomes in insects over long evolutionary periods. Evolution 70:229–234CrossRefPubMedGoogle Scholar
  31. Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry R, Basa S, Walker JA, Smith JJ (2011) Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res, gr 116491:110Google Scholar
  32. White MJD (1977) Animal cytology & evolution. University Press, CambridgeGoogle Scholar
  33. Zenil-Ferguson R, Burleigh JG, Ponciano JM (2018) Chromploid: an R package for chromosome number evolution across the plant tree of life. Appl Plant Sci 6:e1037CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of BiologyTAMU 3258 Texas A&MCollege StationUSA
  2. 2.Department of BiologyUniversity of Texas at ArlingtonArlingtonUSA

Personalised recommendations