Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex

Research output: Contribution to journalArticle


Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and 4 nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.


  • Spiros Papakostas
  • Evangelia Michaloudi
  • Konstantinos Proios
  • Michaela Brehm
  • Laurens Verhage
  • Jadranka Rota
  • Carlos Peña
  • Georgia Stamou
  • Victoria L Pritchard
  • Diego Fontaneto
  • Steven A J Declerck
External organisations
  • Netherlands Institute of Ecology (NIOO-KNAW)
  • Aristotle University of Thessaloniki
  • University of Turku
  • CNR Institute of Ecosystem Study (ISE)
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Zoology
  • Ecology
  • Evolutionary Biology


  • 18S and 28S ribosomal RNA genes, cyclical parthenogens, cytochrome c oxidase subunit I, DNA barcoding, GMYC, haploweb, internal transcribed spacer I, reticulate evolution
Original languageEnglish
Pages (from-to)508-24
Number of pages17
JournalSystematic Biology
Issue number3
Publication statusPublished - 2016 May
Publication categoryResearch
Externally publishedYes