title: Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex.
abstract: 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.
authors.affiliation: Netherlands Institute of Ecology, Department of Aquatic Ecology, Wageningen, Netherlands; Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland;
authors.forename: Spiros
authors.initials: S
authors.lastname: Papakostas
authors.affiliation: Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece;
authors.forename: Evangelia
authors.initials: E
authors.lastname: Michaloudi
authors.affiliation: Netherlands Institute of Ecology, Department of Aquatic Ecology, Wageningen, Netherlands;
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Proios
authors.affiliation: Netherlands Institute of Ecology, Department of Aquatic Ecology, Wageningen, Netherlands;
authors.forename: Michaela
authors.initials: M
authors.lastname: Brehm
authors.affiliation: Netherlands Institute of Ecology, Department of Aquatic Ecology, Wageningen, Netherlands;
authors.forename: Laurens
authors.initials: L
authors.lastname: Verhage
authors.affiliation: Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland; Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Biology, Lund University, Lund, Sweden;
authors.forename: Jadranka
authors.initials: J
authors.lastname: Rota
authors.affiliation: Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland;
authors.forename: Carlos
authors.initials: C
authors.lastname: Peña
authors.affiliation: Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece;
authors.forename: Georgia
authors.initials: G
authors.lastname: Stamou
authors.affiliation: Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland;
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Pritchard
authors.affiliation: National Research Council, Institute of Ecosystem Study, Verbania Pallanza, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Fontaneto
authors.affiliation: Netherlands Institute of Ecology, Department of Aquatic Ecology, Wageningen, Netherlands;
authors.forename: Steven A J
authors.initials: SA
authors.lastname: Declerck
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D050259:Genes, Mitochondrial / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D006824:Hybridization, Genetic; D010802:Phylogeny; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D012403:Rotifera / Q000145:classification* / Q000235:genetics; D013045:Species Specificity
chemical_list: D021903:DNA, Ribosomal Spacer; D005819:Genetic Markers; D012339:RNA, Ribosomal, 28S
keywords: 18S and 28S ribosomal RNA genes; DNA barcoding; GMYC; cyclical parthenogens; cytochrome c oxidase subunit I; haploweb; internal transcribed spacer I; reticulate evolution