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.

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

“…The absence of hybrids in the B. plicatilis complex is in stark contrast with what is known in the B. calyciflorus complex, for which a high level of hybridization and mitonuclear discordance between cryptic species is present (Papakostas et al, 2016). The reasons for such differences in the level of hybridization in the two species complexes of the same genus are still unknown and deserve further investigation.…”

Monogonont rotifers as model systems for the study of micro-evolutionary adaptation and its eco-evolutionary implications

“…The B. plicatilis complex is a strong candidate taxon because it is by far the most well-documented and resolved monogonont species complex. While B. calyciflorus has also been the subject of many studies, its species complex is yet poorly understood although efforts are currently being done to fill this knowledge gap (Papakostas et al, 2016). A major advantage of B. calyciflorus is that it is a common freshwater species in many parts of the world.…”

“…Since the discovery of cryptic species in Brachionus plicatilis (Gómez & Serra, 1995;Gómez et al, 2002), the number of rotifer taxa known to be composed of cryptic species has steadily increased during the last decade (Walsh et al, 2009;Obertegger et al, 2012). Furthermore, several studies have provided evidence for substantial ecological segregation among such species (Gabaldón et al, 2015a;Papakostas et al, 2016). Because cryptic species are often found to be sympatric Gabaldón et al 2015b, Papakostas et al, 2016, the potential occurrence of multiple species in experimental populations of microevolution studies may incur considerable risks.…”

“…Furthermore, several studies have provided evidence for substantial ecological segregation among such species (Gabaldón et al, 2015a;Papakostas et al, 2016). Because cryptic species are often found to be sympatric Gabaldón et al 2015b, Papakostas et al, 2016, the potential occurrence of multiple species in experimental populations of microevolution studies may incur considerable risks. Indeed, when the species identity of genotypes is ignored, trait shifts in populations may not be unequivocally due to microevolutionary responses, but may as well be caused by changes in the relative abundance of cryptic species.…”

Rotifers in Lake Orta: a potential ecological and evolutionary model system

“…Surprisingly, the DNA sequences of the resting eggs of B. calyciflorus from the pre-, during and post-pollution phases represented the same mtDNA haplotype through time. This species is highly variable in the analysed mtDNA fragment (Papakostas et al, 2016); thus, the fact that only one haplotype was found in the lake suggests that this species was able to quickly adapt locally through priority effects and monopolisation (De Meester et al, 2002), and no foreign mtDNA haplotypes managed to colonise the lake during its fluctuating conditions. …”