Genus‐level supertree of Cyprinidae (Actinopterygii: Cypriniformes), partitioned qualitative clade support and test of macro‐evolutionary scenarios

Abstract

We used the supertree approach of matrix representation with parsimony to reconstruct to date the most exhaustive (genus-level) phylogeny of Cyprinidae. The supertree of Cyprinidae, representing 397 taxa (237 nominal genera) and 990 pseudocharacters, was well resolved (96%) through extended consensus majority rule, although 36 nodes (9.4%) were unsupported. The proportion of shared taxa among source trees was very low after calculation of the taxonomic coverage index (TCI = 0.059), which is proposed here as a more accurate alternative to the usual ratios calculated from the number of pseudo-characters or source trees per taxon. We define a new index for the calculation of partitioned qualitative clade support, the partitioned rQS ((p)rQS), which offers a straightforward visualization of the relative supports of source tree partitions at supertree nodes.The use of (p)rQS showed that the molecular source tree partition contributed to most node supports within the supertree of Cyprinidae (73%, contra 21% for the morphological partition) and evidenced a fair proportion of conflict at nodes between the two partitions (21%), notably reflecting (i) the greater number and resolution of molecular source trees, and (ii) potential morphological convergences. Most of the higher-level relationships within Cyprinidae were supported by both morphological and molecular source tree partitions. Our supertree showed a well-supported dichotomy between a clade consisting of a 'barbine' + 'rasborine' lineage, sister group to (Barbinae [paraphyletic], (Cyprininae, Labeoninae)), and a clade consisting of other rasborines (large polytomy) and the two monophyletic groups ((Tincinae, Tanichthys), (Ecocarpia, (Acheilognathinae, (Gobioninae, Leuciscinae)))) and (Squaliobarbinae, (Xenocyprinae, Cultrinae)). Through the non-monophyly of almost all the traditional subfamilies of Cyprinidae and 34 genera, our supertree exemplified the taxonomic chaos that reigns in the classification of the family. It also highlighted that further efforts should aim at increasing taxonomic sampling and generating alternative phylogenetic signals, notably for the still poorly apprehended Tincinae, Squaliobarbinae, Acheilognathinae, Gobioninae, and Rasborinae, the latter representing a key taxon for the understanding of early cyprinid evolution. Our supertree also proved useful for testing macro-evolutionary scenarios at a wide taxonomic scale. Ancestral reconstructions using linear parsimony confirmed that the Oriental tropical region was the centre of origin of Cyprinidae, and identified three Oriental-to-Palaearctic, two Palaearctic-to-Nearctic, and one Oriental-to-Afrotropical major migration events. On the other hand, we almost completely rejected the hypothesis of presence of barbels as a plesiomorphic condition within Cyprinidae (although ambiguous for maxillary barbels of the Barbinae-Cyprininae type). The supertree of Cyprinidae serves as a basis to discuss the applications and bias of the newly proposed (p)rQS, to provide future guidelines for a better a...

Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

“…The connection of drainages between East Asia (China) and Southeast Asia may have contributed to this reverse dispersal. Our biogeographic results of Labeoninae coincide with Gaubert et al (2009) about the Oriental tropical origin of Cyprinidae and our results also verify the Oriental-to-Afrotropical migration events.…”

“…Gaubert et al (2009) proposed that the Oriental tropical region was the centre of origin of Cyprinidae, and identified three Oriental-to-Palaearctic, two Palaearctic-to-Nearctic, and one Oriental-to-Afrotropical major migration events.…”

Revision of Iquius nipponicus Jordan 1919 (Teleostei: Cyprinidae) from the Miocene of Iki Island, Nagasaki, Japan and its phylogenetic position

“…Synapomorphies of other clades were discussed by Cavender and Coburn (1992). There have been many molecular phylogenetic analyses of the family Cyprinidae (e.g., Liu and Chen 2003;Wang et al 2007;Mayden et al 2008;Gaubert et al 2009;Mayden et al 2009). These molecular studies all support a close relationship between xenocyprinins and cultrins.…”

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“…However, the timing is still controversial, as are processes that have led to the key assemblage components of each biogeographic region (Bȃnȃrescu, 2004;Gaubert et al, 2009). The biogeographical boundary of the mid-Aegean trench separating Anatolia from Southern Greece is long established (Poulakakis et al, 2015;Zogaris et al, 2009), but dispersal of freshwater organisms may have occurred either during the MSC or even at an earlier land contact event.…”