First multilocus analysis of the largest Neotropical cichlid genus Crenicichla combining mitochondrial (cytb, ND2, 16S) and nuclear (S7 intron 1) genes and comprising 602 sequences of 169 specimens yields a robust phylogenetic hypothesis. The best marker in the combined analysis is the ND2 gene which contributes throughout the whole range of hierarchical levels in the tree and shows weak effects of saturation at the 3rd codon position. The 16S locus exerts almost no influence on the inferred phylogeny. The nuclear S7 intron 1 resolves mainly deeper nodes. Crenicichla is split into two main clades: (1) Teleocichla, the Crenicichla wallacii group, and the Crenicichla lugubris-Crenicichla saxatilis groups ("the TWLuS clade"); (2) the Crenicichla reticulata group and the Crenicichla lacustris group-Crenicichla macrophthalma ("the RMLa clade"). Our study confirms the monophyly of the C. lacustris species group with very high support. The biogeographic reconstruction of the C. lacustris group using dispersal-vicariance analysis underlines the importance of ancient barriers between the middle and upper Paraná River (the Guaíra Falls) and between the middle and upper Uruguay River (the Moconá Falls). Our phylogeny recovers two endemic species flocks within the C. lacustris group, the Crenicichla missioneira species flock and the herein discovered Crenicichla mandelburgeri species flock from the Uruguay and Paraná/Iguazú Rivers, respectively. We discuss putative sympatric diversification of trophic traits (morphology of jaws and lips, dentition) and propose these species flocks as models for studying sympatric speciation in complex riverine systems. The possible role of hybridization as a mechanism of speciation is mentioned with a recorded example (Crenicichla scottii).

Background: Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole.

Aim We present a molecular phylogenetic and biogeographical analysis of the Mesoamerican cichlid fishes (Cichlidae: Cichlasomatinae: Heroini), a dominant part of the freshwater biodiversity of the region. Based on these analyses we investigate the spatial and temporal origins and diversification of the group. Location Mesoamerica. Methods Model‐based phylogenetic methods (MrBayes) using seven molecular markers with a virtually complete species‐level taxon sampling, together with the Bayesian approach to statistical dispersal–vicariance analysis (S‐DIVA), and fossil‐ and palaeogeography‐calibrated beast molecular clock analyses were used to assess the timing of dispersal, vicariance and diversification events. Results We present a robust multigene phylogeny resolved from the deepest nodes to the species level. Two colonizations of Middle America and one of the Greater Antilles occurred from South America within a narrow time window during the Oligocene epoch. Cichlid colonization of Central America proceeded from the north in the Early–Middle Miocene. Central America later became repeatedly fragmented during the latter half of the Miocene, which led to the formation of the present ichthyological provinces prior to the final closure of the Panama Isthmus. Main conclusions The heroine cichlid fishes colonized the Greater Antilles and Middle America simultaneously through the GAARlandia land bridge during the Oligocene. Central America (including eastern Panama) was colonized from northern Middle America in the Early–Middle Miocene. Thus our results do not support a direct colonization of Middle America from South America, or a Cretaceous–Palaeocene colonization through the proto‐Antilles, or a colonization of the Greater Antilles from Middle America as suggested by previous studies.

Parallel adaptive radiations have arisen following the colonization of islands by lizards and lakes by fishes. In these classic examples, parallel adaptive radiation is a response to the ecological opportunities afforded by the colonization of novel ecosystems and similar adaptive landscapes that favour the evolution of similar suites of ecomorphs, despite independent evolutionary histories. Here, we demonstrate that parallel adaptive radiations of cichlid fishes arose in South American rivers. Speciation-assembled communities of pike cichlids () have independently diversified into similar suites of novel ecomorphs in the Uruguay and Paraná Rivers, including crevice feeders, periphyton grazers and molluscivores. There were bursts in phenotypic evolution associated with the colonization of each river and the subsequent expansion of morphospace following the evolution of the ecomorphs. These riverine clades demonstrate that characteristics emblematic of textbook parallel adaptive radiations of island- and lake-dwelling assemblages are feasible evolutionary outcomes even in labile ecosystems such as rivers.

The Crenicichla mandelburgeri species complex from the Middle Parana ´basin is a diverse group of cichlid species and contains all known ecomorphs found within the entire genus Crenicichla.Here, we study the phylogenetic relationships within the C. mandelburgeri species complex using ddRAD sequencing with focus on its two candidate species flocks endemic to the Iguazu ´and Urugua-ı ´Rivers, and on two putative sympatric species in the Piray Guazu Ŕiver. These species flocks include four and three syntopic species, respectively, which are strongly adapted to different trophic niches and include derived ecomorphs of Crenicichla (molluscivores, a periphyton grazer, and a crevice-feeding thick-lipped invertivore). Our phylogenomic analyses strongly support monophyly and rapid diversification of the Iguazu śpecies flock, but reveal more complex evolutionary histories in the Urugua-ı ´and Piray Guazu ´tributaries. Most species in the Middle Parana ´, including one species in the Urugua-ı ´and both species in the Piray Guazu ´show cytonuclear discordance, and in both of these tributaries, we also found hybridization in one of the resident species. Population-level analyses reveal complete isolation of the Iguazu ´species and coupled with their dramatic ecological diversity, this radiation exemplifies characteristics of a species flock that arose via ecological speciation.