Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla).

Explosive bouts of diversification are one of the most conspicuous features of the tree of life. When such bursts are repeated in similar environments, it suggests some degree of predictability in the evolutionary process. We assess parallel adaptive radiation of South American pike cichlids (Crenicichla) using phylogenomics and phylogenetic comparative methods. We find that species flocks in the Uruguay and Iguazú River basins rapidly diversified into the same set of ecomorphs that reflect feeding ecology. Both adaptive radiations involve expansion of functional morphology, resulting in unique jaw phenotypes. Yet, form and function were decoupled such that most ecomorphs share similar mechanical properties of the jaws (i.e., jaw motion during a feeding strike). Prey mobility explained 6- to 9-fold differences in the rate of morphological evolution but had no effect on the rate of mechanical evolution. We find no evidence of gene flow between species flocks or with surrounding coastal lineages that may explain their rapid diversification. When compared with cichlids of the East African Great Lakes and other prominent adaptive radiations, pike cichlids share many themes, including the rapid expansion of phenotypic diversity, specialization along the benthic-to-pelagic habitat and soft-to-hard prey axes, and the evolution of conspicuous functional innovations. Yet, decoupled evolution of form and function and the absence of hybridization as a catalyzing force are departures from patterns observed in other adaptive radiations. Many-to-one mapping of morphology to mechanical properties is a mechanism by which pike cichlids attain a diversity of feeding ecologies while avoiding exacerbating underlying mechanical trade-offs. [Adaptive radiation; ecological opportunity; feeding kinematics; functional trade-off; hybridization; introgression.].

MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla).

Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65-121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25-40% (Lacustris group), 50-87% (Reticulata group, Teleocichla), 68-168% (Saxatilis group), 125-200% (Wallacii group), and 158-241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon.

Molecular clocks, biogeography and species diversity in Herichthys with evaluation of the role of Punta del Morro as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification.

Using molecular dated phylogenies and biogeographic reconstructions, the species diversity, biogeography and time frame of evolution of the genus Herichthys were evaluated. In particular, we test the role of Punta del Morro (PdM) as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification using several sets of calibrations. Species diversity in Herichthys is complex and the here employed dating methods suggest young age and rapid divergence for many species while species delimitation methods did not resolve these young species including both sympatric species pairs. Based on our molecular clock dating analyses, Herichthys has colonized its present distribution area significantly prior to the suggested vicariance by PdM (10-17.1 Ma vs. 5 to 7.5 Ma). The PdM constraint is in conflict with all other paleogeographic and fossil constraints including novel ones introduced in this study that are, however, congruent among each other. Our study demonstrates that any cichlid datings significantly older or younger than the bounds presented by our analyses and discussion have to be taken as highly questionable from the point of view of Middle American paleogeography and cichlid biogeography unless we allow the option that cichlid biogeography is completely independent from ecological and geological constraints.

The role of head shape and trophic variation in the diversification of the genus Herichthys in sympatry and allopatry.

In the present study we evaluated the putative cases of sympatric speciation in the genus Herichthys by studying the variation in head shape using principal component analysis, phylomorphospace and reconstructions of the ancestral states of feeding preferences. Herichthys includes both allopatric and sympatric sister species, as well as sympatric unrelated species and thus offers great potential for evolutionary studies of putatively sympatric speciation. Herichthys is the northernmost group of cichlids in America and one of the most ecologically disparate genera within Middle American cichlids. Fifteen anatomical points were recorded on the heads of 293 specimens of the 11 species recognized within the genus. The results show that in spite of having wide variation in consumed diets, most species of Herichthys are close in morphospace. However, morphological variation was great among the two pairs of sympatric sister species in agreement with the suggested sympatric model of speciation.

Feeding ecomorphologies in the fish genus Herichthys (Perciformes: Cichlidae) based on stomach content and lower pharyngeal jaw shape

Speciation is a multifactorial process with factors acting at different scales of space and time. Trophic niche segregation has promoted the diversification of cichlids fishes in lentic (lacustrine) environments, whether this is also the case in lotic (riverine) systems remains unknown. Herichthys is the genus of cichlids with the most boreal distribution in the Americas comprising 12 currently recognized species, most micro-endemic and only two with a wide distribution. In the present work, we analyzed the stomach content and lower pharyngeal jaw morphologies of the species of the genus to evaluate the possible role of feeding ecology in the diversification of the group. Trophic strategies varied widely, including omnivores, piscivores, invertivores, molluskivores, detritivores, herbivores and algivores. Low values of Pianka's index of niche overlap were found in the sympatric micro-endemic species, while in the widely distributed species the indices ranged from low to very high. The analysis of lower pharyngeal jaw morphologies allowed discriminating a shape associated with piscivorous species from other foraging groups. The results of this study suggest that trophic niche segregation is a factor that could promotes diversification within the genus Herichthys although additional studies need to be performed to fully understand the speciation process in this group of Neotropical cichlid fishes.

La especiación es un proceso con múltiples factores que actúan a diferentes escalas de espacio y tiempo. La segregación de nichos tróficos es un proceso que ha promovido la diversificación en cíclidos en entornos lacustres, pero en el caso de los ríos no está claro. Herichthys es un género de cíclidos cuya distribución es la más boreal en América, el cual comprende 12 especies actualmente reconocidas, la mayoría microendémicas y solo dos con una amplia distribución. En el presente trabajo, se analizó el contenido estomacal y las morfologías de la mandíbula faríngea inferior de las especies del género para compararlas y evaluar su posible papel en la diversificación del grupo. La dieta en dichas especies es muy variada e incluyó tanto especies que pueden ser consideradas omnívoras como especialistas. Se encontraron valores bajos del índice de solapamiento alimentario (índice de Pianka) en las especies simpátricas microendémicas, mientras que en las especies ampliamente distribuidas el índice fue muy variable. El análisis de morfometría geométrica de la mandíbula faríngea inferior permite discriminar dos formas principales, una que incluye la especie piscívora y otra que incluye a los otros grupos alimentarios. Los resultados encontrados en este estudio sugieren que la segregación de nicho trófico es un factor que promueve claramente la diversificación dentro del género Herichthys, aunque se deben realizar estudios adicionales para comprender completamente el proceso de especiación en este grupo de peces neotropicales.

Description of a new species of the Neotropical cichlid genus Gymnogeophagus Miranda Ribeiro, 1918 (Teleostei: Cichliformes) from the Middle Paraná basin, Misiones, Argentina.

Gymnogeophagus jaryi, new species, is described from Southern tributaries of the Middle Paraná basin in Misiones. It can be distinguished from all other members of the genus, except from G. australis and G. caaguazuensis, by the presence of a hyaline to grey anterior portion of the dorsal fin. Gymnogeophagus jaryi differs from G. caaguazuensis by a longer caudal peduncle, caudal fin not lyrate, central portion of scales on dorsal portion of trunk light iridescent blue and by white spots in soft portion of dorsal fin in adult males, and from G. australis by the light iridescent blue coloration of central portion of scales on the dorsal portion of trunk and tail, and by the lack of scales on the soft portion of the dorsal fin. Additionally, it can be diagnosed by the following unique combination of characters: 10-11 dorsal-fin branched rays, 27-30 E1 scales, absence of lips thickening, and, in males, by the possession of a hump in adults, caudal fin not lyrate, presence of large white spots forming transversal stripes distally and in anterior area of the dorsal fin's soft portion, central area of scales on the dorsal portion of the trunk light iridescent blue, lack of scales on the base of the dorsal fin's soft portion, absence of a conspicuous and oblique dark band from the eye to the anterior border of the head, anterior portion of dorsal fin hyaline to grey, scales of the midlateral spot each bearing a semicircular light blue blotch, head hump starting at the horizontal through the eyes, concave anterior profile in lateral view, base of unpaired fins yellow, and whitish hyaline spots on caudal fin. The new species, based on mtDNA phylogeny, is the sister species of G. caaguazuensis from the Paraguay basin and is closely related to G. australis.

Evolution of the Grey-bellied pygmy mouse group: Highly structured molecular diversity with predictable geographic ranges but morphological crypsis.

The grey-bellied pygmy mouse (Mus triton) from the endemic African subgenus Nannomys is a widespread rodent species inhabiting the highlands of eastern and central Africa. Although it has long been considered as a single species, recent data has suggested the existence of a species complex. In order to evaluate the geographical structure and current taxonomy of M. triton, we analysed one mitochondrial and six nuclear genes from individuals covering most of its distribution range. Our analysis revealed the existence of at least five distinct genetic lineages with only marginal overlaps among their distributional ranges. Morphological comparisons, however, showed large overlaps in external body measurements and only a weak differentiation in skull form. Therefore, we suggest maintaining M. triton as a single taxon with pronounced intraspecific genetic structure. Divergence dating analysis placed the most recent common ancestor of the extant lineages of M. triton to the early Pleistocene (about 2.0 Ma). The phylogeographic structure of the species was likely shaped by Pleistocene climatic oscillations and the highly diverse topography of eastern Africa.

Island- and lake-like parallel adaptive radiations replicated in rivers.

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 (Crenicichla) 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.

Oligosarcus amome (Ostariophysi: Characidae), a new species from the río Uruguay basin, Misiones, Argentina.

Oligosarcus amome is described from tributaries of the arroyo Yabotí-Guazú, río Uruguay basin, Misiones Province, Argentina. This new species can be distinguished from all its congeners by the following combination of characters: presence of two conspicuous series of teeth on premaxilla bearing pentacuspidate teeth in the outer series. Oligosarcus amome is the sister taxon of all remaining analyzed species of the genus excepting O. itau. 

Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe.

The theory of classical and cryptic Pleistocene refugia is based mainly on historical changes in temperature, and the refugia are usually defined within a latitudinal gradient. However, the gradient of oceanic-continental climate (i.e. longitudinal) was also significantly variable during glacial cycles with important biotic consequences. Range-wide phylogeography of the European ground squirrel (EGS) was used to interpret the evolutionary and palaeogeographical history of the species in Europe and to shed light on its glacial-interglacial dynamic. The EGS is a steppe-inhabiting species and the westernmost member of the genus in the Palaearctic region. We have analysed 915 specimens throughout the present natural range by employing mitochondrial DNA sequences (cytochrome b gene) and 12 nuclear microsatellite markers. The reconstructed phylogeography divides the species into two main geographical groups, with deep substructuring within both groups. Bulgaria is the centre of the ancestral area, and it also has the highest genetic diversity within the species. The northernmost group of the EGS survived in the southern part of Pannonia throughout several glacial-interglacial cycles. Animals from this population probably repeatedly colonized areas further to the north and west during the glacial periods, while in the interglacial periods, the EGS distribution contracted back to this Pannonian refugium. The EGS thus represents a species with a glacial expansion/interglacial contraction palaeogeographical dynamics, and the Pannonian and southeastern Balkanian steppes are supported as cryptic refugia of continental climate during Pleistocene interglacials.

Crenicichla taikyra (Teleostei: Cichlidae), a new species of pike cichlid from the middle rio Paraná, Argentina.

Crenicichla taikyra, new species, is described from the middle río Paraná, Argentina. Crenicichla taikyra is distinguished from the other species of the genus by the following combination of characters: lower pharyngeal tooth plate stout, bearing molariform teeth, ascending arm of premaxilla longer than the dentigerous arm, posterior edge of preoperculum serrated, a well developed suborbital stripe, and absence of scattered dark dots on flanks. Molariform teeth on pharyngeal jaws is a derived character among Crenicichla species, however this character state has appeared several times in unrelated species.

Multilocus phylogeny of Crenicichla (Teleostei: Cichlidae), with biogeography of the C. lacustris group: species flocks as a model for sympatric speciation in rivers.

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).

Crenicichla ypo (Teleostei: Cichlidae), a new species from the middle Paraná basin in Misiones, Argentina

A new species of Crenicichla, C. ypo, is described from the Arroyo Urugua-í, a left-hand tributary of the middle Paraná River, Misiones province, Argentina. The new species is recognized by 6 to 8 irregular blotches along the upper lateral line, absence of scattered dark spots on flanks, low number (47-55) of E1 scales, and a slightly prognathous lower jaw. Females have a distinctive coloration of the dorsal fin, with a wide black longitudinal stripe on the distal portion with an equally wide red stripe below it.

Una nueva especie de Crenicichla, C. ypo, es descripta de la cuenca del arroyo Urugua-í, tributaria de la margen izquierda del río Paraná medio, provincia de Misiones, Argentina. La nueva especie es reconocida por tener 6 a 8 manchas irregulares sobre la línea lateral superior, ausencia de pequeñas manchas oscuras dispersas sobre el flanco, bajo número (47-55) de escamas en la serie E1 y la quijada inferior levemente prognata. Las hembras tienen una coloración distintiva en la aleta dorsal con una banda ancha negra en la porción distal y otra roja del mismo ancho por debajo de esta.

Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology.

Heroine cichlids are the second largest and very diverse tribe of Neotropical cichlids, and the only cichlid group that inhabits Mesoamerica. The taxonomy of heroines is complex because monophyly of most genera has never been demonstrated, and many species groups are without applicable generic names after their removal from the catch-all genus Cichlasoma (sensu Regan, 1905). Hence, a robust phylogeny for the group is largely wanting. A rather complete heroine phylogeny based on cytb sequence data is available [Concheiro Pérez, G.A., Rícan O., Ortí G., Bermingham, E., Doadrio, I., Zardoya, R. 2007. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 43, 91-110], and in the present study, we have added and analyzed independent data sets (nuclear and morphological) to further confirm and strengthen the cytb-phylogenetic hypothesis. We have analyzed a combined cytb-nuclear (RAG1 and two S7 introns) data set of 48 species representing main heroine lineages to achieve further resolution of heroine higher taxonomic levels and a combined cytb-morphological data set of 92 species to stabilize generic taxonomy. The recovered phylogenies supported the circumamazonian--CAM--Heroini (sensu Concheiro Peréz et al., 2007) as a monophyletic group, that could be divided into six main clades: (1) australoheroines (the southernmost heroine genus Australoheros), (2) nandopsines (the Antillean genus Nandopsis), (3) caquetaines (including the north western Amazonian genera Caquetaia and Heroina), (4) astatheroines (including Astatheros, Herotilapia and Rocio), (5) amphilophines (including Amphilophus and related genera), and (6) herichthyines (including Herichthyis and related genera). Nuclear and mitochondrial data partitions arrived at highly congruent topologies. Suprageneric relationships were influenced mainly by the nuclear signal, as well as the most basal phylogenetic position of Australoheros within CAM heroines. The new phylogeny of the tribe Heroini provides robust framework to stabilize the taxonomy of the group and for future comparative studies on these morphologically and ecologically diverse freshwater fishes. Morphology was mostly informative at the genus level and aid in determining the monophyly and composition of heroine genera. Upon acceptance of all putative genera, as recovered in this study, the Heroini would be with 35 genera the most genus-rich clade of Neotropical cichlids.

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae).

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.

Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene.

Heroini constitute the second largest tribe of Neotropical cichlids and show their greatest diversity in Mesoamerica. Although heroine species are morphologically and ecologically very diverse, they were all historically assigned to one single genus, Cichlasoma that was never formally revised from a phylogenetic point of view. Here, we present the most comprehensive molecular phylogeny of the tribe Heroini to date, based on the complete DNA sequence of the mitochondrial gene cytochrome b, and the analysis of 204 individuals representing 91 species. Phylogenetic analyses did not support the monophyly of heroines because the genus Pterophyllum was placed as the sister group of all remaining heroines plus cichlasomatines. However, the recovered relative position of Pterophyllum was without strong statistical support. Within the remaining heroines, Hyspelecara and Hoplarchus are recovered with low support in a basal position with respect to a clade that includes Heros, Uaru, Mesonauta, and Symphysodon, and the circumamazonian (CAM) heroines. The first clade is restricted to South America. The largest clade of heroines, the CAM heroines, include more than 85% of the species within the tribe. This clade is mostly Mesoamerican, but also contains four species found in the Greater Antilles (Nandopsis), and three genera found in South America (the 'Heros' festae group, Australoheros, and Caquetaia). Up to eight major lineages can be recovered within the CAM heroines, but the phylogenetic relationships among them remain unresolved. Two large suprageneric groups can be distinguished, the amphilophines and the herichthyines. The amphilophines include Amphilophus, Archocentrus, Hypsophrys, Neetroplus, Parachromis, Petenia, and five additional unnamed genera (the 'Heros' istlanus group, the 'Amphilophus' calobrensis group, the 'Heros' urophthalmus group, the 'Heros' wesseli group, and the 'Heros' sieboldii group). The herichthyines include the crown-group herichthyines (Herichthys, Theraps, Vieja, and Paratheraps) and the genera Tomocichla, Herotilapia, and Thorichthys, together with three unnamed genera (the 'Heros' umbriferus group, the 'Heros' grammodes group, and the 'Heros' salvini group). Amphilophines are prevalent in southern Mesomerica south of the Motagua fault. Herichthyines have basal linages in Central America, whereas crown-group herichthyines and three related genera are found north from the Motagua fault. At least two independent origins are required to explain current Mesoamerican heroine distribution. Dispersal of heroines from South America into Mesoamerica was dated between 24 and 16 million years ago (MYA) based on geological calibrations and on standard fish mitochondrial cytochrome b rates, respectively. These datings cannot be reconciled with currently known geological evidence, and the existence of a connection between Central America and South America in the Miocene needs to be postulated in order to explain the origins of Mesoamerican heroine lineages. However, our datings agree with those estimated for the dispersal of other secondary freshwater fishes (Rivulidae, Synbranchus) into Mesoamerica, and predate the invasion of primary freshwater fishes by at least 10 myr.