Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

Background

With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.

Results

In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses.

Conclusion

A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.     

Phylogenetic relationships among Acestrorhynchus species (Ostariophysi: Characiformes: Acestrorhynchidae)

A total of 104 osteological and external morphological features were examined in 13 species of Acestrorhynchus and 15 outgroup taxa to advance a hypothesis of relationships within the genus. Two most parsimonious hypotheses corroborate the monophyly of Acestrorhynchus but differ in the hypothesized relationships of Acestrorhynchus heterolepis . Three proposed supraspecific assemblages are at least partially correlated with groups of species previously diagnosed on the basis of colour pattern: (1) Acestrorhynchus britskii , Acestrorhynchus grandoculis , Acestrorhynchus microlepis , and Acestrorhynchus minimus ; (2) Acestrorhynchus falcirostris , Acestrorhynchus isalineae , and A. Acestrorhynchus nasutus ; and (3) Acestrorhynchus abbreviatus , Acestrorhynchus altus , Acestrorhynchus falcatus , Acestrorhynchus lacustris , and Acestrorhynchus pantaneiro . In one hypothesis A. heterolepis is proposed as the closest relative of the clade formed by A. falcirostris , A. isalineae , and A. nasutus , and in the alternative hypothesis it is proposed as a sister species of the clade formed by A. abbreviatus , A. altus , A. falcatus , A. lacustris , and A. pantaneiro . Relationships among species of the latter clade remain unresolved. Two independent episodes of reduction of body size are hypothesized to have occurred within the genus: one associated with the clade formed by A. grandoculis and A. minimus , and the other with the clade formed by A. isalineae and A. nasutus . © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 691–757.     

Phylogenetic study of the Characinae (Teleostei: Characiformes: Characidae)

The Characinae is a subunit of the Characidae of special significance in including Charax, the type genus of the family and the order Characiformes. Twelve genera and 79 species have been traditionally assigned to the Characinae, but the subfamily still lacks a phylogenetic diagnosis. Herein, a data matrix including 150 morphological characters and 64 taxa (35 species representing all genera of the Characinae and 29 included in other lineages within the Characiformes) was submitted to two cladistic analyses that differ in the inclusion/exclusion of Priocharax due to the difficulty of coding most of the character states in the miniature species of this genus. Both analyses resulted in a non‐monophyletic Characinae and this subfamily is herein restricted to only seven of the original 12 genera forming the clade (Phenacogaster((Charax Roeboides)(Acanthocharax(Cynopotamus(Acestrocephalus Galeocharax))))), which is supported by ten non‐ambiguous synapomorphies and is more closely related to other genera of the Characidae than those traditionally placed in the subfamily. A second clade includes the members of the tribe Heterocharacini (Lonchogenys(Heterocharax Hoplocharax)) as the sister‐group of Gnathocharax, supported by seven non‐ambiguous synapomorphies. This clade is more closely related to a taxon formed by Roestes and Gilbertolus based on seven non‐ambiguous synapomorphies. Results do not corroborate a close relationship between Roestes–Gilbertolus and the Cynodontinae. Inclusion of the genus Priocharax suggests that it is related more closely to the Heterocharacini, but the profound modifications in its anatomy possibly related to ontogenetic truncations obscure a better understanding of its relationships. A new classification of the Characinae and the Heterocharacinae is proposed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 809–915.     

A new species of Acestrocephalus (Characiformes: Characidae) from Venezuela

A new species of Acestrocephalus is described from 60 specimens collected in the Río Orinoco and Río Negro drainages, Venezuela. This species is distinguished from all other Acestrocephalus by the combination of the following characters: anal rays, 29-36; 63-71 perforated scales on the lateral line; 10-12 scales above and 9-12 below the lateral line; 39-52 teeth on the maxillary; 9-12 premaxillary teeth; 8-12 teeth in the inner row on the dentary; 5-7 gill rakers on the lower part of the first gill arch; humeral, peduncular and caudal blotch absent.     

Spermiogenesis and spermatozoa ultrastructure in Salminus and Brycon, two primitive genera in Characidae (Teleostei: Ostariophysi: Characiformes)

In Salminus, spermiogenesis is cystic and gives origin to a type I aquasperm. Spermatid differentiation is characterized by chromatin condensed into thick fibres, nuclear rotation, nuclear fossa formation, cytoplasmic channel formation, mitochondrial fusion producing long and ramified mitochondria, and the presence of several membranous concentric rings around the plasma membrane that encircles the cytoplasmic channel. In Salminus and Brycon, spermatozoa are very similar. They exhibit a spherical nucleus and chromatin condensed into fibre clusters, and a deep nuclear fossa. They show a long midpiece with few elongate mitochondria at the initial region and a cytoplasmic channel completely encircled by one or two membranous concentric rings. The flagellar axis is perpendicular to the nucleus and exhibits the classic axoneme (9 + 2). The very strong similarity observed between Salminus and Brycon spermatozoa supports the hypothesis that these subfamilies are likely to have a monophyletic origin.     

Comparative development in Moenkhausia pittieri and Paracheirodon innesi (Ostariophysi: Characiformes) with comments on heterochrony and miniaturization in the Characidae

Developmental heterochronies between the small‐sized Moenkhausia pittieri and the miniature Paracheirodon innesi were determined by describing and comparing external morphological development in both species. Despite being classified as miniature, P. innesi was larger and more developed in the flexion and post‐flexion larval stages than M. pittieri. Broader patterns within the Characidae suggest that body size reduction in P. innesi is tied to accelerated development and higher growth rate along with early maturation and precocious cessation of growth, which are characteristic of miniature species. Comments on adipose‐fin loss in Characidae as a consequence of developmental truncation are included.     

A new fish species Hemibrycon (Characiformes: Characidae)

Hemibrycon pautensis (Characiformes, Characidae), a new fish species from Paute River, eastern Ecuador is described. Diagnostic characteristics: eight to nine branched rays in the dorsal fin (vs. six to seven), and 27 - 28 in the anal fin (vs. 16 - 26, except in H. dariensis which presents 22 - 27, in H. metae 26 - 31 and H. jabonero 23 - 28); a no occurrence of dorsal pharyngeal plate (vs. occurrence); a cartilaginous and divided-in-two basihial (vs. an osseous base and a cartilaginous upper part). Hemibrycon pautensis resembles H. metae by its oblique external edge of the pelvic fins. They can be distinguished by the position of the pectoral fins in relation to the snout (38.24-41.6% in H. pautensis vs. 21.21-25.87) and by the position of the pectoral fins in relation to the origin of the dorsal fin (20.95-24.30 in Hemibrycon pautensis vs. 35.89-42.63), and by the number of proximate radials in the pectoral girdle (five in Hemibrycon pautensis vs. three to four). In addition, the geographic distribution of H. metae is restricted to the upper part of the Meta River in Colombia and can be distinguished of H. boquiae by: the number of scales between the lateral-line and the origin of the dorsal fin (eight in H. pautensis vs. 5-7); the distance between the snout and the pelvic fins (38.00-42.90 % in H. pautensis vs. 42.9-46.19%); the pelvic fins length (13.77-17.96% in H. pautensis vs. 10.72-13.21%); and the snout length (21.34-27.88 in H. pautensis vs. 26.92-33.66%).     

Morphological and molecular evidence for two new species of Tetragonopterus (Characiformes: Characidae) from central Brazil

The combination of morphological and molecular data of Tetragonopterus species collected in the Rio Araguaia basin allows the recognition of two undescribed species that are presented in this article. These species are distinguished from their congeners (Tetragonopterus anostomus, Tetragonopterus argenteus, Tetragonopterus carvalhoi, Tetragonopterus chalceus and Tetragonopterus rarus) by characters related to the number and morphology of the teeth, the numbers of gill rakers on the upper and lower limbs of the first gill arch, the number of predorsal scales and the overall colour pattern. In addition, the analysis of mitochondrial DNA sequences identified an accentuated genetic distance between these two new species and their congeners. A discussion of the phylogenetic relationships within Tetragonopterus is provided.     

Morphological and Molecular Phylogenetic Data Reveal a New Species of Primula (Primulaceae) from Hunan,China

A new species of Primulaceae, Primula undulifolia, is described from the hilly area of Hunan province in south-central China. Its morphology and distributional range suggest that it is allied to P. kwangtungensis, both adapted to subtropical climate, having contiguous distribution and similar habitat, growing on shady and moist cliffs. Petioles, scapes and pedicels of them are densely covered with rusty multicellular hairs, but the new species can be easily distinguished by its smaller flowers and narrowly oblong leaves with undulate margins. Molecular phylogenetic analysis based on four DNA markers (ITS, matK, trnL-F and rps16) confirmed the new species as an independent lineage and constitutes a main clade together with P. kwangtungensis, P. kweichouensis, P. wangii and P. hunanensis of Primula sect. Carolinella.     

Phylogenetic Relationships of the Macaques (Cercopithecidae: Macaca), Inferred from Mitochondrial DNA Sequences

To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.     

A New Genus of Marine Scuticociliate (Protozoa, Ciliophora) from Northern China, with a Brief Note on Its Phylogenetic Position Inferred from Small Subunit Ribosomal DNA Sequence Data

ABSTRACT. The morphology, infraciliature, and silverline system of a new marine scuticociliate, Wilbertia typica n. g., n. sp., collected from coastal waters off northern China, were investigated. The new genus Wilbertia is characterized as follows: sculptured and dorso-ventrally flattened body; dominant buccal field that is almost completely surrounded by the paroral membrane; three apically positioned long membranelles, arranged in parallel; membranelle (M)1 and M2 prominent, M3 small; reticulate silverline system. The type species W. typica n. sp. is defined by having a conspicuous anterior beak-like protrusion; five to eight caudal cilia; M1 four-rowed, M2 two-rowed; M3, single-rowed, bipartite; 15 or 16 somatic kineties; contractile vacuole positioned just posterior to the buccal field; globular macronucleus. The small subunit ribosomal DNA sequence of W. typica is 98.5% similar to the similar morphotype, Eurystomatella sinica . Phylogenetic analyses indicate that Wilbertia groups with Eurystomatella sinica forming a branch that diverges at a deep level from all other pleuronematid scuticociliates. The molecular and morphological data indicate that Wilbertia should be placed within the family Eurystomatidae, which is closely related to the well-known Cyclidiidae.     

A new species of Creagrutus Günther (Teleostei: Ostariophysi: Characiformes), from the upper Rio Paraná basin, central Brazil

Creagrutus varii n. sp. is described based on material from the Rio São Marcos basin, in the upper Rio Paraná system, Goiás State, Brazil. This is the first record of Creagrutus in the upper Rio Paraná. The new species is proposed to be the sister group of the remaining species of Creagrutus . Creagrutus varii differs from congeners in the morphology of the maxilla, primordial ligament, premaxillary dentition and other features. The evolution of premaxillary tooth morphology in Piabina and Creagrutus and the biogeography of the Rio Paranaíba basin are discussed.     

Molecular phylogeny of Aphyocharacinae (Characiformes, Characidae) with morphological diagnoses for the subfamily and recognized genera

The subfamily Aphyocharacinae was recently redefined to comprise eight genera: Aphyocharax, Prionobrama, Paragoniates, Phenagoniates, Leptagoniates, Xenagoniates, Rachoviscus and Inpaichthys. This new composition, however, is partially incongruent with published results of molecular studies especially concerning the positions of Rachoviscus and Inpaichthys. Our goal was to investigate the monophyly of Aphyocharacinae and its interrelationships using three distinct phylogenetic methodologies: Maximum-likelihood and Bayesian analyses of molecular data, and also Parsimony analysis of a concatenated molecular and morphological dataset. All tree topologies recovered herein suggest that Rachoviscus, Inpaichthys and Leptagoniates pi do not belong to the Aphyocharacinae. The remaining aphyocharacin taxa analyzed do form a monophyletic group, which is itself composed of two subgroups being one comprised of Paragoniates, Phenagoniates, Leptagoniates and Xenagoniates, and the other comprised of Aphyocharax and Prionobrama. Internal relationships among these genera are statistically well supported and morphological synapomorphies are presented at the generic level. All tree topologies also indicate that Aphyocharacidium is closely related to Aphyocharacinae suggesting that it should be included in this subfamily. As recognized in the present study, the Aphyocharacinae is diagnosed by a single morphological synapomorphy: two dorsal-fin rays articulating with the first dorsal pterygiophore.     

Algae or Protozoa: Phylogenetic Position of Euglenophytes and Dinoflagellates as Inferred from Mitochondrial Sequences

The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes, but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts are remnants of endosymbiotic algae. Received: 24 March 1997 / Accepted: 21 April 1997     

Are characiform Fishes Gondwanan in Origin? Insights from a Time-Scaled Molecular Phylogeny of the Citharinoidei (Ostariophysi: Characiformes)

Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma) of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary histories could have been strongly and similarly influenced by Miocene geotectonic events that modified the landscape and produced the drainage pattern of Central Africa seen today.     

A new species of Hemigrammus (Characiformes: Characidae) from western Amazon River basin,Colombia

A new species of Hemigrammus is described from the Amazon Basin near Leticia, Departamento Amazonas, Colombia. In common with some congeners and some Hyphessobrycon spp., the new species colour pattern lacks a humeral blotch but has a caudal-peduncle blotch. It can be distinguished from congeners with a similar colour pattern by having: a relatively deep body (30.2%–39.0% L_S), 20–24 branched anal-fin rays, 6–8 perforated scales of the lateral line, anal-fin base without a conspicuous black stripe, 3–5 maxillary teeth, maxillary teeth with 1–3 cusps, a thin longitudinal midlateral line and a well-defined oval shaped caudal blotch, extending from caudal peduncle into the lower caudal-fin rays. Comparisons with congeners and with Hyphessobrycon species sharing the same general colour pattern are presented.