Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei)

Nucleotide sequences from the mitochondrial ND4 gene and the nuclear RAG2 gene were used to derive the most extensive molecular phylogeny to date for the Neotropical cichlid subfamily Geophaginae. Previous hypotheses of relationships were tested in light of these new data and a synthesis of all existing molecular information was provided. Novel phylogenetic findings included support for : (1) a 'Big Clade' containing the genera Geophagus sensu lato, Gymnogeophagus, Mikrogeophagus, Biotodoma, Crenicara, and Dicrossus; (2) a clade including the genera Satanoperca, Apistogramma, Apistogrammoides, and Taeniacara; and (3) corroboration for Kullander's clade Acarichthyini. ND4 demonstrated saturation effects at the third code position and lineage-specific rate heterogeneity, both of which influenced phylogeny reconstruction when only equal weighted parsimony was employed. Both branch lengths and internal branch tests revealed extremely short basal nodes that add support to the idea that geophagine cichlids have experienced an adaptive radiation sensu Schluter that involved ecomorphological specializations and life history diversification.     

Diet-morphology correlations in the radiation of South American geophagine cichlids (Perciformes: Cichlidae: Cichlinae)

Genera within the South American cichlid tribe Geophagini display specialized feeding and reproductive strategies, with some taxa specialized for both substrate-sifting and mouth brooding. Several lineages within the clade also possess an epibranchial lobe (EBL), a unique pharyngeal structure that has been proposed to have a function in feeding and/or mouth brooding. A recently published genus-level phylogeny of Neotropical cichlids was used as the evolutionary framework for investigating the evolution of morphological features presumably correlated with diet and mouth brooding in the tribe Geophagini. We tested for possible associations between the geophagine epibranchial lobe and benthic feeding and mouth brooding. We also addressed whether the EBL may be associated with unique patterns of diversification in certain geophagine clades. Tests of binary character correlations revealed the EBL was significantly associated with mouth brooding. We also tested for a relationship between diet and morphology. We analyzed stomach contents and morphometric variation among 21 species, with data for two additional species obtained from the literature. Principal Components Analysis revealed axes of morphological variation significantly correlated with piscivory and benthivory, and both morphology and diet were significantly associated with phylogeny. These results suggest that the EBL could be an adaptation for either feeding or mouth brooding. The EBL, however, was not associated with species richness or accelerated rates of phyletic diversification.     

Molecular phylogeny and biogeography of the Malagasy and South Asian cichlids (Teleostei: Perciformes: Cichlidae)

Phylogenetic relationships of the Malagasy and South Asian cichlids are investigated using nucleotide characters from two mitochondrial genes, a 544 bp region of the large ribosomal subunit (16S) and a 649 bp region of cytochrome c oxidase subunit I (COI). This is the first molecular analysis to include a thorough taxonomic sampling of all Malagasy-South Asian genera, and a near complete taxonomic inventory of all valid species. Parsimony analysis of the combined data set (1193 aligned nucleotide positions) results in a single, completely resolved phylogenetic hypothesis. Results of this analysis, and that based on more comprehensive taxonomic sampling across Cichlidae for 16S alone (554 bp for 73 taxa), indicate that the Malagasy cichlids are paraphyletic, whereas the Malagasy and South Asian cichlids comprise a monophyletic group. In both analyses, the African and Neotropical assemblages are monophyletic. The Malagasy-South Asian cichlids are not recovered as plesiomorphic members of the family in either analysis. Two major clades are recovered within the Malagasy-South Asian assemblage and given subfamilial rank, Etroplinae, comprising Paretroplus (Madagascar) and Etroplus (southern India and Sri Lanka), and Ptychochrominae, comprising Ptychochromis, Ptychochromoides, and Oxylapia, all endemic Malagasy genera. Placement of the endemic Malagasy genus Paratilapia is equivocal depending on the gene fragment(s) analyzed. Inter- and intrageneric relationships within Ptychochrominae and Etroplinae are presented and discussed. The hypothesis of relationships for Cichlidae based on nucleotide characters from 16S alone, arguably the most comprehensive and broadly sampled data set across all major geographic assemblages to date, is congruent with prevailing hypotheses regarding the sequence of Gondwanan fragmentation and a vicariance scenario to explain the current distribution of cichlid fishes.     

Morphology,phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes,Viperidae)

Carrasco, P.A., Mattoni, C.I., Leynaud, G.C. & Scrocchi, G.J. (2012). Morphology, phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes, Viperidae). —Zoologica Scripta, 41, 109–124. South American bothropoids comprise a monophyletic and greatly diverse group of pitvipers that were initially included in the genus Bothrops and later assigned to five genera. Until recently, most phylogenetic analyses of bothropoids used exclusively mitochondrial DNA sequences, whereas few of them have included morphological traits. Moreover, the systematic affinities of some species remain unclear. In this study, we performed a parsimony analysis of morphological data obtained from the examination of 111 characters related to lepidosis, colour pattern, osteology, and hemipenial morphology of 35 of the 48 species that compose the bothropoid group. The morphological data analysed contain novel information about several species, including the incertae sedis. Morphology was analysed separately and combined with 2393 molecular characters obtained from published sequences of four mitochondrial genes. Five characters of the ecology were also included. A sensitivity analysis was performed using different weighting criteria for the characters. The congruence among different sources of evidence was evaluated through partitioned and total evidence analyses, the analyses of reduced datasets and the use of incongruence length difference test. With few exceptions, results showed groups of species similar to those obtained in previous studies; however, incongruences between morphological and molecular characters, and within the molecular partition, were revealed. This conflict affects the relationship between particular groups of species, leading to alternative phylogenetic hypotheses for bothropoids: hierarchical radiation or two major lineages within the group. The results also showed that Bothrops sensu stricto is paraphyletic. We discuss previous taxonomic approaches and, considering both phylogenetic hypotheses, we propose an arrangement that rectifies the paraphyly of Bothrops: maintaining Bothrocophias, assigning Bothrops andianus to this genus; and recognising the sister clade as Bothrops, synonymising Bothriopsis, Bothropoides and Rhinocerophis.     

Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution

Diversity and disparity are unequally distributed both phylogenetically and geographically. This uneven distribution may be owing to differences in diversification rates between clades resulting from processes such as adaptive radiation. We examined the rate and distribution of evolution in feeding biomechanics in the extremely diverse and continentally distributed South American geophagine cichlids. Evolutionary patterns in multivariate functional morphospace were examined using a phylomorphospace approach, disparity-through-time analyses and by comparing Brownian motion (BM) and adaptive peak evolutionary models using maximum likelihood. The most species-rich and functionally disparate clade (CAS) expanded more efficiently in morphospace and evolved more rapidly compared with both BM expectations and its sister clade (GGD). Members of the CAS clade also exhibited an early burst in functional evolution that corresponds to the development of modern ecological roles and may have been related to the colonization of a novel adaptive peak characterized by fast oral jaw mechanics. Furthermore, reduced ecological opportunity following this early burst may have restricted functional evolution in the GGD clade, which is less species-rich and more ecologically specialized. Patterns of evolution in ecologically important functional traits are consistent with a pattern of adaptive radiation within the most diverse clade of Geophagini.     

Squamation and scale character stability in cichlids, examined in Sarotheroden galilaeus (Linnaeus, 1758) (Perciformes, Cichlidae)

Squamation and scale morphology provide interesting characters for phyletic analysis within the Cichlidae. It is not known, however, to what extent these characters are genetically fixed or determined by environmental parameters. To clarify this point, a study on Sarotherodon galilaeus was conducted. This species has an extensive distribution and lives in markedly different environments. Most scale characters were found to be remarkably stable within the species. The only large variations occur in scale counts, extent of caudal fin Squamation, number of circuli and radii, and the extent of scale granulation. The Squamation pattern, the form of the circuli and radii, the shape of interradial rostrad projecting tongues, the denticles on the circuli in the rostral field, and especially the kind of granulation in the caudal field is similar in all specimens examined and is also retained in fish bred in aquaria for several generations. Thus it seems justified to assume that these characters are strongly determined by genetic factors and that their analysis can be useful in the determination of phyletic relationships.     

Morphology,molecules and the phylogeny of Characidae (Teleostei,Characiformes)

This is the most comprehensive phylogenetic analysis of the Characidae to date and the first large-scale hypothesis of the family, combining myriad morphological data with molecular information. A total of 520 morphological characters were analysed herein, of which 98 are newly defined. Among the analysed taxa, 259 species were coded by examining specimens, three fossil species were coded from the literature, one species was coded almost completely from published figures, 122 were partially coded from the literature, and 88 were analysed exclusively from molecular data. The total number of species in the analysed dataset is 473. Analyses were made by parsimony under equal and extended implied weighting with a broad range of parameters. The final hypothesis was selected using a stability criterion that chooses among the most parsimonious trees of all searches. It was found by weighting molecular characters with the average homoplasy of entire partitions (markers). The resulting hypothesis is congruent with previous molecular-based phylogenies of the family. The Characidae are monophyletic, with four main clades: the Spintherobolinae new subfamily; an expanded Stethaprioninae including the Grundulini, Gymnocharacini, Rhoadsiini and Stethaprionini; the Stevardiinae; and a clade composed of the Aphyocharacinae, Characinae, Cheirodontinae, Exodontinae and Tetragonopterinae. Also, a stem Characidae was found, as formed by the Eocene–Oligocene genera †Bryconetes and †Paleotetra as successive sister groups of extant members of the family. A subfamilial classification is proposed, but deep changes in the systematics that are beyond the scope of this study are still needed to classify the Characidae into monophyletic genera.     

Scale morphology and squamation patterns in cichlids (Teleostei, Perciformes): A comparative study

Problems in cichlid systematics call for new characteristics to be exploited. Scale surface morphology and squamation patterns could provide novel and useful information. A comparative study comprising 105 African, 10 American, and eight outgroup species was conducted to identify the most useful scale and squamation characters within the family and to clarify their phylogenetic significance. A great number of obviously genetically fixed characters were established. At least IS scale granulation types could be identified, proving to be ofparticular value for systematic purposes. Squamation patterns on the head, breast and fins were also found to be of interest in this context. Different character states are described and their distribution is reviewed, together with a discussion of their plesiomorphic status. From the results it can be concluded that for the Cichlidae scale and squamation studies can be valuable tools in investigating phylogenetic relationships.     

Spermiogenesis and sperm ultrastructure in Cichla intermedia with some considerations about Labroidei spermatozoa (Teleostei, Perciformes, Cichlidae)

Spermiogenesis and spermatozoal structure were studied in Cichla intermedia, a primitive species of Neotropical Cichlids. The analysis shows that spermiogenesis is characterized by chromatin compaction, flagellum development, nuclear rotation, nuclear fossa formation and residual cytoplasm elimination. In the spermatozoa, the head is round, the nucleus contains highly condensed filamentous clusters of chromatin and an acrosome is absent. The nuclear fossa is slightly eccentric and shows a projection that penetrates into the nuclear outline. The proximal centriole is located in the initial segment of the nuclear fossa. The midpiece and the cytoplasmic channel are long. The mitochondria, about 10 in number, are round or slightly elongated, disposed in two layers around the initial segment of the flagellum. The flagellum has a classical 9+2 axoneme and two lateral fins. The data available show that no characteristics of spermiogenesis or spermatozoa are exclusively found in members of the suborder Labroidei. However, three characteristics seem to be exclusively observed in Cichlidae: (1) compact filamentous clusters of chromatin; (2) slightly eccentric nuclear fossa; and, (3) number of mitochondria.     

Molecular phylogeny of the South American land slug Phyllocaulis (Mollusca,Soleolifera, Veronicellidae)

Gomes, S. R., Britto da Silva, F., Mendes, I. L. V., Thomé, J. W. & Bonatto, S. L. (2009). Molecular phylogeny of the South American land slug Phyllocaulis (Mollusca, Soleolifera, Veronicellidae). —Zoologica Scripta, 39, 177–186. Our main objectives were investigate the phylogenetic relationships between the species of the land slug Phyllocaulis and the monophyly of the genus based on mitochondrial (16S and COI) and nuclear (ITS2) DNA sequences from multiple individuals from each species. Evolutionary trees were constructed using Bayesian inference, maximum likelihood, maximum parsimony and neighbor‐joining methods. All species accepted in the current taxonomy based on penial characteristics and radular measurements were reciprocally monophyletic. Five species out of six formed a clade with the following highly supported relationship: Phyllocaulis gayi, Phyllocaulis soleiformis, Phyllocaulis renschi, Phyllocaulis variegatus, Phyllocaulis boraceiensis. The position of Vaginulus taunaisii changed according to the analysis, appearing as sister‐group of Phyllocaulis or as sister‐group of Phyllocaulis tuberculosus. Divergence times estimated from the 16S tree indicated that the extant species of Phyllocaulis shared a common ancestor around 1.3 Ma and that most species originated between 0.8 and 0.6 Ma.     

Echinoderm phylogeny: Morphology and molecules approach accord

Phylogenetic relationships of echinoderms at various taxonomic levels have come under intense focus recently from both a morphological and a molecular standpoint. Initial conflict between molecular and morphological results is gradually being resolved to produce a consensus that places echinoderm Phylogeny on a new robust footing.     

Karyotype and mitochondrial 16S gene characterizations in seven South American Cichlasomatini species (Perciformes, Cichlidae)

The family Cichlidae constitutes most of the freshwater fish fauna of South America; its taxonomy is at present mainly based on morphological characters. Here, relationships among seven Cichlasomatini species have been investigated by studying their karyotype structure and by sequencing a 520 bp fragment of the mitochondrial 16S gene. Molecular data sets point to a high affinity of Cichlasoma amazonarum with Aequidens sensu stricto group, in particular with Aequidens tetramerus . Aequidens never form a single monophyletic clade: molecular trees group together ' Aequidens pulcher ' and ' Aequidens rivulatus ' and suggest their close relationship with Bujurquina and Laetacara , rather than with the A. sensu stricto group. Both molecular and karyotypic data confirm that Cleithracara maronii belongs to a distinct clade, thus supporting its generic differentiation based on morphological characters. Chromosome number, karyotype structure and molecular data suggest that Laetacara dorsigera is related to Bujurquina vittata and confirm their generic level of differentiation. From a cytotaxonomic point of view, a karyotype of 2 n  = 48 with most acrocentric or subacrocentric chromosomes could be the ancestral one from which the others might have derived.     

Multilocus phylogeny of the widely distributed South American lizard clade Eulaemus (Liolaemini,Liolaemus)

The lizard genus Liolaemus and different clades within it have been the focus of several recent phylogenetic studies mainly based on morphology and mtDNA. Although there is general consensus for recognizing two clades (subgenera) within the genus, [Liolaemus (sensu stricto) and Eulaemus], phylogenetic relationships within each subgenus remain difficult to elucidate, given incomplete taxonomic sampling and large discordance between published studies. Here, new phylogenetic relationships for the Eulaemus subgenus are proposed based on the largest molecular data set ever used for this clade, which includes 188 individuals and 14 loci representing different parts of the genome (mtDNA, anonymous nuclear loci and nuclear protein‐coding loci). This data set was analysed using two species tree approaches (*beast and MDC). Levels of discordance among methods were found, and with previously published studies, but results are robust enough to propose new phylogenetic hypotheses for the Eulaemus clade. Specifically well‐resolved and well‐supported novel hypotheses are provided within the lineomaculatus section, and we formally recognize the zullyae clade, the sarmientoi clade and the hatcheri group. We also resolve species relationships within the montanus section, and particularly within the melanops series. We found discordance between mitochondrial and nuclear trees and discussed alternative hypotheses for the lineomaculatus and montanus sections, as well as the challenge in resolving phylogenetic relationships for large clades in general.     

Morphology and evolution of the wing bullae in South American Leptophlebiidae (Ephemeroptera)

Insects were the first animals to take to the skies, and have been flying for over 320 million years. The order Ephemeroptera is, or at least is part of, the most early-diverging lineage of extant winged insects. The extant species present a very short adult life span, mainly dedicated to reproduction and dispersal of eggs. Mating and egg-laying behavior depend on flight. Wings are structures to fly and as such face a number of physical and physiological challenges. The convex curvature along the anterior–posterior axis of the wing generates a camber that must be carefully regulated. One of the most interesting ways of wing bending is provided by the bullae, which have been defined as short sections of flexible chitin, where the flexion lines cross veins. Although the bullae have been frequently used as taxonomic characters, there is no study focused on their morphology, although their prevalence on the wings of mayflies strongly suggests a role in flight. In order to identify evolutionary trends of these structures within Ephemeroptera, we constructed a matrix with comparative anatomy data of the bullae from whole mounts of the wings of 300 specimens belonging to 70 species of several mayfly families, as well as scanning microscopy samples of selected specimens. We also surveyed the number of bullae and their distribution in the wings of the different species within the South American Leptophlebiidae clade. We optimized the characters onto the latest published phylogeny for Leptophlebiidae.     

Molecular phylogeny and speciation of the surfperches (Embiotocidae, Perciformes).

Labroid fishes include a variety of families, such as wrasses (Labridae), odacids (Odacidae), damselfishes (Pomacentridae), parrotfishes (Scaridae), cichlids (Cichlidae), and surfperches (Embiotocidae). With only 23 species, the small embiotocid family exhibits a remarkably low species diversity compared to the large species diversity of the Cichlidae. Using mitochondrial DNA sequences of all 14 extant embiotocid genera, we established a molecular phylogeny of the family and compared it with a previously proposed morphological phylogeny. Genetic differentiation among embiotocids was compared to that among cichlids. Although species numbers are extremely different between these two families, the degrees of genetic differentiation within each family was found to be very similar.     

A phylogeny of sparoid fishes (Perciformes, Percoidei) based on morphology

 The putative percoid superfamily Sparoidea includes the Nemipteridae, Lethrinidae, Sparidae, and Centracanthidae. Although a rigorous cladistic analysis has never been attempted, two hypotheses regarding relationships among these families have been proposed. One early noncladistic hypothesis considered the Sparidae to be intermediate between the more primitive Nemipteridae and the more derived Lethrinidae. A later nonformal phylogenetic treatment provided evidence for a close relationship between Sparidae and Centranthidae and suggested a closer affinity between the Nemipteridae and Lethrinidae. We examine 54 osteological, ligament, and squamation characters in representatives of all 45 genera of these families and 4 outgroup taxa. The results of our cladistic analysis are congruent with a cladistic interpretation of the earlier hypothesis, with strong support for the phyletic sequence Nemipteridae, Lethrinidae, Sparidae plus Centracanthidae, with placement of centracanthids unresolved with respect to sparid genera. Received: May 21, 2001 / Revised: October 26, 2001 / Accepted: November 19, 2001     

Morphology and molecular phylogeny of three new oligotrich ciliates (Protozoa,Ciliophora) from the South China Sea

The present paper documents the morphology and systematic positions of three new oligotrich ciliates, P arallelostrombidium obesum sp. nov. , P arallelostrombidium ellipticum sp. nov. , and S trombidium tropicum sp. nov. , which were sampled from habitats with different salinities in southern China. P arallelostrombidium obesum sp. nov. is characterized by a fat body and the posterior portions of the girdle and ventral kineties extending transversely on the dorsal side. P arallelostrombidium ellipticum sp. nov. is recognizable by the anterior ends of the girdle and ventral kineties being close to each other and the posterior ends of the girdle and ventral kineties intersecting on the dorsal side. S trombidium tropicum sp. nov. is distinguished by a ventrally opened girdle kinety that is slightly spiralled with the right end shifted posteriad. Small subunit rRNA gene trees show that P . obesum sp. nov. and P . ellipticum sp. nov. fall into a mixed group composed of Parallelostrombidium and some Novistrombidium species, and that S . tropicum sp. nov. branches at the base of the clade containing non‐Strombidium species. The relationships of Parallelostrombidium species and that of Strombidium species are both not resolved considering their low support values in our phylogenetic analysis. © 2015 The Linnean Society of London     

Proposed chromosomal phylogeny for the South American primates of the Callitrichidae family (Platyrrhini)

Cytogenetic and cytotaxonomic studies (G, C, sequential G/C, and NOR banding) were performed on 110 specimens representing the four genera of South American primates of the family Callitrichidae: Cebuella (C. pygmaea), Callithrix, groups argentata (C. argentata, C. emiliae, C. chrysoleuca, C. humeralifera, C. mauesi), and jacchus (C. aurita, C. geoffroyi, C. jacchus, C. kuhli, C. penicillata), Leontopithecus (L. chrysomelas, L. rosalia), and Saguinus (S. midas midas, S. m. niger). Mitotic chromosomes are characterized, and the rearrangements distinguishing the karyotypes of the taxa are inferred from arm homologies. The results were then converted into numerical data and submitted to cladistic analysis. The following conclusions were achieved: 1) Five karyotypic classes were observed, which correspond to the five taxa studied. Differences between them are as follows: a) Cebuella (2n = 44, 10 acrocentrics, A + 32 bi‐armed autosomes, bi) and the argentata group (2n = 44, 10A + 32bi) are different from each other due to a reciprocal translocation; b) both can be distinguished from the jacchus group (2n = 46, 14A + 30bi) by a centric fusion/fission rearrangement and a paracentric inversion; c) Leontopithecus (2n = 46, 14A + 30bi) and Saguinus (2n = 46, 14A + 30bi) differ from the jacchus group by a reciprocal translocation and three paracentric inversions; and d) Saguinus is different from the others by one paracentric inversion and pericentric inversions in at least four pairs of acrocentric autosomes. 2) The cladistic analysis separates Cebus (used as an outgroup) from the Callitrichidae groups, which forms a clade. Among the Callitrichidae, marmosets (Cebuella and Callithrix) form a sub‐clade, Cebuella and the argentata group being more closely related to each other than both are to the jacchus group. Tamarins (Leontopithecus and Saguinus) are also quite close, so that if one was not derived from the other, they with the marmosets share a common ancestor. Among the tamarins, Leontopithecus is karyotypically closest to the marmosets, specifically to the jacchus group. 3) Based on the chromosome information and considering the possible direction of the evolutionary changes (primitivity or phyletic dwarfism hypothesis, previously advanced by other authors), it was possible to propose the ancestral karyotypes and to develop two alternatives for the origin, differentiation and dispersion of the callitrichid. Both proposals are plausible, but when the geographical distribution is considered, the phyletic dwarfism hypothesis seems to be the most probable. Am. J. Primatol. 49:133–152, 1999. © 1999 Wiley‐Liss, Inc.