Molecular phylogeny of advanced snakes (Serpentes, Caenophidia) with an emphasis on South American xenodontines: A revised classification and descriptions of new taxa

We present a molecular phylogenetic analysis of caenophidian (advanced) snakes using sequences from two mitochondrial genes (12S and 16S rRNA) and one nuclear (c-mos) gene (1681 total base pairs), and with 131 terminal taxa sampled from throughout all major caenophidian lineages but focussing on Neotropical xenodontines. Direct optimization parsimony analysis resulted in a well-resolved phylogenetic tree, which corroborates some clades identified in previous analyses and suggests new hypotheses for the composition and relationships of others. The major salient points of our analysis are: (1) placement of Acrochordus, Xenodermatids, and Pareatids as successive outgroups to all remaining caenophidians (including viperids, elapids, atractaspidids, and all other colubrid groups); (2) within the latter group, viperids and homalopsids are sucessive sister clades to all remaining snakes; (3) the following monophyletic clades within crown group caenophidians: Afro-Asian psammophiids (including Mimophis from Madagascar), Elapidae (including hydrophiines but excluding Homoroselaps), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae, and Xenodontinae. Homoroselaps is associated with atractaspidids. Our analysis suggests some taxonomic changes within xenodontines, including new taxonomy for Alsophis elegans, Liophis amarali, and further taxonomic changes within Xenodontini and the West Indian radiation of xenodontines. Based on our molecular analysis, we present a revised classification for caenophidians and provide morphological diagnoses for many of the included clades; we also highlight groups where much more work is needed. We name as new two higher taxonomic clades within Caenophidia, one new subfamily within Dipsadidae, and, within Xenodontinae five new tribes, six new genera and two resurrected genera. We synonymize Xenoxybelis and Pseudablabes with Philodryas; Erythrolamprus with Liophis; and Lystrophis and Waglerophis with Xenodon.

Molecular phylogeny of Moenkhausia (Characidae) inferred from mitochondrial and nuclear DNA evidence

Moenkhausia is one of the most speciose genera in Characidae, currently composed of 75 nominal species of small fishes distributed across South American hydrographic basins, primarily the Amazon and Guyanas. Despite the large number of described species, studies involving a substantial number of its species designed to better understand their relationships and putative monophyly are still lacking. In this study, we analysed a large number of species of Moenkhausia to test the monophyly of the genus based on the phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes. The in-group included 29 species of Moenkhausia, and the out-group was composed of representatives of Characidae and other members of Characiformes. All species of Moenkhausia belong to the same clade (Clade C); however, they appear distributed in five monophyletic groups along with other different genera, which means that Moenkhausia is polyphyletic and indicates the necessity of an extensive revision of the group. © 2013 Blackwell Verlag GmbH.

Multilocus molecular phylogeny of Gasteropelecidae (Ostariophysi: Characiformes) reveals the existence of an unsuspected diversity

The characiform family Gasteropelecidae, the so-called freshwater hatchetfishes, is comprised of three genera and nine species found in Panama and all South American countries except Chile. Our goal was to investigate the molecular characteristics, phylogenetic relationships among the species and genera of Gasteropelecidae and phylogenetic relationships between the Gasteropelecidae family with other Characiformes. DNA fragments from two mitochondrial (16S rRNA and Cytochrome B) and three nuclear genes (Rag1, Rag2 and Myh6) were sequenced. Our results corroborate the morphology-based hypothesized monophyly of the Gasteropelecidae family and most of the relationships among its genera. However, the genus Gasteropelecus is polyphyletic because G. maculatus is placed as the sister group to all other gasteropelecids, whereas G. sternicla is more closely related to species of Carnegiella. Similarly, the species Carnegiella strigata is not monophyletic, which suggests that the family needs a taxonomic review. Moreover, the species Thoracocharax stellatus was composed by four distinct lineages suggesting the this species may represents a species complex. © 2013 Elsevier Inc.

Molecular phylogeny of the genus Saguinus (Platyrrhini, Primates) based on the ND1 mitochondrial gene and implications for conservation

The systematics of the subfamily Callitrichinae (Platyrrhini, Primates), a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae) using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes) and one Cebus monkey (the outgroup) and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.

Molecular phylogeny resolves a taxonomic misunderstanding and places Geisleria close to Absconditella s. str. (Ostropales: Stictidaceae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The first molecular phylogeny of Chilodontidae (Teleostei: Ostariophysi: Characiformes) reveals cryptic biodiversity and taxonomic uncertainty

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Molecular Phylogeny and Biogeographic History of the Armored Neotropical Catfish Subfamilies Hypoptopomatinae, Neoplecostominae and Otothyrinae (Siluriformes: Loricariidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Taxonomic revision and molecular phylogeny of Gymnocorymbus Eigenmann, 1908 (Teleostei, Characiformes, Characidae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic diversity and molecular phylogeny of Anaplasma marginale studied longitudinally under natural transmission conditions in Rio de Janeiro, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Differentiation and species status of the Neotropical yellow-eared bats Vampyressa pusilla and V. thyone (Phyllostomidae) with a molecular phylogeny and review of the genus

A systematic re-evaluation of Vampyressa pusilla warrants the elevation of V. p. thyone from subspecies to species rank based on its distinction from the allopatric V. p. pusilla. Morphological, mensural, chromosomal, and mitochondrial differences define each of these two taxa as divergent lineages. Vampyressa pusilla is endemic to the Atlantic Forest of southeastern South America and V. thyone is found allopatrically in northwestern South America, Central America, and southern Mexico. A molecular phylogenetic analysis of the mtDNA ND3-4 gene region using restriction endonuclease cut sites resulted in a monophyletic, although weakly supported Vampyressa ingroup with Chiroderma, and a clade of Mesophylla and Ectophylla as successive basal outgroup lineages. The phylogeny within Vampyressa, with the exception of V. melissa which is most similar to V. thyone based on karyotypes and morphology, had a topology of ((pusilla + thyone) + ((brocki + nymphaea) + bidens))).

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus

Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups. (C) 2011 Elsevier Inc. All rights reserved.

Molecular phylogeny of the New World Dipsadidae (Serpentes: Colubroidea): a reappraisal

We present a phylogenetic analysis of the New World dipsadids based on an expanded data matrix that includes 246 terminal taxa including 196 dipsadids. The species are sampled for eight genes (12S, 16S, cytb, nd2, nd4, bdnf, c-mos, rag2). The data are explored using two distinct optimality proceduresmaximum parsimony and maximum likelihoodand two alignment strategiesdynamic homology and static homology. Two previously unsampled dipsadid genera, Sordellina and Rhachidelus, are now included in the analysis. The definitions of the genera, Erythrolamprus, Clelia, Hypsirhynchus, Philodryas and Phimophis, and the tribes Alsophiini, Echinantherini and Conophiini, are revised. In order to maintain monophyly, the genus Umbrivaga is synonymized with Erythrolamprus, and two new genera are erected to accommodate Phimophis iglesiasi and Clelia rustica, as well as their closely related species. The West Indian genera Schwartzophis, Darlingtonia, Antillophis and Ocyophis are resurrected. (c) The Willi Hennig Society 2012.

Ontogenetic and evolutionary change of external morphology of the neotropical shrimp potimirim (Holthuis, 1954) explained by a molecular phylogeny of the genus

A phylogenetic analysis of a fragment of the mitochondrial gene 16S was used to test the monophyletic status of Potimirim. Existing doubts on the taxonomic status of brasiliana (once P glabra) and P potimirim (once P mexicana) were clarified. Potimirim mexicana and P potimirim are distinct species according to molecular data and appendix masculina morphology. A new species (Potimirim sp. 1) from Puerto Rico was revealed with molecular data, and it is evolutionarily related to P potimirim and P mexicana according to our analysis. We found out three distinct species under the name P glabra. Then, we recommend the application of the name P glabra for the populations of the Pacific slope of Central America and revalidation of P brasiliana for the Brazilian ones. The need for a new name to those "P glabra" of the Caribbean is highlighted, and it was provisionally referred as Potimirim sp. 2. The ontogenetic (juveniles to adults) development of the appendix masculina of P brasiliana was observed and compared to the other species of Potimirim (adults). In the light of our phylogenetic hypothesis, we postulate a pattern of character addition for the evolution of the appendix masculina of Potimirim. This hypothesis is plausible for two key reasons. First. Potimirim is a monophyletic group according to our hypothesis. Second, the shape of appendix masculina found in adults of P. americana is similar and comparable to those found in the earliest juvenile stages of P brasiliana, a derived species according to our phylogeny (P americana, ((P mexicana, Potimirim sp. 1. P potimirim), (P glabra, (brasiliana, Potimirim sp. 2)))). As so, the basal P americana retain the ancestral morphological state of the appendix masculina when compared to the other species of Potimirim. In our interpretation the ontogeny of the appendix masculina recapitulated the proposed phylogeny, giving further support to it.