Phylogeny of the Neotropical genus Acestrorhynchus (Ostariophysi: Characiformes) based on nuclear and mitochondrial gene sequences and morphology: a total evidence approach.
ABSTRACT Acestrorhynchus is the sole genus of the family Acestrorhynchidae which includes 14 species currently recognized as valid. Species of Acestrorhynchus comprise small-to-medium sized piscivorous fishes and have been traditionally grouped on the basis of well-defined color patterns. A recent phylogeny, based on morphological characters, could not resolve the phylogenetic affinities of A. heterolepis and the relationships among the species of the clade formed by A. abbreviatus, A. altus, A. falcatus, A. lacustris, and A. pantaneiro. The simultaneous analysis of two mitochondrial genes (16S and ATP synthase subunits 6 and 8) and one nuclear intron (S7) was able to resolve the latter clade, but the position of A. heterolepis remained unresolved. The combination of the molecular and morphological data sets in a total evidence analysis resulted in a well-resolved hypothesis regarding the phylogenetic relationships of Acestrorhynchus species.
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ABSTRACT: A phylogenetic analysis is provided for representatives of more than one hundred species of the catfish family Loricariidae, including nearly all genera of the subfamilies Neoplecostominae and Hypoptopomatinae. This analysis is based on fragments of the subunit 1 of the cytochrome c oxidase gene (COI), the recombination activating genes 1 (RAG1) and 2 (RAG2), and the F-Reticulon 4 gene. We obtained an alignment of 4678 contiguous nucleotides for 136 species of 50 loricariid genera from five loricariid subfamilies, and ten outgroup species from five loricarioid families. Our results from Maximum Parsimony, Maximum Likelihood, and Bayesian analyses show the following set of interrelationships ((((Hypoptopomatinae, Neoplecostominae) Hypostominae), Loricariinae) Delturinae). However, neither Hypoptopomatinae nor Neoplecostominae were recovered as monophyletic groups. A previously hypothesized monophyly of Hypoptopomatini and Otothyrini was refuted. Furthermore, the genera Pareiorhaphis, Pareiorhina, Hisonotus and Parotocinclus were recovered as polyphyletic.Molecular Phylogenetics and Evolution 01/2011; 59(1):43-52. · 4.07 Impact Factor
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ABSTRACT: The present paper is an argument in support of the continued importance of morphological systematics and a plea for improving molecular phylogenetic analyses by addressing explicit character transformations. We use here the inference of key innovations and adaptive radiations to demonstrate why morphological systematics is still relevant and necessary. After establishing that theories of phylogenetic relationship offer robust explanatory bases for discussing evolutionary diversification, the following topics are addressed: (1) the inference of key innovations grounded in phylogenetic analyses; (2) the epistemic distinction between character ‘mapping’ and relevant evidence in systematic and evolutionary studies; and (3) key innovations in molecular phylogenetics. We emphasize that the discovery of key innovations, in fossil or extant taxa, further strengthens the importance of morphology in systematic and evolutionary inferences, as they reveal scenarios of character transformation that have led to asymmetrical sister-group diversification. Our main conclusion is that understanding characters in and of themselves, when properly contextualized systematically, is what evolutionary biologists should be concerned with, whereas the analysis of tree topology alone, in which statistical nodal support measures are the sole indicators of phylogenetic affinity, does not lead to a fuller understanding of key innovations. KeywordsCharacter transformation series-Congruence test-Fossils-Homology-Molecular data-Phylogeny-Synapomorphy-TopologyEvolutionary Biology 01/2010; 37(4):247-254. · 2.39 Impact Factor
Conference Paper: Broadcast news transcription[Show abstract] [Hide abstract]
ABSTRACT: We describe our work on automatic transcription of radio and television news broadcasts. This problem is very challenging for large vocabulary speech recognition because of the frequent and unpredictable changes that occur in speaker, speaking style, topic, channel, and background conditions. Faced with such a problem, there is a strong tendency to try to carve the input into separable classes and deal with each one independently. In our early work on this problem, however, we are finding that the rewards for condition-specific techniques are disappointingly small. This is forcing us to look for general, robust, and adaptive algorithms for dealing with extremely variable data. We describe the BBN BYB-LOS recognition system configured to handle off-line transcription and we characterize the speech contained in the 1996 DARPA Hub-4 testbed. On the partitioned development test set, we achieved a 29.4% overall word error rateAcoustics, Speech, and Signal Processing, 1997. ICASSP-97., 1997 IEEE International Conference on; 05/1997