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      Evolutionary history of the Lake Tanganyika cichlid tribe Lamprologini (Teleostei: Perciformes) derived from mitochondrial and nuclear DNA data

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          Abstract

          Lake Tanganyika comprises a cichlid species flock with substrate-breeding and mouthbrooding lineages. While sexual selection via mate choice on male mating color is thought to boost speciation rates in mouthbrooding cichlids, this is not the case in substrate-breeding lamprologines, which mostly form stable pairs and lack sexual dichromatism. We present a comprehensive reconstruction of the evolution of the cichlid tribe Lamprologini, based upon mtDNA sequences and multilocus nuclear DNA (AFLP) markers. Twelve mtDNA clades were identified, seven of which were corroborated by the AFLP tree. The radiation is likely to have started about 5.3 MYA, contemporarily with that of the mouthbrooding C-lineage, and probably triggered by the onset of deep-water conditions in Lake Tanganyika. Neither the Congo- nor the Malagarazi River species form the most ancestral branch. Several conflicts in the mtDNA phylogeny with taxonomic assignments based upon color, eco-morphology and behavior could be resolved and complemented by the AFLP analysis. Introgressive hybridization upon secondary contact seems to be the most likely cause for paraphyly of taxa due to mtDNA capture in species involving brood-care helpers, while accidental hybridization best explains the para- or polyphyly of several gastropod shell breeders. Taxonomic error or paraphyly due to the survival of ancestral lineages appear responsible for inconsistencies in the genera Lamprologus and Neolamprologus.

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

            With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
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              Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.

              Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.
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                Author and article information

                Journal
                Mol Phylogenet Evol
                Mol. Phylogenet. Evol
                Molecular Phylogenetics and Evolution
                Academic Press
                1055-7903
                1095-9513
                October 2010
                October 2010
                : 57
                : 1
                : 266-284
                Affiliations
                [a ]Department of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
                [b ]Zoological Institute, Evolutionary Biology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
                [c ]Division of Vertebrate Zoology (Ichthyology), American Museum of Natural History, Central Park West at 79th Street, NY 10024, USA
                Author notes
                [* ]Corresponding author. Fax: +43 316 380 9875. Christian.Sturmbauer@ 123456uni-graz.at
                Article
                YMPEV3681
                10.1016/j.ympev.2010.06.018
                2997427
                20601006
                ba68300e-e767-4aac-b281-31e6dbe43e9d
                © 2010 Elsevier Inc.

                This document may be redistributed and reused, subject to certain conditions.

                History
                : 19 January 2010
                : 14 June 2010
                : 23 June 2010
                Categories
                Article

                Evolutionary Biology
                cichlid fishes,speciation,molecular phylogeny,hybridization,adaptive radiation

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