@article {7634, title = {Doubly uniparental inheritance (DUI) of mitochondrial DNA in Donax trunculus (Bivalvia: Donacidae) and the problem of its sporadic detection in Bivalvia}, journal = {Evolution}, volume = {62}, number = {4}, year = {2008}, note = {PDF}, pages = {959-970}, keywords = {bivalvia, dui, mollusca, mtDNA, reproduction}, author = {Theologidis, Ioannis and Fodelianakis, Stilianos and Gaspar, Miguel B. and Zouros, Eleftherios} } @article {7563, title = {Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA}, journal = {Molecular Phylogenetics and Evolution}, volume = {13}, number = {1}, year = {1999}, month = {October}, pages = {31-49}, keywords = {16S, bivalvia, corbiculoidea, dreissenoidea, mollusca, mtDNA, phylogenetics, phylogeny}, author = {Stepien, Carol A. and Hubers, Allyson N. and Skidmore, Jennifer L.} } @article {7499, title = {Mitochondrial intergenic spacer in fairy basslets (Serranidae: Anthiinae) and the simultaneous analysis of nucleotide and rearrangement data}, journal = {American Museum Novitates}, volume = {3652}, year = {2009}, note = {PDF}, pages = {1-10}, keywords = {dna rearrangement, molecular characters, mtDNA, poy}, author = {Smith, W. L. and Smith, K. R. and Wheeler, W. C.} } @article {7500, title = {Polyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data}, journal = {Molecular Phylogenetics and Evolution}, volume = {32}, number = {2}, year = {2004}, note = {PDFTimes Cited: 8ReviewEnglishCited References Count: 118838ry}, month = {AUG}, pages = {627-646}, abstract = {Mitochondrial and nuclear DNA sequence data for 105 acanthomorph taxa are analyzed to address questions of scorpaeniform monophyly and relationships. The combination of 3425 aligned base pairs from the mitochondrial small subunit rDNA (12S), large subunit rDNA (16S), and tRNA-Val and the nuclear large subunit rDNA (28S), histone H3, and TMO-4c4 loci are analyzed. Representatives of all scorpaeniform suborders and 32 of 36 scorpaeniform families are included with most suborders represented by multiple species. In addition to 69 scorpaeniform taxa, 36 outgroup taxa, including representatives of most families previously conjectured to be related to the Scorpaeniformes, are analyzed due to serious concerns of scorpaeniform monophyly. The traditionally recognized scorpaeniform fishes are recovered as polyphyletic, The 13 representatives of the Atheriniformes, Blennioidei, Gasterosteoidei, Grammatidae, Notothenioidei, Percidae, Trichodontidae, and Zoarcoidei included in the analysis are all nested within the least inclusive clade that includes all traditionally recognized scorpaeniforms. The scorpaenoid lineage is widely polyphyletic, and its intrarelationships differed significantly from previous hypotheses. The cottoid lineage is paraphyletic with only the presence of the Trichodontidae, as the sister-taxon of the Cottoidei, disrupting the traditional subordinal hypothesis of relationships. (C) 2004 Elsevier Inc. All rights reserved.}, keywords = {direct optimization, evolution, mtDNA, nuDNA, phylogenetics, poy, taxonomy}, url = {://000222732000016}, author = {Smith, W. L. and Wheeler, W. C.} } @article {7421, title = {Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis}, journal = {Cladistics}, volume = {18}, number = {5}, year = {2002}, note = {PDFTimes Cited: 18ArticleEnglishCited References Count: 88612el}, month = {OCT}, pages = {455-484}, abstract = {The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000-2700 by for each taxon) from the nuclear genes 18S and 285 and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA. sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae + Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))). (C) 2002 Elsevier Science (USA). All rights reserved.}, keywords = {alignment, congruence, direct optimization, morphology, mtDNA, optimization, phylogenetics, poy, sensitivity}, url = {://000179061500001}, author = {Schulmeister, S. and Wheeler, W. C. and Carpenter, J. M.} } @inbook {7143, title = {Nucleic acids II: the polymerase chain reaction}, booktitle = {Molecular systematics}, year = {1996}, pages = {205-247}, publisher = {Sinauer Associates, Inc.}, organization = {Sinauer Associates, Inc.}, edition = {2}, address = {Sunderland, Massachusetts}, keywords = {molecules, mtDNA, nuDNA, pcr, systematics}, author = {Palumbi, Stephen R.}, editor = {Hillis, David M. and Moritz, Craig and Mable, Barbara K.} } @article {6896, title = {Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences}, journal = {Molecular Phylogenetics and Evolution}, volume = {27}, year = {2003}, note = {PDF}, pages = {429-440}, keywords = {bivalvia, CO1, mollusca, mtDNA, phylogenetics, phylogeny, Pterineidae, pteriomorphia}, author = {Matsumoto, Masahiro} } @article {6897, title = {Phylogenetic analysis of the family Pectinidae (Bivalvia) based on mitochondrial cytochrome C oxidase subunit I}, journal = {Journal of Molluscan Studies}, volume = {66}, year = {2000}, note = {PDF}, pages = {477-488}, keywords = {CO1, molecular clock, mollusca, mtDNA, pectinidae, pectinoidea, phylogeny}, author = {Matsumoto, Masahiro and Hayami, Itaru} } @article {6668, title = {Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system}, journal = {Molecular Ecology}, volume = {13}, year = {2004}, note = {PDF}, pages = {2749{\textendash}2762}, keywords = {biogeography, dispersal, gastropoda, mollusca, mtDNA, phylogeny}, author = {Kirkendale, Lisa A. and Meyer, Christopher P.} } @article {6385, title = {The evolution of brooding characters among the freshwater pearly mussels (Bivalvia : Unionoidea) of North America}, journal = {Journal of Molluscan Studies}, volume = {66}, year = {2000}, note = {PDFTimes Cited: 11ArticleEnglishCited References Count: 95320lkPart 2}, month = {MAY}, pages = {157-170}, abstract = {Brooding characters have figured prominently in the classification of North American freshwater pearly mussels (Bivalvia: Unionoidea). The purpose of our study was to evaluate phylogenetic hypotheses of brooding character evolution in order to test homology statements suggested by earlier taxonomic systems of the Unionoidea. Parsimony analysis of partial COI sequences from 29 species of freshwater mussels and 13 outgroups were used to derive a phylogeny. Thirteen brooding characters (e.g., brooding period, marsupium arrangement, structure of interlamellar septa, etc.) were traced onto this phylogeny. Results indicate that long-term brooding (bradytictia) is the derived state among North American freshwater mussels: short-term brooding (tachytictia) is plesiomorphic. Bradytictia evolved independently in the Anodontinae and Lampsilini, with unique morphological modifications derived in those clades to facilitate long-term brooding.}, keywords = {anatomy, bivalvia, CO1, ecology, evolution, mollusca, mtDNA, neotrigonia, trigonioida, unionidae, unionoidea}, url = {://000087402500004}, author = {Graf, Daniel L. and {\'O} Foighil, Diarmaid} } @article {6034, title = {Evolutionary history of Northern Hemisphere Nucella (Gastropoda, Muricidae): molecular, morphological, ecological, and paleontological evidence}, journal = {Evolution}, volume = {50}, number = {6}, year = {1996}, note = {PDF}, pages = {2287-2304}, keywords = {biogeography, character evolution, ecology, gastropoda, invasive species, mollusca, mtDNA, muricidae, phylogeny, speciation, vicariance}, author = {Collins, Timothy M. and Frazer, Kenneth and Palmer, A. Richard and Vermeij, Geerat J. and Brown, Wesley M.} } @article {5971, title = {Phylogeny of North American amblemines (Bivalvia, Unionoida): prodigious polyphyly proves pervasive across genera}, journal = {Invertebrate Biology}, volume = {124}, number = {2}, year = {2005}, pages = {131-164}, keywords = {16S, bivalvia, CO1, molecules, mollusca, mtDNA, ND1, phylogeny, unionoida}, author = {Campbell, David C. and Serb, Jeanne M. and Buhay, Jennifer E. and Roe, Kevin and Minton, Russell L. and Lydeard, Charles} } @article {5972, title = {Phylogenetic analysis of Veneridae (Bivalvia): Comparison of molecular and palaeontological data}, journal = {Journal of Molecular Evolution}, volume = {43}, number = {5}, year = {1996}, note = {Times Cited: 17ArticleEnglishCited References Count: 24Vt330}, month = {NOV}, pages = {517-522}, abstract = {An approximately 400-bp-long portion of the 16s rRNA gene sequence has been determined for the venerid clams Chamelea gallina (Chioninae), Dosinia lupinus (Dosiniinae), Pitar rudis, Callista chione (Pitarinae), Tapes decussatus, T. philippinarum, Venerupis (= Paphia) aurea (Tapetinae), and Venus verrucosa (Venerinae). Neighbor-joining and maximum parsimony trees support the results of traditional classification methods at the subfamily level but do not support the concept of a genus Tapes. The transversion divergence rate estimated on the basis of the palaeontological record for the C. gallina/V. verrucosa separation and for the Pitarinae is very close (0.14-0.16\% per Myr, respectively) to that of ungulates and cetaceans, while the Tapetinae exhibit a much higher (0.36\% per Myr) rate.}, keywords = {16S, bivalvia, evolution, molecular clock, mtDNA, systematics, veneridae}, url = {://A1996VT33000011}, author = {Canapa, A. and Marota, I. and Rollo, F. and Olmo, E.} } @article {5841, title = {Mitochondrial DNA reveals genetic differentiation between Australian and Indonesian pearl oyster Pinctada maxima (Jameson, 1901) populations}, journal = {Journal of Shellfish Research}, volume = {22}, number = {3}, year = {2003}, note = {PDF}, pages = {781-787}, keywords = {biogeography, bivalvia, mollusca, mtDNA, pinctada, pinctada maxima, population genetics, pteriidae, pterioidea}, author = {Benzie, John A. H. and Smith, Carolyn and Sugama, Ketut} } @article {5851, title = {A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences}, journal = {Cladistics}, volume = {21}, year = {2005}, note = {PDF}, pages = {209-239}, keywords = {aves, biogeography, character evolution, combined data analyses, molecules, morphology, mtDNA, phylogeny, poy}, author = {Bertelli, Sara and Giannini, Norberto P.} } @article {5811, title = {Molecular phylogeny of the family Pectinidae (Mollusca : Bivalvia) based on mitochondrial 16S and 12S rRNA genes}, journal = {Molecular Phylogenetics and Evolution}, volume = {31}, number = {1}, year = {2004}, note = {PDFTimes Cited: 0ArticleEnglishCited References Count: 41807ym}, month = {APR}, pages = {89-95}, abstract = {Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features. (C) 2003 Elsevier Inc. All rights reserved.}, keywords = {12S, 16S, 18S, bivalvia, dna, evolution, mollusca, morphology, mtDNA, multiple sequence alignment, pectinidae, position, substitution}, url = {://000220536800008}, author = {Barucca, M. and Olmo, E. and Schiaparelli, S. and Canapa, A.} } @article {5789, title = {Cryptic species and morphological plasticity in long-lived bivalves (Unionoida: Hyriidae) from inland Australia}, journal = {Molecular Ecology}, volume = {12}, year = {2003}, note = {PDF}, pages = {2707-2717}, keywords = {biodiversity, bivalvia, cryptic species, hybridization, hyriidae, isozymes, mollusca, mtDNA, plasticity}, author = {Baker, Andrew M. and Bartlett, Chris and Bunn, Stuart E. and Goudkamp, Katrina and Sheldon, Fran and Hughes, Jane M.} } @article {1386, title = {Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences}, journal = {Molecular Phylogenetics and Evolution}, volume = {27}, year = {2003}, pages = {429-440}, keywords = {bivalvia, CO1, mollusca, mtDNA, phylogenetics, phylogeny, pteriomorphia}, issn = {1055-7903}, doi = {10.1016/S1055-7903(03)00013-7}, author = {Matsumoto, Masahiro} }