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Showing papers in "Molecular Phylogenetics and Evolution in 2004"


Journal ArticleDOI
TL;DR: The various phylogenetic analyses carried out on the data sets allowed us to conclude that: the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient.

394 citations


Journal ArticleDOI
TL;DR: It is argued that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.

333 citations



Journal ArticleDOI
TL;DR: Better taxonomic resolution and recovery of established taxa were obtained here, especially with Bayesian inference, than in previous parsimony-based studies that used 18S rRNA sequences, and should revive interest in using rRNA genes to study arthropod and ecdysozoan relationships.

302 citations


Journal ArticleDOI
TL;DR: It is asserted that similarity is the appropriate homology criterion for sequence alignment, as it is with morphology, and the severity of this test is compromised when congruence with other characters is favored when selecting among alignment parameters.

279 citations


Journal ArticleDOI
TL;DR: It is estimated that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval, and polyploidization occurred at least six times in clawed frogs.

278 citations


Journal ArticleDOI
TL;DR: DNA sequences from the first exon of the IRBP gene are used to infer phylogenetic relationships within and among the major lineages of muroid rodents and a preliminary examination of molar tooth morphology suggests the triserial murid molar pattern as conceived by evolved at least three times during the course of muraid evolution.

272 citations


Journal ArticleDOI
TL;DR: Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus.

259 citations


Journal ArticleDOI
TL;DR: Parsimony, maximum likelihood, and Bayesian inference methods suggest that both the Ranoidea and Hyloidea are well-supported monophyletic groups.

249 citations



Journal ArticleDOI
TL;DR: The mtDNA data do not support the traditional classification of red deer as only one species nor its division into numerous subspecies, and the discrepancies between the geographical pattern of differentiation based on mtDNA cytochrome b and the existing specific and subspecific taxonomy based on morphology are discussed.

Journal ArticleDOI
TL;DR: Nearly the entire carbomoylphosphate synthase (CPS) domain of CAD is sequenced from 29 species of flies representing all major clades within Eremoneura, or higher flies, and several orthorrhaphous brachyceran outgroups, and exhibits considerable phylogenetic utility.

Journal ArticleDOI
TL;DR: Several strongly supported groupings within the Geoemydidae demonstrate non-monophyly of some genera and possible interspecific hybrids, and it is found that adding data for a subset of taxa improved resolution of some deeper nodes in the tree.

Journal ArticleDOI
TL;DR: The analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae.

Journal ArticleDOI
TL;DR: This paper presents the first phylogenetic hypothesis for the Latrodectus genus and is generated from DNA sequences of the mitochondrial gene cytochrome c oxidase subunit I, recovering two well-supported reciprocally monophyletic clades within the genus.

Journal ArticleDOI
TL;DR: The topology derived from molecular data provides a basis for proposing a new classification of Demospongiae s.s., and suggests a reverse polarity of some characters, with respect to traditional conceptions: viviparity, presence of monaxon spicules and of spongin appear to be ancestral, whereas ovip parity, and presence of tetraxon spicule appear as derived characters.

Journal ArticleDOI
TL;DR: Parsimony and Bayesian analyses yielded identical relationships for the diploids, and these are consistent with other data, producing the best-supported phylogenetic assessment currently available for the genus Nicotiana.

Journal ArticleDOI
TL;DR: A comprehensive molecular phylogeny for the family Sciuridae is reported on and Parsimony, likelihood, and Bayesian analyses reveal five major lineages and refute the conventional elevation of the flying squirrels (Pteromyinae) to subfamily status.

Journal ArticleDOI
TL;DR: PCR amplification, sequencing and phylogenetic analysis of nodA gene sequences revealed the monophyletic character with the possible exception of photosynthetic Bradyrhizobium, despite high sequence diversity, and indicated that the spread and maintenance of nodulation genes within the Bradyrnobia genus occurred through vertical transmission, although lateral gene transfer also played a significant role.

Journal ArticleDOI
TL;DR: All analyses strongly support the monophyly of the three amphibian Orders and the Batrachia hypothesis (Gymnophiona, (Anura, Caudata) receives moderate or good support depending on the method of analysis).

Journal ArticleDOI
TL;DR: This study examined mitochondrial displacement loop sequence variation and frequencies of Bos taurus and Bos indicus Y chromosome haplotypes in Japanese, Mongolian, and Korean native cattle to clarify the origin and genetic diversity of cattle in North Eastern Asia.

Journal ArticleDOI
TL;DR: The utility of the trnC-trnD region for lower-level phylogenetic studies in flowering plants is demonstrated, which provides a similar number of informative phylogenetic characters as the ITS regions and a slightly higherNumber of informative characters than the chloroplast ndhF gene.

Journal ArticleDOI
TL;DR: Parsimony and Bayesian analyses of the combined ITS/trnL-F dataset show Loliinae to be monophyletic but unresolved for a weakly supported clade of 'broad-leaved Festuca,' while Vulpia is polyphyletic within the 'fine-leaves' fescues as revealed by the two genome analyses.

Journal ArticleDOI
TL;DR: The Bayesian method of phylogenetic reconstruction was applied to the data, because even with a large number of sequences it is an efficient means of analysis that provides intuitive measures of support for tree topologies and for the parameters of the nucleotide substitution model.

Journal ArticleDOI
TL;DR: This article used 269 Genbank sequences of mitochondrial DNA and nuclear DNA (from 16 genes) to infer phylogenies for 30 species of salmonids using maximum parsimony and maximum likelihood to analyze each gene separately, the mtDNA data combined, the nuclear data combined and all of the data together.

Journal ArticleDOI
TL;DR: A phylogeny of the Asian pitvipers, based on 2403 bp of four mitochondrial gene regions, indicates the existence of distinct species groups within Trimeresurus s.s. Although all but two species currently referred to this genus form a monophyletic group, morphological and molecular analyses identify four subgroups that warrant recognition at the generic level.

Journal ArticleDOI
TL;DR: Phylogenetic analysis among insect orders confirmed a monophyletic Endopterygota, a monphyletic Mecopterida, a Monophyletics Diptera, amonophyletsic Lepidoptera, and a monophysletic ColeopterA, suggesting that the complete insect mt genome sequence has a resolving power in the diversification events within Endoperygota.

Journal ArticleDOI
TL;DR: Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus, with an unresolved basal polytomy, and indicates that the subgenus Mus contains three distinct 'species groups'.

Journal ArticleDOI
TL;DR: Several cases of probable LBA are found by analyzing subsamples from an alignment of 18S rDNA sequences for 133 metazoans, demonstrating that LBA problems can occur in real data sets, and they provide an opportunity to investigate causes of incorrect inferences.

Journal ArticleDOI
TL;DR: Phylogenetic analysis shows that the ancient sequences form a clade that is most closely related to the extant lions from Africa and Asia; at the same time, cave lions appear to be highly distinct from their living relatives.