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310
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
- Syst
, 2005
"... Abstract.-Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of a ..."
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Cited by 112 (7 self)
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Abstract.-Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean −lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2ln Bayes factor >10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.
Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches
- Syst. Biol
, 2002
"... Abstract.—Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer con�dence values by way of nonparametric bootstrapping. Recent developments in phylogenetics sugg ..."
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Cited by 91 (8 self)
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Abstract.—Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer con�dence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the ef�ciency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wideranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required �80 % less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and
IM: FH3, a domain found in formins, targets the fission yeast formin Fus1 to the projection tip during conjugation
- J Cell Biol
, 1998
"... Abstract. Formins are involved in diverse aspects of morphogenesis, and share two regions of homology: FH1 and FH2. We describe a new formin homology region, FH3. FH3 is an amino-terminal domain that differs from the Rho binding site identified in Bni1p and p140mDia. The Schizosaccharomyces pombe fo ..."
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Cited by 37 (0 self)
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Abstract. Formins are involved in diverse aspects of morphogenesis, and share two regions of homology: FH1 and FH2. We describe a new formin homology region, FH3. FH3 is an amino-terminal domain that differs from the Rho binding site identified in Bni1p and p140mDia. The Schizosaccharomyces pombe formin Fus1 is required for conjugation, and is localized to the projection tip in cells of mating pairs. We replaced genomic fus1 � with green fluorescent protein (GFP)tagged versions that lacked either the FH1, FH2, or FH3 domain. Deletion of any FH domain essentially abolished mating. FH3, but neither FH1 nor FH2, was required for Fus1 localization. An FH3 domain–GFP fusion protein localized to the projection tips of mating pairs. Thus, the FH3 domain alone can direct protein
Relationships and evolution of the North African geckos Geckonia and Tarentola (Reptilia: Gekkonidae), based on mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution
, 2002
"... on mitochondrial and nuclear DNA sequences ..."
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Incipient speciation in sympatric Nicaraguan crater lake cichlid fishes: sexual selection versus ecological diversification
- Proc. R. Soc
"... ecological diversi cation ..."
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M (2003) Climatic oscillations triggered post-Messinian speciation
- of Western Palearctic brown frogs (Amphibia, Ranidae). Molecular Phylogenetics and Evolution
"... Oscillating glacial cycles over the past 2.4 million years are proposed to have had a major impact on the diversity of contem-porary species communities. We used mitochondrial and nuclear DNA sequence data to infer phylogenetic relationships within Western Palearctic brown frogs and to test the infl ..."
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Cited by 32 (1 self)
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Oscillating glacial cycles over the past 2.4 million years are proposed to have had a major impact on the diversity of contem-porary species communities. We used mitochondrial and nuclear DNA sequence data to infer phylogenetic relationships within Western Palearctic brown frogs and to test the influence of Pliocene and Pleistocene climatic changes on their evolution. We se-quenced 1976 bp of the mitochondrial genes 16S rRNA and cytochrome b and of the nuclear rhodopsin gene for all current species and subspecies. Based on an established allozyme clock for Western Palearctic water frogs and substitution rate constancy among water frogs and brown frogs, we calibrated a molecular clock for 1425 bp of the 16S and rhodopsin genes. We applied this clock to date speciation events among brown frogs. Western Palearctic brown frogs underwent a basal post-Messinian radiation about 4 million years ago (mya) into five major clades: three monotypic lineages (Rana dalmatina, Rana latastei, Rana graeca), an Anatolian lineage, and a lineage comprising Rana italica, Rana arvalis, and all Iberian taxa. Polytypic lineages radiated further in concordance with the onset of climatic oscillations ca. 3.2, 2.0, and 1.0–0.6 mya, respectively. The dated fossil record corroborates our paleo-biogeographic scenario. We conclude that drastic climatic changes followed by successive temperature oscillations ‘‘trapped’ ’ most brown frog species in their southern European glacial refugia with enough time to speciate. Substantial dispersal was only possible during extensive interglacial periods of a constant subtropical climate.
Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe: Anatini). Molecular Phylogenetics and Evolution
, 1998
"... Rates of sequence evolution were estimated for the cytochrome b (cyt b) and NADH dehydrogenase sub-unit 2 (ND2) genes using a phylogeny of the dabbling ducks (Tribe: Anatini) and outgroups. This speciose group was densely sampled, reducing the impact of undetected homoplasy on rate comparisons. Phyl ..."
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Cited by 28 (9 self)
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Rates of sequence evolution were estimated for the cytochrome b (cyt b) and NADH dehydrogenase sub-unit 2 (ND2) genes using a phylogeny of the dabbling ducks (Tribe: Anatini) and outgroups. This speciose group was densely sampled, reducing the impact of undetected homoplasy on rate comparisons. Phylog-enies based on sequences of the two gene regions and various weighting schemes differed, but most of the differences involved weakly supported nodes. In addi-tion, partition homogeneity tests show that these differ-ences were not due to statistically significant conflict between the data sets. Cyt b and ND2 also showed similar rates and types of both nucleotide and amino acid substitutions. For both genes, substitutions be-tween isoleucine and valine and between alanine and threonine were most common; both of these substitu-tion types are the result of A–G transitions at first positions of codons. Rates of sequence evolution var-ied substantially and significantly among nucleotide positions, and even within a given codon position (first, second, or third), rates were significantly hetero-geneous among sites. Within Anatini, cyt b and ND2 show similar levels of variation and homoplasy, and are equally useful for reconstructing the species level phylogeny of this group. r 1998 Academic Press Key Words: mtDNA coding gene evolution; weighting;
Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates
- Mol. Phylogenet. Evol
, 2003
"... The study of Amazonian biodiversity requires detailed knowledge of the phylogenetic relationships of closely related taxa dis-tributed across Amazonia. The Amazonian poison frogs of the genus Dendrobates have undergone many taxonomic revisions, but the phylogenetic relationships within this group re ..."
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Cited by 24 (6 self)
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The study of Amazonian biodiversity requires detailed knowledge of the phylogenetic relationships of closely related taxa dis-tributed across Amazonia. The Amazonian poison frogs of the genus Dendrobates have undergone many taxonomic revisions, but the phylogenetic relationships within this group remain poorly understood. Most previous classifications were based on morphology and skin toxin analyses, with limited use of DNA sequence data. Using mtDNA sequence data from four gene regions (cytochrome b, cytochrome oxidase I, 16S rRNA, and 12S rRNA), we present a molecular phylogenetic analysis of the evolutionary relationships within a representative group of Amazonian Dendrobates. We use the resulting phylogenetic hypothesis to investigate different biogeographic hypotheses concerning genetic divergence and species diversity in Amazonia. The results of the analysis support the presence of ancient paleogeographic barriers to gene flow between eastern and western Amazonia, and indicate substantial genetic divergence between species found in the northern and southern regions of western Amazonia. 2002 Elsevier Science (USA). All rights reserved.
Nuclear and mitochondrial genes contain similar phylogenetic signal for pigeons and doves
, 2000
"... Molecular systematic studies generally assume that gene trees are reasonable estimates of species trees. We tested the validity of this assumption in the pigeons and doves (Aves: Columbiformes) by comparing phylogenies derived from nuclear (�-fibrinogen intron 7) and mitochondrial (cytochrome b) gen ..."
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Cited by 23 (8 self)
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Molecular systematic studies generally assume that gene trees are reasonable estimates of species trees. We tested the validity of this assumption in the pigeons and doves (Aves: Columbiformes) by comparing phylogenies derived from nuclear (�-fibrinogen intron 7) and mitochondrial (cytochrome b) genes. Trees derived from the two genes when analyzed separately contained many nodes in common. A partition homogeneity test revealed no significant incongruence between trees derived from the two genes; so, we combined nuclear and mitochondrial data in subsequent phylogenetic analyses. The resulting tree, which was highly resolved and generally well supported, contained a strong biogeographic component. The rate of nucleotide substitution for the nuclear intron was approximately six times slower than that of cytochrome b. This resulted in a much higher consistency index for trees derived from the intron because of the low level of multiple substitution. However, the degree of resolution and support for trees reconstructed from the two genes was similar. We also examined the transition and transversion substitution rates for the genes. Third position transversions for cytochrome b accumulated linearly with intron divergence, suggesting low levels of multiple substitution for third position transversions.
Historical biogeography of the western rattlesnake (Serpentes: Viperidae: Crotalus viridis), inferred from mitochondrial DNA sequence information
- Mol. Phylogenet. Evol
, 2000
"... We infer the phylogeography of the Western Rattlesnake (Crotalus viridis) using phylogenetic analysis of mitochondrial DNA sequences from 1345 bp of the genes for cytochrome b and NADH dehydrogenase subunit 4. Two main clades are revealed: one includes populations from east and south of the Rocky Mo ..."
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Cited by 20 (3 self)
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We infer the phylogeography of the Western Rattlesnake (Crotalus viridis) using phylogenetic analysis of mitochondrial DNA sequences from 1345 bp of the genes for cytochrome b and NADH dehydrogenase subunit 4. Two main clades are revealed: one includes populations from east and south of the Rocky Mountains (conventionally referred to as Crotalus viridis viridis and C. v. nuntius), and the other consists of populations west of the Rocky Mountains. Within the western clade, a population from southern Arizona (C. v. cerberus) represents the sister taxon to the remaining western populations. The conventional subspecies recognized in this species do not fully correspond to the phylogenetic pattern, and a review of the systematic status of several populations is needed. Our data allow the inferences that small body size evolved twice and that the ability of one population (C. v. concolor)to secrete highly lethal toxins related to Mojave toxin arose within the complex. Our phylogeny should represent the basis for further studies on the causes of geographical variation in this complex.
