Gene–Gene Concordance and the Phylogenetic Relationships among Rare and Widespread Pygmy Sunfishes (Genus Elassoma)

Quattro, Joseph M.; Jones, William J.; Grady, James M.; Rohde, Fred C.

doi:10.1006/mpev.2000.0884

Cited by 16 publications

(9 citation statements)

References 26 publications

(23 reference statements)

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“…The claim is often made that mitochondrial sequences are more useful for resolving recent nodes while nuclear sequences are more appropriate for resolving older nodes (e.g., Johnson and Clayton, 2000;Quattro et al, 2001). Because nuclear genes evolve more slowly, they are postulated to have greater utility at levels of divergence where the signal from mitochondrial sequences has become saturated.…”

Section: Properties and Relative Utility Of The Nuclearmentioning

confidence: 98%

Type I Sts Markers Are More Informative than Cytochrome b in Phylogenetic Reconstruction of the Mustelidae (Mammalia: Carnivora)

Koepfli

Wayne

2003

Systematic Biology

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We compared the utility of five nuclear gene segments amplified with type I sequence-tagged site (STS) primers versus the complete mitochondrial cytochrome b (cyt b) gene in resolving phylogenetic relationships within the Mustelidae, a large and ecomorphologically diverse family of mammalian carnivores. Maximum parsimony and likelihood analyses of separate and combined data sets were used to address questions regarding the levels of homoplasy, incongruence, and information content within and among loci. All loci showed limited resolution in the separate analyses because of either a low amount of informative variation (nuclear genes) or high levels of homoplasy (cyt b). Individually or combined, the nuclear gene sequences had less homoplasy, retained more signal, and were more decisive, even though cyt b contained more potentially informative variation than all the nuclear sequences combined. We obtained a well-resolved and supported phylogeny when the nuclear sequences were combined. Maximum likelihood and Bayesian phylogenetic analyses of the total combined data (nuclear and mitochondrial DNA sequences) were able to better accommodate the high levels of homoplasy in the cyt b data than was an equally weighted maximum parsimony analysis. Furthermore, partition Bremer support analyses of the total combined tree showed that the relative support of the nuclear and mitochondrial genes differed according to whether or not the homoplasy in the cyt b gene was downweighted. Although the cyt b gene contributed phylogenetic signal for most major groupings, the nuclear gene sequences were more effective in reconstructing the deeper nodes of the combined tree in the equally weighted parsimony analysis, as judged by the variable-length bootstrap method. The total combined data supported the monophyly of the Lutrinae (otters), whereas the Melinae (badgers) and Mustelinae (weasels, martens) were both paraphyletic. The American badger, Taxidea taxus (Taxidiinae), was the most basal taxon. Because hundreds of type I STS primer sets spanning the complete genomes of the human and mouse have been published and thus represent many independently segregating loci, the potential utility of these markers for molecular systematics of mammals and other groups is enormous.

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Section: Properties and Relative Utility Of The Nuclearmentioning

confidence: 98%

Type I Sts Markers Are More Informative than Cytochrome b in Phylogenetic Reconstruction of the Mustelidae (Mammalia: Carnivora)

Koepfli

Wayne

2003

Systematic Biology

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“…Our ultimate goal is to reconstruct the phylogenetic relationships among all currently recognized western North American cyprinid genera (natural or not) through observed variation in one mitochondrial and three nuclear DNA genes analyzed using diverse phylogenetic methods. The variable rates of evolution in these four genes has been demonstrated by several authors to make them highly informative in analyses done in large clades with deep and shallow nodes and across a broad range of evolutionary divergences (Quattro et al 2001). This study also extends phylogenetic hypotheses beyond previously published analyses of western cyprinids that potentially suffer from incomplete taxon and character sampling through the addition of multiple species within genera (i.e.…”

Section: Introductionmentioning

confidence: 99%

Molecular systematics of western North American cyprinids (Cypriniformes: Cyprinidae)

Schönhuth

Shiozawa

Dowling

et al. 2012

Zootaxa

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The phylogenetic or evolutionary relationships of species of Cypriniformes, as well as their classification, is in a era of flux. For the first time ever, the Order, and constituent Families are being examined for relationships within a phylogenetic context. Relevant findings as to sister-group relationships are largely being inferred from analyses of both mitochondrial and nuclear DNA sequences. Like the vast majority of Cypriniformes, due to an overall lack of any phylogenetic investigation of these fishes since Hennig's transformation of the discipline, changes in hypotheses of relationships and a natural classification of the species should not be of surprise to anyone. Basically, for most taxa no properly supported phylogenetic hypothesis has ever been done; and this includes relationships with reasonable taxon and character sampling of even families and subfamilies. As such, like others, many western North American cyprinid genera have had a controversial taxonomic and systematic history.Our effort to better understand the evolutionary history of this artificial geographic grouping of species (Western) surveyed taxa and characters broadly. We analyzed 127 taxa (71 species) from 36 genera, including representative taxa from all 22 western genera hypothesized to form the Western Clade sensu Coburn and Cavender (1992). Our evaluation also included additional sampling from a heterogeneous array of species from the western genera Algansea, Gila, Lepidomeda, Ptychocheilus and Siphateles. Resulting phylogenetic inferences, based on one mitochondrial and three nuclear genes (mtDNA: cytb; nDNA: Rag1, Rhod, S7), consistently resolved a well-supported Western Clade, but one inclusive of Chrosomus erythrogaster. This taxon, always formed the sister group to the extant species of Gila plus 10 other western genera. Our Western Clade is qualitatively different from that of prior studies and does not include the genera Agosia, Algansea, Iotichthys, Lepidomeda, Meda, Mylocheilus, Plagopterus, Pogonichthys, Rhinichthys, Tiaroga or Yuriria. All of these taxa were, however, included in Coburn and Cavender´s (1992) Western Clade. Our broader-scale survey and increased character sampling were always resolved these latter taxa within one of two different major clades: the OPM Clade (sensu Mayden 1989) and the Creek Chub-Plagopterin Clade (sensu Simons et al. 2003). Our hypothesized Western Clade places Orthodon sister to a Western Chub-Pikeminnow Clade also inclusive of Acrocheilus, Eremichthys, Gila, Hesperoleucus, Lavinia, Moapa, Mylopharodon, Ptychocheilus, Relictus and Siphateles. The latter taxa have traditionally been recognized at the generic level, simply on the basis of their morphological distinctiveness and not on the basis of a phylogenetic evaluation of relationships. Composition of our Western Chub-Pikeminnow Clade also reveals genetic divergences between species of some genera (Gila, Ptychocheilus, Siphateles) comparable to genetic divergences documented between genera within the Western Clade. Relationships for th...

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“…Our sampling of taxa is biased towards those on which our lab currently works; we have not fully explored the taxonomic breadth over which these primer sets might be useful. However, the Ald-B locus described here, along with other single-copy loci [6,7], might prove useful as markers for studies of intra- and inter-specific phylogeny in many acanthopterygian fishes.…”

Section: Discussionmentioning

confidence: 99%

“…Although each locus would provide an independent estimate of phylogenetic relationship, the amplification of multiple loci might cause confusion regarding relationships among loci across taxa. Developing primer sets that target single loci [6,7] or refining existing primer sets that amplify multiple loci to target a single locus could circumvent this problem. We demonstrate the latter approach by redesigning 'universal' primers to target the aldolase-B (Ald-B) locus in a sample of acanthopterygian fishes.…”

Section: Introductionmentioning

confidence: 99%

PCR primers for an aldolase-B intron in acanthopterygian fishes

2001

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Background: Nuclear DNA sequences provide genetic information that complements studies using mitochondrial DNA. Some 'universal' primer sets have been developed that target introns within protein-coding loci, but many simultaneously amplify introns from paralogous loci. Refining existing primer sets to target a single locus could circumvent this problem.Results: Aldolase intron 'G' was amplified from four fish species using previously described primer sets that target several loci indiscriminately. Phylogenetic analyses were used to group these fragments and other full-length aldolase proteins from teleost fishes into orthologous clades and a primer set was designed to target specifically an intron within the aldolase-B locus in acanthopterygian fishes. DNA amplifications were tried in a variety of acanthopterygian fishes and amplification products, identifiable as aldolase-B intron 'G', were observed in all atherinomorph and percomorph taxa examined. Sequence variation within this locus was found within and among several species examined. Conclusions:Using 'universal' primer sets coupled with phylogenetic analyses it was possible to develop a genetic assay to target a specific locus in a variety of fish taxa. Sequence variation was observed within and among species suggesting that this targeted assay might facilitate interspecific and intraspecific comparisons.

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Gene–Gene Concordance and the Phylogenetic Relationships among Rare and Widespread Pygmy Sunfishes (Genus Elassoma)

Cited by 16 publications

References 26 publications

Type I Sts Markers Are More Informative than Cytochrome b in Phylogenetic Reconstruction of the Mustelidae (Mammalia: Carnivora)

Type I Sts Markers Are More Informative than Cytochrome b in Phylogenetic Reconstruction of the Mustelidae (Mammalia: Carnivora)

Molecular systematics of western North American cyprinids (Cypriniformes: Cyprinidae)

PCR primers for an aldolase-B intron in acanthopterygian fishes

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