Molecular systematics of North American phoxinin genera (Actinopterygii: Cyprinidae) inferred from mitochondrial 12S and 16S ribosomal RNA sequences

Abstract

The cyprinid fish fauna of North America is relatively large, with approximately 300 species, and all but one of these are considered phoxinins. The phylogenetic relationships of the North American phoxinins continue to pose difficulties for systematists. Results of morphological analyses are not consistent owing to differences interpreting and coding characters. Herein, we present phylogenetic analyses of mitochondrial 12S and 16S ribosomal RNA sequence data for representatives of nearly all genera of North American phoxinins. The data were analysed using parsimony, weighted parsimony, maximum likelihood and bayesian analyses. Results from weighted parsimony, likelihood and the bayesian analysis are largely consistent as they all account for differing substitution rates between transitions and transversions. Several major clades within the fauna can be recognized and are strongly supported by all analyses. These include the western clade, creek chub-plagopterin clade and the open posterior myodome clade. The shiner clade is nested in the open posterior myodome clade and is the most species-rich clade of North American phoxinins. Relationships within this clade were not well resolved by our analyses. This may reflect the inability of the mitochondrial RNA genes to resolve recent speciation events or taxon sampling within the shiner clade.

Phylogenetic relationships in the genus Cyprinella (Actinopterygii: Cyprinidae) based on mitochondrial and nuclear gene sequences

“…Morphological characters have been traditionally used to resolve the phylogenetic relationships of Cyprinella (Gibbs, 1957; Mayden, 1989;Coburn and Cavender, 1992), but recently molecular approaches using mitochondrial genes have been used to test previous hypotheses, existing classifications, and resolve relationships (Broughton and Gold, 2000;Simons et al, 2003). However, across these studies there is limited agreement in major clades within Cyprinella and sister-species relationships of taxa in the phylogeny (Fig.…”

“…within the Notropin clade in the shiner clade (Coburn and Cavender, 1992). Mitochondrial data (12S, 16S rDNA) did not clearly resolve relationships of Cyprinella with other taxa within the shiner clade, recovering the two Cyprinella species analyzed close to some species of Notropis, but relationships were collapsed in basal positions of the shiner clade (Simons et al, 2003). Recently, the phylogeny of 24 species of Cyprinella based on two mitochondrial (ND2 and ND4L) genes was reconstructed, plus four species from four related genera (Broughton and Gold, 2000).…”

“…This study recognized two major clades within Cyprinella: the C. lutrensis clade composed by 10 species endemic to northern Mexico and southwestern United States; and the C. whipplei clade including 17 species from east-central United States. Later, phylogenetic inferences based on morphology (Coburn and Cavender, 1992) and molecular sequence data (Simons et al, 2003) of North American Cyprinids, placed the genus Cyprinella within a larger group of North American species identified by Mayden (1989) as the ''open posterior myodome clade" (OPM) and a member of the shiner Clade. However, these latter two studies focused on higher-level systematic relationships for North American Cyprinidae and sampling within Cyprinella was limited.…”

“…With these factors in mind we examined mitochondrial DNA sequence variation for all species currently included in Cyprinella with a more exhaustive sampling in problematic taxa, and produced the first nuclear DNA sequence data for the genus in an effort to clarify major clades, relationships of these clades, and terminal nodes in this taxonomically controversial genus. Our analysis also includes all the hypothesized closely related taxa following revisionary analyses by Mayden's (1989) and Coburn and Cavender's (1992) based on morphology and recent phylogenies based on mitochondrial characters (Simons et al, 2003;Schönhuth et al, 2006). Herein, we offer phylogenetic hypotheses for the genus and related species together with another example illustrating the importance of both thorough taxon sampling and the importance of nuclear genes for the phylogenetic inferences.…”

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

“…Therefore, the 16S rRNA gene has great potential for the inference of divergences among the cyprinid lineages and resolution of relationships within Cyprininae. Some recent analyses using the mitochondrial 16S rRNA gene, however, have depicted limited resolution of relationships within the Cyprinidae because of low nodal support (Gilles et al, 1998;Simons and Mayden, 1998;Simons et al, 2003;Li et al, 2005). It is well known that phylogenetic inferences depend not only on the appropriate choice of the marker, but also rely on comparative studies of the inherent phylogenetic contents of the molecular markers, such as base compositions, structural characteristics, parameter estimations and the adopted methods (Rosenberg and Kumar, 2003;Telford et al, 2005).…”