Application of hypervariable genetic markers to forensic identification of 'wild' from hatchery-raised red drum, Sciaenops ocellatus.

Forensic identification of 'wild' versus hatchery-produced (cultured) red drum (Sciaenops ocellatus), an economically important marine fish in the southern United States, was assessed using hypervariable nuclear-encoded microsatellites and sequences of mitochondrial DNA. Both genotype exclusion and likelihood-ratio tests successfully identified 'wild' and 'cultured' individuals within requisite error bounds and within the context of complete parental sampling. Of the two, genotype exclusion was more effective, producing satisfactory results with fewer microsatellites and larger allowable error rates. Assignment tests proved ineffective, most likely because of the low level of genetic divergence between the sampled populations. An optimal, minimum set of ten markers that will reduce potential genotyping costs is identified. Results of the study should allay concerns regarding identification of 'wild'-caught fish sold illegally.

The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA.

We describe the complete sequence of the 16,596-nucleotide mitochondrial genome of the zebrafish (Danio rerio); contained are 13 protein genes, 22 tRNAs, 2 rRNAs, and a noncoding control region. Codon usage in protein genes is generally biased toward the available tRNA species but also reflects strand-specific nucleotide frequencies. For 19 of the 20 amino acids, the most frequently used codon ends in either A or C, with A preferred over C for fourfold degenerate codons (the lone exception was AUG: methionine). We show that rates of sequence evolution vary nearly as much within vertebrate classes as between them, yet nucleotide and amino acid composition show directional evolutionary trends, including marked differences between mammals and all other taxa. Birds showed similar compositional characteristics to the other nonmammalian taxa, indicating that the evolutionary trend in mammals is not solely due to metabolic rate and thermoregulatory factors. Complete mitochondrial genomes provide a large character base for phylogenetic analysis and may provide for robust estimates of phylogeny. Phylogenetic analysis of zebrafish and 35 other taxa based on all protein-coding genes produced trees largely, but not completely, consistent with conventional views of vertebrate evolution. It appears that even with such a large number of nucleotide characters (11,592), limited taxon sampling can lead to problems associated with extensive evolution on long phyletic branches.

Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis.

Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplastic and consistent transition and transversion changes in mitochondrial protein coding genes were determined from character-state reconstructions on a highly corroborated phylogeny of mammals. We found that although homoplasy was related to evolutionary rates and was greater for transitions, the absolute number of consistent transitions greatly exceeded the number of consistent transversions. Consequently, transitions provided substantially more useful phylogenetic information than transversions. These results suggest that down-weighting transitions may be unwarranted in many cases. This conclusion was supported by the fact that a range of transition: transversion weighting schemes applied to various mitochondrial genes and genomic partitions rarely provided improvement in phylogenetic estimates relative to equal weighting, and in some cases weighting transitions more heavily than transversions was most effective.

Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera.

Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprinid fish Cyprinella spiloptera. Variation at different nucleotide positions in individual repeats supported different models of repeat evolution. One set of characters included several nucleotide variants found in all copies from a limited number of individuals, while the other set included an 8-bp deletion found in a limited number of copies in all individuals. The deletion and an associated nucleotide change appear to be the result of a deterministic, rather than stochastic, mutation process. Parallel origins of repeat arrays in different mitochondrial lineages, possibly coupled with a homogenization mechanism, best explain the distribution of nucleotide variation.

Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera.

Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation.

Temporal effects of infused corticosterone and aldosterone on plasma glucose levels in the American bullfrog (Rana catesbeiana).

The effects of a single infusion of corticosterone or aldosterone on plasma glucose levels were compared in the American bullfrog (Rana catesbeiana). The corticoids were administered, and serial blood samples were collected, via a cannula placed in the common iliac artery. Plasma glucose was estimated by the glucose oxidase method. Plasma glucose levels were essentially unchanged from the time-zero levels at 3 hr after the infusion of 1.0 mg/100 g body wt of corticosterone. The levels subsequently increased to maxima that were approximately 45% greater than the time-zero levels at 9 through 24 hr and then declined to approximately the initial levels by 48 hr after treatment. Infusion of 0.24 mg/100 g body wt of aldosterone did not significantly alter plasma glucose levels. The results suggest that elevated circulating corticosterone is not involved in the primary hyperglycemic response to a stress, but may function synergistically and sequentially with elevated circulating catecholamines in subsequent compensatory adjustments.