Biomedical subjects

W K Thomas

Publications and source records attributed to W K Thomas.

25 records · Page 2Linked to original sources

PubMed1991

Mode and tempo of molecular evolution in the nematode caenorhabditis: cytochrome oxidase II and calmodulin sequences.

Through direct sequencing methods, the mitochondrial gene for cytochrome oxidase subunit two (CO II) and the single-copy nuclear gene for calmodulin were compared among strains of Caenorhabidits elegans and two other Caenorhabditis species (C. remanei and C. briggsae). In addition the CO II sequence was determined from a distantly related nematode, Steinernema intermedii. Among the 11 strains of C. elegans tested, there are four types of CO II gene, arising from two major lineages. Levels of intraspecific difference in the CO II gene are low (less than 2.0%) compared to the extraordinary divergence between congeneric species, which is about 50% when corrected for multiple hits. Concordant with the increase in divergence between taxa is a change in the pattern of substitution from a strong transition bias (24 transitions compared to two transversions) within species to a substitution pattern that appears to reflect the base composition of the mitochondrial genome when more divergent nematodes are compared. The base composition of the Caenorhabditis CO II gene is strongly biased toward A + T at all three positions of codons and appears to constrain the amino acid composition of the protein. Both the CO II and calmodulin genes show extreme conservation of amino acid sequences. When the accumulation of changes at silent sites in the two genes is compared among strains, it becomes evident that the mitochondrial gene is changing faster than the nuclear gene.

Amino Acid Sequence↗

PubMed1990

Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens.

The advent of direct sequencing via the polymerase chain reaction (PCR) has opened up the possibility of molecular studies on museum specimens. Here we analyze genetic variation in populations over time by applying PCR to DNA extracted from museum specimens sampled from populations of one species over the last 78 years. Included in this study were 43 museum specimens of the Panamint kangaroo rat Dipodomys panamintinus from localities representing each of three geographically distinct subspecies. These specimens were originally collected and prepared as dried skins in 1911, 1917, or 1937. For each specimen, a 225-bp segment of the mitochondrial genome was sequenced. These mitochondrial DNA sequences were compared to those of 63 specimens collected at the same localities in 1988. The three subspecies were nearly completely distinct. Only 2 of the 106 individuals shared mitochondrial types between subspecies. For all three localities, the diversity levels were maintained between the two temporal samples. The concordance observed between the two temporally separate phylogenies supports the use of museum specimens for phylogenetic inference. This study demonstrates the accuracy and routine nature of the use of museum specimens in the analysis of mitochondrial sequence variation in natural populations and, importantly, that a temporal aspect can now be added to such studies.

Animals↗

PubMed1990

Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model.

Extensive length polymorphism and heteroplasmy (multiple forms within an individual) of the D-loop region are observed in mitochondrial DNA of the white sturgeon (Acipenser transmontanus). The nucleotide sequence of this region, for both a short and a long form, shows that the differences are due to variable numbers of a perfect 82-bp direct repeat. We propose a model for the replicative origin of length differences, involving a competitive equilibrium between the heavy strand and the D-loop strand. This model suggests that frequent misalignment in the repeat region prior to elongation, facilitated by a stable secondary structure in the displaced strand, can explain both the polymorphism and heteroplasmy in this species.

Animals↗

PubMed1990

Intraspecific sequence variation in the mitochondrial genome of rainbow trout (Oncorhynchus mykiss).

We examined the sequence of a 2214 base pair HindIII fragment from the mitochondrial genome of six rainbow trout. The fragment encodes four proteins and two tRNAs. Sequences for two fish from a single locality were identical. Those from separate localities differed by from 1 to 7 nucleotide substitutions. Of 13 variable sites, 12 were synonymous and 1 led to a conservative amino acid substitution. Transitions accounted for 12 of the 13 variants. In contrast to interspecific comparisons (Thomas and Beckenbach. 1989. J. Mol. Evol. 29: 233-245), the intraspecific divergence estimates based on sequence are less than those estimated from restriction fragment analysis, suggesting a complex, dynamic process for the accumulation of variation in the mitochondrial genome.

Amino Acid Sequence↗

PubMed1989

Variation in salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution.

Sequence comparisons were made from 2214 bp of mitochondrial DNA cloned from six Pacific salmonid species. These sequences include the genes for ATPase subunit 6, cytochrome oxidase subunit 3, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4L, tRNA(GLY), and tRNA(ARG). Variation is found at 338 silent and 12 nonsilent positions of protein coding genes and 10 positions in the two tRNA sequences. A single 3-bp length difference was also detected. In all pairwise comparisons the sequence divergence observed in the fragment was higher than that previously predicted by restriction enzyme analysis of the entire molecule. The inferred evolutionary relationship of these species is consistent between methods. The distribution of silent variation shows a complex pattern with greatly reduced variation at the junctions of genes. The variation in the tRNA sequences is concentrated in the DHU loop. The close relationship of these species and extensive sequence analyzed allows for an analysis of the spectrum of substitutions that includes the frequencies of all 12 possible substitutions. The observed spectrum of substitutions is related to potential pathways of spontaneous substitution. The salmonid sequences show an extremely high ratio of silent to replacement substitutions. In addition the amino acid sequences of the four proteins coded in this fragment show a consistently high level of identity with the Xenopus sequences. Taken together these data are consistent with a slower rate of amino acid substitution among the cold-blooded vertebrates when compared to mammals.

Adenosine Triphosphatases↗

PubMed1989

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.

Amino Acid Sequence↗

PubMed1989

Shifting constraints on tRNA genes during mitochondrial DNA evolution in animals.

During the evolution of echinoderm mitochondrial (mt) DNA, a transfer RNA gene lost its tRNA function and became part of a protein-coding gene. To examine the evolutionary consequences of this event, we sequenced 961 bp of mtDNA in five sea urchin species. This enabled us to build a tree relating the mtDNAs and use it for analyzing the pattern and process of evolutionary substitutions in the former leucine tRNA gene, which now is a 5' extension of the gene for NADH dehydrogenase subunit 5 (ND5). This 5' extension is now evolving at the same rate and under the same protein-coding constraints as the rest of ND5. The adjacent (upstream) serine tRNA gene, however, has been evolving at a reduced rate, consistent with the possibility that it has assumed a punctuation role in processing of the primary transcript that was once fulfilled by the former leucine tRNA gene.

Animals↗