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W K Thomas

Publications and source records attributed to W K Thomas.

At least 19 recordsLinked to original sources
PubMed1998

A molecular evolutionary framework for the phylum Nematoda.

Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.

Animals↗
PubMed1998

Embryonic axis specification in nematodes: evolution of the first step in development.

In 1828, von Baer proposed that the early stages of development must be the most conserved [1]. Others have since countered that the middle stages of development are the most conserved [2]. To address whether the earliest step in pattern formation can evolve, we have examined how asymmetry along the antero-posterior (AP) axis is generated in various nematode species. AP asymmetry is specified in Caenorhabditis elegans at fertilization by the sperm, which directs a cytoplasmic rearrangement that segregates critical factors such as the P granules to one side of the uncleaved embryo [3,4]. We found that AP asymmetry is generated differently in another nematode species: the sperm is not used to specify AP asymmetry, there are no signs of cytoplasmic movements, and P granules are segregated differently. Despite these differences, development from the two-cell stage is remarkably similar in the two species. We have reconstructed the evolutionary history of these mechanisms by analyzing the development of 30 nematode species and mapping the results onto a molecular phylogeny of the nematodes [5]. The results suggest that a new mechanism for axis specification evolved in an ancestor of some of the relatives of C. elegans. We conclude that this fundamental step in development can evolve without affecting other aspects of development.

Animals↗
PubMed1997

An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans.

Nematodes are known to be a useful system for studies of comparative development. Here we perform a molecular phylogenetic analysis to allow for the independent interpretation of the developmental and morphological changes observed among a selected set of nematode species. Our molecular phylogenetic analysis is based on coding regions of the genes for RNA polymerase II, the small subunit rRNA and an expansion segment of the large subunit rRNA. Sequences were compared from five species in the family (Rhabditidae) that includes the developmental model organism Caenorhabditis elegans and from an outgroup taxon Aduncospiculum halicti (Diplogasterina). The phylogenetic analysis does not support the monophyly of the subfamily Mesorhabditinae and identifies the unnamed strain PS1010 as a sister taxon of C. elegans despite its morphologically divergent buccal capsule. On the basis of the inferred framework, we can begin to interpret the evolution of vulval development and of morphological differences among these nematode species.

Animals↗
PubMed1994

A molecular evolutionary framework for eukaryotic model organisms.

BACKGROUND: Implicit in the characterization of a model organism is the hope that insights into its biology can be extended to other species. For this hope to be fulfilled, the phylogenetic position of the model organism within a larger evolutionary framework must be known. We focus here on major model organisms of developmental genetics and cell biology. We first consider the positions of the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster within a phylogeny of the major advanced metazoan groups. Then we consider the evolutionary relationships between fungi (represented by Saccharomyces cerevisiae and Schizosaccharomyces pombe), plants, and animals. RESULTS: We show, by a direct comparison with small subunit ribosomal RNA (18 S rRNA), that RNA polymerase II is an appropriate molecule for addressing the phylogenetic branchings in the early evolution of eukaryotes. The results from the analyses of newly determined and previously published sequences of the two largest subunits of RNA polymerase II suggest the following. Firstly, that plants and animals share a last common ancestor that excludes fungi, the lineage of which originated earlier. Secondly, that the lineage leading to the nematode Caenorhabditis elegans diverged earlier from the Metazoa than the lineages of arthropods, deuterostomes, annelids and molluscs. Finally, that deuterostomes arose from within protostomes. CONCLUSIONS: RNA polymerase II is well-suited for the elucidation of the evolutionary relationships among eukaryotes. We emphasize the implications of our results for other biological disciplines in addition to molecular evolution, as a phylogenetic framework allows predictions and inferences to be made about the existence of fundamental biological mechanisms elucidated in model organisms.

Amino Acid Sequence↗
PubMed1994

Phylogenetic analysis of the Coscoroba coscoroba using mitochondrial srRNA gene sequences.

In order to study the phylogenetic relationships among Coscoroba, goose, and swan lineages, sequences for the complete mitochondrial small ribosomal RNA (srRNA) gene were determined from five waterfowl species. Parsimony and distance analyses support the branching of Coscoroba prior to the divergence of geese and swans, and maximum likelihood analyses give almost equal support to that pattern and to the sister group relationship between Coscoroba and swans. The monophyly of the geese was confirmed at a statistically significant level. In sequence comparisons among waterfowl, transitions increase linearly with transversions, and so we conclude that the lack of complete resolution of Coscoroba's position is not due to sequence saturation alone, but also reflects relatively close branching times.

Animals↗
PubMed1994

The marsupial mitochondrial genome and the evolution of placental mammals.

The entire nucleotide sequence of the mitochondrial genome of the American opossum, Didelphis virginiana, was determined. Two major features distinguish this genome from those of other mammals. First, five tRNA genes around the origin of light strand replication are rearranged. Second, the anticodon of tRNA(Asp) is posttranscriptionally changed by an RNA editing process such that its coding capacity is altered. When the complete protein-coding region of the mitochondrial genome is used as an outgroup for placental mammals it can be shown that rodents represent an earlier branch among placental mammals than primates and artiodactyls and that artiodactyls share a common ancestor with carnivores. The overall rates of evolution of most of the mitochondrial genome of placentals are clock-like. Furthermore, the data indicate that the lineages leading to the mouse and rat may have diverged from each other as much as 35 million years ago.

Amino Acid Sequence↗
PubMed1994

Transgenic cattle resulting from biopsied embryos: expression of c-ski in a transgenic calf.

Producing transgenic cattle by microinjection of DNA into pronuclei has been inefficient and costly, in large part because of the cost of maintaining numerous nontransgenic pregnancies to term. We designed a system for early identification of transgenic embryos in which biopsies of embryos were assayed by polymerase chain reaction for presence of the transgene before embryo transfer. A total of 2555 embryos were microinjected with one of two DNA constructs. Of the 533 embryos biopsied, 112 were judged to be potentially transgenic and were transferred nonsurgically to recipients, resulting in production of 29 putative transgenic fetuses. One fetus and one calf (7% of offspring) were subsequently shown to be definitively transgenic. The calf was transgenic for a chicken c-ski cDNA, and several months after birth developed dramatic muscular hypertrophy followed by muscle degeneration. This phenotype was associated with expression of high levels of mRNA from the transgene.

Animals↗
PubMed1993

A recent origin of marmots.

The complete mitochondrial cytochrome b genes from four ground squirrels, a marmot, and a tree squirrel were sequenced and compared. A level of divergence three times lower than expected based on fossil evidence was found between the marmot and the ground squirrels. The observed divergence was similar to that found within the ground squirrels and is consistent with a recent divergence of marmots (Marmota) from true ground squirrels (Spermophilus).

Animals↗
PubMed1993

Effects of cumulus cells on culture of bovine embryos derived from oocytes matured and fertilized in vitro.

Bovine zygotes derived from oocytes matured and fertilized in vitro were cultured in vitro. In Exp. 1, zygotes were vortexed to remove cumulus cells and then cultured in oviduct epithelial cell-conditioned TCM-199 medium with or without added cumulus cells. Embryos cultured without cumulus cells developed to blastocysts significantly less often than those cultured with added cumulus cells, 3 vs 38% of cleaved ova (P < .05). Co-culture of embryos with cumulus cells during the first 48 h only, or for the duration of the culture period, resulted in development rates similar to those of controls that were not vortexed. In Exp. 2, denuded zygotes were centrifuged (15,850 x g, 3 min) at room temperature to facilitate visualization of pronuclei. Centrifuged zygotes were either placed directly into conditioned medium for culture (with or without added cumulus cells) or DNA was first microinjected into their cytoplasm or a pronucleus. All microinjected embryos were co-cultured with added cumulus cells. Centrifugation and microinjection did not reduce viability significantly when embryos were co-cultured with cumulus cells. Development was reduced significantly when embryos were cultured without cumulus cells. Thus, when oviduct epithelial cell-conditioned medium was used, cumulus cell co-culture was beneficial during the early cleavage stages of in vitro-derived zygotes, including those that received DNA microinjection.

Animals↗
PubMed1992

Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent.

Initial amplification and sequencing of a 366-bp fragment of the cytochrome b gene by a conserved primer pair (MVZ 03 and MVZ 04) revealed a nonfunctional copy of the gene with two deletions (one of which is 17 bp in length and the other of which is 3 bp in length) in Chroeomys jelskii, a South American akodontine rodent. By means of an alternative primer to MVZ 03--namely, MVZ 05--from the region of the tRNA for glutamic acid, a functional copy of cytochrome b was subsequently amplified. Both primer pairs amplify functional sequence when applied to purified mitochondrial DNA (mtDNA). Restriction-endonuclease digestion of purified mtDNA from C. jelskii did not reveal any additional sets of bands that would suggest heteroplasmy in the mitochondrial genome. When probed with both functional and nonfunctional gene fragments, MboI restriction digests revealed the same pattern, providing further evidence that the nonfunctional copy must be located in the nucleus. Observed differences in the mitochondrial and nuclear sequences from two populations are consistent with a faster rate of change in mtDNA than in nuclear DNA.

Animals↗
PubMed1991

Rearrangements of mitochondrial transfer RNA genes in marsupials.

The nucleotide sequences of the mitochondrial origin of light-strand replication and the five tRNA genes surrounding it were determined for three marsupials. The region was found to be rearranged, leaving only the tRNA(Tyr) gene at the same position as in placental mammals and Xenopus. Distribution of the same rearranged genotype among two marsupial families indicates that the events causing the rearrangements took place in an early marsupial ancestor. The putative mitochondrial light-strand origin of replication in marsupials contains a hairpin structure similar to other vertebrate origins and; in addition, extensive flanking sequences that are not found in other vertebrates. Sequence comparisons among the marsupials as well as placentals indicate that the tRNA(Tyr) gene has been evolving under more constraints than the other tRNA genes.

Animals↗
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↗