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R DeSalle

Publications and source records attributed to R DeSalle.

71 records · Page 4Linked to original sources
PubMed1992

Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.

Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.

Animals↗
PubMed1992

The origin and possible time of divergence of the Hawaiian Drosophilidae: evidence from DNA sequences.

The origins and times of divergence of the speciose Hawaiian Drosophilidae are examined using mtDNA sequences. The Hawaiian Drosophilidae are resolved as the sister group to the subgenus Drosophila. No one member of the subgenus Drosophila could be determined to be more closely related to the Hawaiian Drosophilidae than could any other. This result suggests that the Hawaiian Drosophilidae arose before the diversification of the subgenus Drosophila and after the divergence of the subgenus Sophophora. In light of fossil evidence, this phylogenetic scenario suggests that the Hawaiian Drosophilidae lineages are no younger than 30 Myr.

Alcohol Dehydrogenase↗
PubMed1991

Nucleolus organizer-suppressed position-effect variegation in Drosophila melanogaster.

The white locus is inactivated in a cell-by-cell variegated pattern when juxtaposed with the proximal or distal parts of the nucleolus organizer region (NO) by X chromosome inversion. Recombinants for two such inversions, wm51b and wm4, were obtained and randomized for genetic background. White locus activity was much higher in the wm4 recombinant duplicated for most of the NO and much lower in the wm51b recombinant deficient for it. Although there may be other molecular differences between the heterochromatic regions of the recombinants, the most obvious is the dosage of NO. Suppression of a NO region-evoked variegated phenotype by additional NO doses is discussed in relation to four different classes of models for position-effect variegation (PEV): chromatin structure, nuclear geometry, incomplete transposition of mobile elements, and heterochromatin promoter-driven transcription. A corollary of the structural model is functional subdivision of heterochromatin, which would enable the use of PEV as a tool for its study.

Animals↗
PubMed1988

Calibration of the change in thermal stability of DNA duplexes and degree of base pair mismatch.

One method of determining the degree of base pair divergence between two sources of DNA (different strains, species, etc.) is to determine the decrease in thermal stability of hybrid duplex DNA due to mismatching of base pairs. Attempts to calibrate the change in median melting temperature (delta Tm) to base pair mismatch have led to conflicting results. We have studied the delta Tm between DNAs of known sequence over a range of from 0.55% to 7.2% base pair mismatch. The relationship of delta Tm and percent base pair mismatch is remarkably linear over this range with a correlation coefficient greater than 0.98. A delta Tm of 1 degree C corresponds to 1.7% base pair mismatch. This conversion is higher than that usually assumed and, therefore, rates of DNA evolution estimated by DNA-DNA hybridization studies are likely faster than previously thought.

Animals↗
PubMed1987

Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila.

Sequence comparisons were made for up to 667 bp of DNA cloned from 14 kinds of Hawaiian Drosophila and five other dipteran species. These sequences include parts of the genes for NADH dehydrogenase (subunits 1, 2, and 5) and rRNA (from the large ribosomal subunit). Because the times of divergence among these species are known approximately, the sequence comparisons give insight into the evolutionary dynamics of this molecule. Transitions account for nearly all of the differences between sequences that have diverged by less than 2%: for these sequences the mean rate of divergence appears to be about 2%/Myr. In comparisons involving greater divergence times and greater sequence divergence, relatively more of the sequence differences are due to transversions. Specifically, the fraction of these differences that are counted as transversions rises from an initial value of less than 0.1 to a plateau value of nearly 0.6. The time required to reach half of the plateau value, about 10 Myr, is similar to that for mammalian mtDNA. The mtDNAs of flies and mammals are also alike in the shape of the curve relating the percentage of positions at which there are differences in protein-coding regions to the time of divergence. For both groups of animals, the curve has a steep initial slope ascribable to fast accumulation of synonymous substitutions and a shallow final slope resulting from the slow accumulation of substitutions causing amino acid replacements. However, the percentage of all sites that can experience a high rate of substitution appears to be only about 8% for fly mtDNA compared to about 20% for mammalian mtDNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1987

Temporal and spatial heterogeneity of mtDNA polymorphisms in natural populations of Drosophila mercatorum.

Restriction endonuclease analysis of mtDNA was used to examine the genetic relatedness of several geographically separated isolines of the Drosophila mercatorum subgroup. In addition, we examined the temporal and spatial distribution of two mtDNA restriction site polymorphisms produced by the enzymes BstEII and BstNI at a single locality--Kamuela, Hawaii. Due to small sample sizes of some collections and the undesirable dependance of the estimation of polymorphism frequency on its variance, an arcsin square root transformation of the frequency data was used. We also use an Fst estimator of our transformed frequencies to demonstrate considerable spatial and temporal differentiation within the Kamuela population. In contrast, isozyme data from the same population reveals no pattern of differentiation. The temporal and geographic heterogeneity and population subdivision detected with mtDNA analysis also is consistent with the known dispersal behavior and ecological constraints of this species. The mtDNA data in conjunction with the isozyme data show that the population structure of the Kamuela D. mercatorum is close to the boundary line separating panmixia from subdivision, a conclusion that could not be made from isozyme data alone.

Alleles↗
PubMed1986

Mitochondrial DNA variability in natural populations of Hawaiian Drosophila. I. Methods and levels of variability in D. silvestris and D. heteroneura populations.

We describe techniques by which mitochondrial DNA (mtDNA) restriction site information can be obtained for up to 16 different restriction endonucleases on individual Hawaiian Drosophila, in particular D. silvestris and D. heteroneura. We have constructed mtDNA restriction site maps for a total of forty-eight wild caught genomes of both species, from seven major collecting sites on the island of Hawaii. Levels of variability are, in general, high in D. silvestris (p of Ewens et al., 1981 = 0.0486) and lower in D. heteroneura (p = 0.0327). Measures of population subdivision using Nei's Gst indicate that about 50-60 per cent of the observed variability is due to interdemic subdivision. In accordance, populations within a species show a much lower level of variability, however some populations harbour individuals that are very divergent from the rest of their conspecifics at the same locality. We review two possible mechanisms that could explain the presence of these divergent individuals, hybridisation and the effects of stochastic branching processes.

Animals↗
PubMed1986

Mitochondrial DNA variability in natural populations of Hawaiian Drosophila. II. Genetic and phylogenetic relationships of natural populations of D. silvestris and D. heteroneura.

Restriction site mapping of mitochondrial DNA with 23 restriction endonucleases was used to examine the genetic and phylogenetic relationships of populations of D. silvestris and D. heteroneura from the island of Hawaii. Two morphological races of D. silvestris are known on the island of Hawaii. One has three bristle rows on the tibia of the foreleg and is found on the east side of the island. The other is found on the west side of the island and has the ancestral bristle row character of two rows on the tibia of the foreleg. All D. heteroneura have the ancestral bristle row character state. We demonstrate that mtDNA restriction site analysis can also differentiate the two D. silvestris races, and that the two bristle row D. silvestris are more closely related to D. heteroneura than they are to their three bristle row conspecifics using both distance and character state analysis. Our study (which uses six base recognition restriction endonucleases) is not sensitive enough to determine the phylogenetic relationships of populations within either of the D. silvestris lineages.

Animals↗
PubMed1986

Discordance of nuclear and mitochondrial DNA phylogenies in Hawaiian Drosophila.

Drosophila differens, endemic to Molokai, Drosophila planitibia of Maui, and Drosophila silvestris and Drosophila heteroneura from the island of Hawaii are chromosomally homosequential species that presumably have colonized the newer islands of the Hawaiian archipelago by sequential founder events. We have examined the phylogenetic relationships of these four species by using mitochondrial DNA restriction site data for 23 enzymes. Both distance and character-state analyses indicate that a sequential or monotonic branching relationship exists for mtDNA restriction site data from the four species. The mtDNA data suggest that the maternal lineage that gave rise to D. differens is ancestral to the D. planitibia maternal lineage, which in turn shares the most recent common ancestor with the D. silvestris and D. heteroneura maternal lineages [with Drosophila hemipeza (Oahu) and Drosophila neopicta (Molokai and Maui) as outside references]. We also discuss the phylogenetic implications of the mtDNA data in comparison with other sources of phylogenetic data. We conclude that hybridization of the species in this group has been an important factor in the evolution of the nuclear genomes. Because of small population sizes and mating asymmetries, it is possible that the nuclear genetic distance of species that are physically capable of hybridizing (e.g., on the same island or island complex) is depressed. Consequently the mtDNA genetic distance appears to be more sensitive in establishing the sequence of evolutionary events responsible for the present distribution and population structure of these species.

Animals↗
PubMed1986

The molecular through ecological genetics of abnormal abdomen. II. Ribosomal DNA polymorphism is associated with the abnormal abdomen syndrome in Drosophila mercatorum.

Restriction endonuclease cleavage analyses of cloned and genomic DNA samples indicate that the structure of the DNA encoding the large cytoplasmic RNAs (rDNAs) is altered in Drosophila mercatorum lines which exhibit an abnormal abdomen (aa) phenotype. In a majority of the rDNA repeat units from aa flies, the 28S coding sequence is interrupted by a large [5-6 kilobase pairs (kbp)] insert. A subclone containing this inserted DNA (ins 3) hybridizes primarily to rDNA-containing sequences in in situ and genomic blot hybridization experiments. Additionally, genomic nitrocellulose blot hybridization analyses show that ins- containing rDNA repeat units are clustered in a spontaneously arising aa mutant. This rDNA alteration in D. mercatorum flies with the aa phenotype more closely resembles the bobbed (bb) defect of D. hydei than the bb defect of D. melanogaster, which involves alterations in rDNA copy number. By analogy with the other Drosophila systems, we propose that the altered D. mercatorum rDNA repeat units are defective in rRNA production at a critical stage. The lowered levels of rRNA ultimately would limit the concentration of ribosomes needed to produce large quantities of a protein (in these cases, juvenile hormone esterase) needed for normal development.

Abdomen↗
PubMed1986

The molecular through ecological genetics of abnormal abdomen. III. Tissue-specific differential replication of ribosomal genes modulates the abnormal abdomen phenotype in Drosophila mercatorum.

The abnormal abdomen (aa) syndrome in Drosophila mercatorum is controlled by two major X-linked genetic elements. We have previously shown that the major X-linked element of aa is associated with the presence of large inserts in the 28S gene of the ribosomal RNA (rDNA) genes. We show that, in polytene tissue of wild-type D. mercatorum, the uninterrupted rDNA repeats are overreplicated relative to interrupted repeats. Uninterrupted rDNA repeats are also overreplicated in polytene tissue of hybrid larval offspring from wild-type and aa parents. This overreplication of uninterrupted repeats is not observed in diploid tissues of wild-type hybrids (of wild-type and aa parents) and homozygous aa larvae or in polytene tissue of aa larvae. Furthermore, molecular analysis of an aa line that has reverted to the wild type indicates that the reversion phenomenon is associated with the ability to overreplicate uninterrupted rDNA repeats in polytene tissues. The patterns of differential replication of rDNA genes in wild-type hybrids and aa larvae of D. mercatorum offer a possible mechanism for the tissue-specific control of the aa phenotype and suggest that the molecular basis for the second X-linked genetic element of aa is involved in the control of differential replication in polytene tissues.

Abdomen↗
PubMed1985

Homogenization of geographical variants at the nontranscribed spacer of rDNA in Drosophila mercatorum.

rDNA nontranscribed spacer (NTS) lengths of Drosophila mercatorum have been measured in individuals from several geographic regions. Individuals from the different geographic subpopulations share some length fragments but are in general distinct. The length differences, both within and between individuals, arise from different copy numbers of a 250-bp repeating unit that is localized to one part of the NTS. In addition to the length differences caused by the 250-bp repeat, there is a Y chromosome (male)-specific length variant elsewhere in the NTS that is approximately 70 bp shorter than the NTS fragment from the X chromosome. Sexual dimorphism seems to be present in all Drosophila. Also, D. mercatorum has fewer NTS length variants per individual than does D. melanogaster while possessing comparable levels of restriction-site polymorphism. The mechanisms that may cause this pattern of variation are selection, gene conversion, and unequal recombination.

Animals↗
PubMedDate not supplied

Molluscan engrailed expression, serial organization, and shell evolution.

Whether the serial features found in some molluscs are ancestral or derived is considered controversial. Here, in situ hybridization and antibody studies show iterated engrailed-gene expression in transverse rows of ectodermal cells bounding plate field development and spicule formation in the chiton, Lepidochitona cavema, as well as in cells surrounding the valves and in the early development of the shell hinge in the clam, Transennella tantilla. Ectodermal expression of engrailed is associated with skeletogenesis across a range of bilaterian phyla, suggesting a single evolutionary origin of invertebrate skeletons. The shared ancestry of bilaterian-invertebrate skeletons may help explain the sudden appearance of shelly fossils in the Cambrian. Our interpretation departs from the consideration of canonical metameres or segments as units of evolutionary analysis. In this interpretation, the shared ancestry of engrailed-gene function in the terminal/posterior addition of serially repeated elements during development explains the iterative expression of engrailed genes in a range of metazoan body plans.

Animals↗
PubMedDate not supplied

The effect of differential reproductive success on population genetic structure: correlations of life history with matrilines in humpback whales of the gulf of maine.

To examine whether demographic and life-history traits are correlated with genetic structure, we contrasted mtDNA lineages of individual humpback whales (Megaptera novaeangliae) with sighting and reproductive histories of female humpback whales between 1979 and 1995. Maternal lineage haplotypes were obtained for 323 whales, either from direct sequencing of the mtDNA control region (n = 159) or inferred from known relationships along matrilines from the sequenced sample of individuals (n = 164). Sequence variation in the 550 bp of the control region defined a total of 19 maternal lineage haplotypes that formed two main clades. Fecundity increased significantly over the study period among females of several lineages among the two clades. Individual maternal lineages and other clades were characterized by significant variation in fecundity. The detected heterogeneity of reproductive success has the potential to substantially affect the frequency and distribution of maternal lineages found in this population over time. There were significant yearly effects on adult resighting rates and calf survivorship based on examination of sighting histories with varying capture-recapture probability models. These results indicate that population structure can be influenced by interactions or associations between reproductive success, genetic structure, and environmental factors in a natural population of long-lived mammals.

Animals↗
PubMedDate not supplied

The mtDNA genealogy of closely related Drosophila silvestris.

Genetic, morphological, and behavioral analyses have been used to examine the evolutionary dynamics and phylogeny of the rare Hawaiian Drosophila species, D. silvestris. Critical to understanding the evolution of this species is the examination of the distribution of populations of D. silvestris on the Big Island of Hawaii. Behavioral analysis using mating asymmetries and the Kaneshiro hypothesis as an indicator of ancestral behavioral state has suggested that flies from the northern part of the island are ancestral to those on the southern part of the island. Consequently, a sequential pattern of colonization going from north to south is predicted for these flies on the east side of the Island of Hawaii. We have examined this prediction using mitochondrial DNA (mtDNA) restriction site analysis with four-base cutters and DNA sequencing. The resulting mtDNA phylogeny based on 23 phylogenetically informative restriction sites and two phylogenetically informative DNA sequence characters agrees in part with the phylogeny predicted from the behavioral data.

Animals↗