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R DeSalle

Publications and source records attributed to R DeSalle.

At least 55 records · Page 3Linked to original sources
PubMed1995

Origin of the foraminifera.

We report nuclear small-subunit rDNA sequences for two species of the benthic foraminifer Ammonia. Because of their abundance in present and past seas, the foraminifera are a very important group of organisms used in a wide range of geologic studies; however, the ancestry of this group was, until now, unknown. Difficulties in purifying foraminiferal DNA and avoiding PCR contamination led us to develop DNA.DNA in situ hybridization techniques to verify our sequence data. Phylogenetic analysis of verified foraminiferal DNA sequence indicates these taxa are a divergent, "alveolate" lineage, within the major eukaryotic radiation. Our findings cast doubt upon the assumption that all foraminifera are derived from an amoebalike ancestor. Cytological features and the DNA sequences presented herein suggest that the foraminifera were derived from a heterokaryotic flagellated marine protist, probably sometime in the later Proterozoic.

Animals↗
PubMed1995

Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites.

The process of multiple sequence alignment provides homology statements for the phylogenetic analysis of molecular data. Unfortunately, multiple alignments are frequently nonunique. Two sources of these multiple alignments are analysis based on different sets of alignment parameter values (gap:change cost ratios) and nonunique equally costly alignments based on a single set of alignment parameters. By "eliding" these individual alignments into a single grand alignment, phylogeny that is weighted toward those positions that align more consistently can be reconstructed. Positions that show greater variation among alignments will be relatively downweighted. The technique results in a weighting procedure that is a posteriori and based on the evidence established from the original sequence alignments.

Alligators and Crocodiles↗
PubMed1995

Class-level relationships in the phylum Cnidaria: molecular and morphological evidence.

The evolutionary history of cnidarian life cycles has been debated since the 1880s, with different hypotheses favored even by current textbooks. Contributing to the disagreement is the fact that the systematic relationships of the four cnidarian classes have received relatively little examination using modern systematic methods. Here we present analyses of class-level relationships based on 18S ribosomal DNA (rDNA) sequence, mitochondrial 16S rDNA sequence, mitochondrial genome structure, and morphological characters. DNA sequences were aligned using a repeatable parsimony-based approach incorporating a range of alignment parameters. Analyses of individual data sets and of all data combined are unanimous in grouping the classes possessing a medusa stage, leaving the holobenthic Anthozoa basal within the phylum.

Animals↗
PubMed1994

Implications of ancient DNA for phylogenetic studies.

The utility of DNA sequence characters from fossil specimens is examined from a phylogenetic perspective. Four ways that fossil characters can alter phylogenetic hypotheses are discussed. Two empirical examples and a third hypothetical example concerning amber-preserved insects are presented to illustrate these phenomena. Fossil DNA sequences as characters will be affected by the problem of missing data and missing taxa. In general, cladogram accuracy will be more greatly affected by missing taxa and cladogram resolution will be affected more acutely by missing data. Due to these points, an examination of the importance of the phylogenetic question being addressed, the utility of the fossil DNA sequences and the rarity of the fossil should be considered before damage of a fossil is undertaken.

Animals↗
PubMed1994

Flies and congruence.

Competing phylogenetic hypotheses have become the rule in modern systematics. While the problem of incongruence between character sets has become extremely acute due to the generation of molecular data, it is by no means specific to molecular and morphological comparisons. The role of the modern systematist is to interpret incongruence between character sets and to come to some conclusion regarding a phylogenetic hypothesis of the organisms in question. Two aspects of congruence analysis are examined using the Drosophilidae as an example. The first includes the quantification of congruence and the types of phylogenetic inference that can be made from such analyses. The second aspect concerns an examination of character evolution in order to identify characters and taxa that might be contributing to incongruence in phylogenetic analysis.

Animals↗
PubMed1994

Computational problems in molecular systematics.

The development of extremely powerful computer programs and the ready availability of microcomputers has revealed several computational problems with data analysis. These problems occur in the handling of systematic data in general and molecular systematic data in particular. This paper examines three areas of controversy in molecular systematics resulting from increased computer power. We start by examining the first step in DNA sequence analysis, the establishment of homology via sequence alignment. Next we examine several problems in phylogenetic analysis that have arisen in the last few years due to use of the PAUP (Swofford, 1991), HENNIG86 (Farris, 1988), and PHYLIP programs. These problems include limitations on the number of taxa examined in a given analysis and the accuracy of the parsimony trees in such analyses. The final subject is an examination of programs used for assessing tree robustness. We concentrate on certain programs (such as MALIGN (Wheeler and Gladstein, 1993), PAUP (Swofford, 1991), HENNIG86 (Farris, 1988), PHYLIP (Felsenstein, 1990), CLADOS (Nixon, 1993), MacClade (Maddison and Maddison, 1993), etc.), but similar comments about other programs could also be made.

Animals↗
PubMed1994

Very old DNA.

The verification of DNA sequences obtained from very old tissue sources as indeed ancient is a major point of discussion in the ancient DNA field. Proper controls and the use of the phylogenetic approach are the general methods employed for verification of the ancient DNA. Most studies have reported the recovery of extremely small amounts of nucleic acids which are sheared into rather small fragments. In addition, problems such as 'PCR jumping' can produce spurious sequence information. These observations suggest that random amplification techniques and the development of primers for highly informative but short target regions are essential for the further development of the ancient DNA field.

Amber↗
PubMed1994

Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis.

Sequence divergence in the internal transcribed spacer region 1 (ITS-1) of the ribosomal DNA locus was assessed in subspecies of the coastal North American tiger beetle, Cicindela dorsalis. The spacer region was amplified using the polymerase chain reaction and cloned for sequencing. Of a total of 50 clones obtained from 12 specimens, 42 clones were different in at least one nucleotide position. In a parsimony analysis of these sequences, the main phylogenetic distinction was found to separate sequences from the Gulf of Mexico and the Atlantic Ocean. Within these two assemblages phylogenetic resolution was low, and the variation within individuals was almost as high as the variation within the entire lineage. The pattern of sequence variation suggests the existence of two forms of the ITS-1 that are maintained on different chromosomes. Polymorphisms of limited geographical distribution could be detected, and 41 additional clones were partly sequenced, to assess the geographic distribution of these polymorphisms in more detail. In a population aggregation analysis, the geographic pattern of ITS-1 distribution was basically congruent with that obtained in earlier studies from mitochondrial DNA in the same C. dorsalis populations.

Animals↗
PubMed1994

Phylogenetic utility of ubiquitin DNA sequence from 3 marine protist lineages.

The foraminifera are one of the last major groups of eukaryotes for which no published DNA sequences exist. DNA sequence of ubiquitin repeat units from 5 foraminifera (representing 3 suborders), a diatom, and a dinoflagellate were characterized using the polymerase chain reaction, cloning, and sequencing. The phylogenetic utility of ubiquitin DNA sequence is discussed in reference to a full eukaryote data base. The foraminifera are possibly a polyphyletic group, whereas the phylogenetic placement of the diatom and the dinoflagellate are congruent with existing hypotheses. The lack of a noneukaryote root and limited phylogenetically informative sequence information indicate that polyubiquitin may not be useful for phylogenetic reconstruction of all eukaryotes.

Amino Acid Sequence↗
PubMed1993

PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus).

DNA from 30-million-year-old amber preserved termites (Mastotermes electrodominicus) was PCR amplified with nuclear ribosomal RNA small subunit primers and cloned into the TA vector (INVITROGEN). We obtained several classes of recombinant clones as a result. Authentic Mastotermes electrodominicus clones were identified. The source of other classes of clones was identified as contaminants of the ancient DNA template. Several of the clones appeared to be chimeric in structure with half of the clone identical to the termite sequence and the other half identical to contaminant sequences. The phenomenon of PCR jumping was identified as a possible source for the chimeric clones.

Animals↗
PubMed1993

Alignment-ambiguous nucleotide sites and the exclusion of systematic data.

Molecular systematists generally rely on computer algorithms to establish the alignment of DNA sequences. However, when alignment regions are characterized by multiple insertions and deletions, these gap-filled stretches of DNA are often excised before phylogenetic reconstruction. This exclusion of systematic data is generally determined by subjective criteria. We explore a replicable methodology in which the comparison of several multiple sequence alignments can be used to eliminate regions of unstable sequence alignment. Using crocodilian and insect mitochondrial (mt) ribosomal (r) DNA as examples, we caution against the removal of sequence data prior to phylogenetic reconstruction.

Algorithms↗
PubMed1993

Collection and storage of invertebrate samples.

The validity of any comparative study is dependent on the reliability of the identification of the samples in the study. Not all researchers are experts in the field of identification of samples, nor do all researchers have quick and ready access to expert systematists who can accomplish the task of identification. The importance of verification of sample identity for comparative studies is vital. We describe several methods by which researchers can obtain and identify samples from the wild, and we suggest methods by which voucher samples can be obtained for future reference to these collected samples. We outline alternatives to collection of samples from the wild, such as purchase from stock centers and biological supply companies. Museum collections can also be extremely helpful in obtaining complete organismal samples for comparative studies.

Academies and Institutes↗
PubMed1993

Determination of paternity in dragonflies by Random Amplified Polymorphic DNA fingerprinting.

We used Random Amplified Polymorphic DNA (RAPD) fingerprinting to address issues of paternity in two odonate species. Amplification artifacts of RAPD markers were controlled by assessing paternity patterns relative to the banding patterns generated by quantitative mixtures of DNA from putative parents ('synthetic offspring'). In the aeshnid dragonfly Anax parthenope, for which the mating histories of both males and females were unknown, we found strong evidence for complete paternity success for the contact guarding male. In the highly polygamous libellulid dragonfly Orthetrum coerulescens, we detected and quantified mixed paternity in sequentially produced offspring clutches and demonstrated that fertilization success is correlated with the duration of copulation. Our results suggest that RAPD fingerprinting is suitable to address issues of paternity in systems which are genetically uncharacterized and produce large offspring clutches.

Animals↗
PubMed1992

DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications.

DNA was extracted from the fossil termite Mastotermes electrodominicus preserved in Oligo-Miocene amber (25 million to 30 million years old). Fragments of mitochondrial [16S ribosomal DNA (rDNA)] and nuclear (18S rDNA) genes were amplified by polymerase chain reaction. Phylogenetic analysis of fossil and extant 18S rDNA confirmed morphological cladistic analyses of living dictyopterans (termites, cockroaches, and mantids). The fossil termite shares several sequence attributes with Mastotermes darwiniensis. Addition of this fossil to living-species phylogeny is required to substantiate Mastotermes monophyly and affects molecular phylogenetic hypotheses of termites in this, the oldest DNA yet characterized.

Animals↗
PubMed1992

Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.

The phylogenetic relationships of the Recent cnidarian classes remain one of the classic problems in invertebrate zoology. We survey the structure of the mitochondrial genome in representatives of the four extant cnidarian classes and in the phylum Ctenophora. We find that all anthozoan species tested possess mtDNA in the form of circular molecules, whereas all scyphozoan, cubozoan, and hydrozoan species tested display mtDNA in the form of linear molecules. Because ctenophore and all other known metazoan mtDNA is circular, the shared occurrence of linear mtDNA in three of the four cnidarian classes suggests a basal position for the Anthozoa within the phylum.

Animals↗
PubMed1992

The phylogenetic relationships of flies in the family Drosophilidae deduced from mtDNA sequences.

The phylogenetic relationships of several taxa from representative genera, subgenera, groups, and subgroups in the Drosophilidae were examined using sequences from a 905-bp mtDNA fragment. Conventional cloning and sequencing techniques were used to obtain nucleotide sequences. In addition, polymerase chain reaction primers were designed for the rapid amplification and sequencing of this region for the species examined in the Drosophilidae. Phylogenetic analysis was done by cladistic techniques. Because of the coding nature of the 905-bp mtDNA fragment, several separate analyses of these sequences were performed. The genera Scaptomyza and Hirtodrosophila occupy ancestral branching positions in the molecular phylogeny. The genera Chymomyza and Zaprionus have intermediate branching positions, while the subgenera Drosophila and Sophophora are in the most derived position in the molecular phylogeny. Within the subgenus Sophophora, there is little resolution using these sequences, while within the subgenus Drosophila, D. melanica, D. funebris, and D. pinicola form a clade in a derived part of the phylogeny, with D. robusta and D. immigrans branching in an intermediate position in the phylogeny. D. mercatorum, a member of the repleta species group, occupies an ancestral position in the molecular phylogeny.

Animals↗
PubMed1992

The molecular through ecological genetics of abnormal abdomen. IV. Components of genetic variation in a natural population of Drosophila mercatorum.

Natural populations of Drosophila mercatorum are polymorphic for a phenotypic syndrome known as abnormal abdomen (aa). This syndrome is characterized by a slow-down in egg-to-adult developmental time, retention of juvenile abdominal cuticle in the adult, increased early female fecundity, and decreased adult longevity. Previous studies revealed that the expression of this syndrome in females is controlled by two closely linked X chromosomal elements: the occurrence of an R1 insert in a third or more of the X-linked 28S ribosomal genes (rDNA), and the failure of replicative selection favoring uninserted 28S genes in larval polytene tissues. The expression of this syndrome in males in a laboratory stock was associated with the deletion of the rDNA normally found on the Y chromosome. In this paper we quantify the levels of genetic variation for these three components in a natural population of Drosophila mercatorum found near Kamuela, Hawaii. Extensive variation is found in the natural population for both of the X-linked components. Moreover, there is a significant association between variation in the proportion of R1 inserted 28S genes with allelic variation at the underreplication (ur) locus such that both of the necessary components for aa expression in females tend to cosegregate in the natural population. Accordingly, these two closely linked X chromosomal elements are behaving as a supergene in the natural population. Because of this association, we do not believe the R1 insert to be actively transposing to an appreciable extent. The Y chromosomes extracted from nature are also polymorphic, with 16% of the Ys lacking the Y-specific rDNA marker. The absence of this marker is significantly associated with the expression of aa in males. Hence, all three of the major genetic determinants of the abnormal abdomen syndrome are polymorphic in this natural population.

Abdomen↗