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R DeSalle

Publications and source records attributed to R DeSalle.

At least 37 records · Page 2Linked to original sources
PubMed2000

A new method to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily.

When a data set is partitioned, the resulting subsets may contain phylogenetically conflicting signals if they have different evolutionary histories. In a data set with many taxa, a single taxon that contains multiple phylogenetic histories may result in global incongruence, but no methods are available in a parsimony framework to localize incongruence to specific clades in a phylogeny or to test the significance of incongruence on a local scale. Here we present a new method to quantify the conflict between data partitions for any clade in a phylogeny and to test the statistical significance of that conflict by using a metric called the local incongruence length difference. We apply this method to the evolutionary history of the nuclear receptor superfamily, a large group of transcriptional regulators that play essential roles in metazoan development and physiology. All nuclear receptors are composed of several discrete domains, including one that binds to DNA response elements on specific target genes and another that binds to the appropriate ligand. We have performed combined and separate phylogenetic analyses of these two domains and have tested the hypothesis that nuclear receptors evolved by a simple process of lineage splitting and divergence, without domain shuffling or other forms of sequence transfer between proteins. Our analysis indicates that significant conflict exists between the partitined domains at a few nodes on the tree, suggesting that several groups of receptors are "hybrid proteins" formed by domain shuffling or other forms of sequence transfer between more ancient nuclear receptors.

Animals↗
PubMed1999

Molecular evolution of the synapsin gene family.

Synapsins, a family of synaptic vesicle proteins, play a crucial role in the regulation of neurotransmission and synaptogenesis. They have been identified in a variety of invertebrate and vertebrate species, including human, rat (Rattus norvegicus), cow (Bos taurus), longfin squid (Loligo pealei), and fruit fly (Drosophila melanogaster). Here, synapsins were cloned from three additional species: frog (Xenopus laevis), lamprey (Lampetra fluviatilis), and nematode (Caenorhabditis elegans). Synapsin protein sequences from all these species were then used to explore the molecular phylogeny of these important neuronal phosphoproteins. The ancestral condition of a single synapsin gene probably gave rise to the vertebrate synapsin gene family comprised of at least three synapsin genes (I, II, and III) in higher vertebrates. Synapsins possess multiple domains, which have evolved at different rates throughout evolution. In invertebrate synapsins, the most conserved domains are C and E. During the evolution of vertebrates, at least two gene duplication events are hypothesized to have given rise to the synapsin gene family. This was accompanied by the emergence of an additional conserved domain, termed A. J. Exp. Zool. ( Mol. Dev. Evol. ) 285:360-377, 1999.

Amino Acid Sequence↗
PubMed1999

Development, evolution, and corroboration.

The cloning of genes involved in pathways fundamental to morphogenesis has opened the door to visualizing expression of developmental regulatory genes in many organisms. Expression data have become technical commonplace in analysis of mutants of Drosophila melanogaster and a handful of other genetic model systems. Many researchers have used probes and extended the logic from studies of D. melanogaster for comparisons of expression patterns to infer developmental bases for homologous structures among animals with diverse body plans. This research program has led to exciting but sweeping generalizations about how development evolves. Here we examine several underlying assumptions of this approach in terms of comparative and historical biology. First, we evaluate the logic that underlies the equation of gene expression similarity with homologous morphology. Second, we examine epistemological issues surrounding the descriptive visualization of gene expression patterns. We conclude by examining the role of phylogenetic coding and mapping of these patterns to examine the evolution of complex gene regulatory networks.

Animals↗
PubMed1999

Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged.

We performed a genealogical analysis of the ionotropic glutamate receptor (iGluR) gene family, which includes the animal iGluRs and the newly isolated glutamate receptor-like genes (GLR) of plants discovered in Arabidopsis. Distance measures firmly placed the plant GLR genes within the iGluR clade as opposed to other ion channel clades and indicated that iGluRs may be a primitive signaling mechanism that predated the divergence of animals and plants. Moreover, phylogenetic analyses using both parsimony and neighbor joining indicated that the divergence of animal iGluRs and plant GLR genes predated the divergence of iGluR subtypes (NMDA vs. AMPA/KA) in animals. By estimating the congruence of the various glutamate receptor gene regions, we showed that the different functional domains, including the two ligand-binding domains and the transmembrane regions, have coevolved, suggesting that they assembled together before plants and animals diverged. Based on residue conservation and divergence as well as positions of residues with respect to functional domains of iGluR proteins, we attempted to examine structure-function relationships. This analysis defined M3 as the most highly conserved transmembrane domain and identified potential functionally important conserved residues whose function can be examined in future studies.

Amino Acid Sequence↗
PubMed1999

The evolution and development of dipteran wing veins: a systematic approach.

In this review, we use the wing veins of dipteran insects as potential models for understanding the evolution of development. We briefly discuss previous work in this field and examine the genetic complexity of wing formation, discussing the genes involved in wing formation and their roles in Drosophila wing development and vein formation. Furthermore, patterns of wing vein formation, addition, and reduction are discussed as they occur throughout the Diptera. Using the phyletic phenocopy paradigm, we draw attention to many wing vein morphologies that phenocopy various wing mutants in Drosophila melanogaster. The systematic issues of the nature of characters, homology, and the role of modern developmental approaches to evolutionary studies, which has recently become important, can be addressed from the perspective of the wing. We argue that further developmental evolutionary studies, and the interpretation of data therefrom, must be conducted within the context of a well-supported phylogeny of the organisms under study.

Animals↗
PubMed1998

Molecular phylogeny of Acipenserinae.

The family Acipenseridae consists of 25 extant sturgeon species (19 species of Acipenserinae and 6 species of Scaphirhynchinae). Together with two extant paddlefish species, Polyodon spathula and Psephurus gladius (Polyodontidae), it composes the order Acipenseriformes, the most numerous of all living "fossil" fishes. This paper presents results of sequencing of three regions of the cytochrome b gene (650 bp), and fragments of 12S (150 bp) and 16S (350 bp) rRNA genes, from all extant species of Acipenserinae (species of Acipenser and Huso) and Scaphirhynchus albus (Scaphirhynchinae). The phylogenetic tree obtained for combined data is the first comprehensive treatment of phylogeny within the Acipenserinae. Three general conclusions are inferred from the tree: (1) The pallid sturgeon, S. albus, is the sister-species of all species of Acipenser and Huso. (2) The two species of Huso are embedded within the genus Acipenser. It also appears that Huso is not a separate taxonomic unit. (3) There are at least three main clades within Acipenser: A. sturio-A. oxyrinchus, A. schrenckii-A. transmontanus, and all Ponto-Caspian species plus A. dabryanus and A. brevirostrum. There is congruence between ploidy and the branching patterns of the sturgeon species. A hypothetical evolutionary history of the Acipenseriformes based on the paleontological, geological, and molecular data is discussed.

Animals↗
PubMed1998

Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae.

We address two systematic questions, the origin and monophyly of the Hawaiian Drosophilidae and the question of how to analyze multiple data partitions containing disparate kinds of information, in this study. New evidence, from analysis of characters from morphology, mitochondrial DNA, and nuclear DNA suggests that the Hawaiian Drosophilidae are a monophyletic assemblage. Although we are not able to suggest a single species group which may represent the continental sister taxon to the Hawaiian Drosophilidae, the candidates suggested by our analysis, the melanicarobusta lineage and the virilis-repleta lineage, have been suggested by other investigators as probable sister taxa. Through analyses of our data partitions separately and in a variety of combinations, we conclude that the best phylogenetic hypothesis to be generated from multiple data partitions will be obtained if the data from these partitions are combined and analyzed simultaneously. We advocate performing tests for congruence between and among data partitions not to justify keeping them apart, but for understanding the interactions among the signals included in the analysis and how they affect the topology of, and support for, the total evidence tree.

Animals↗
PubMed1998

Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees.

We examined the contribution of morphological and molecular character information for 15 systematics studies in which these two kinds of data were used in combined or simultaneous analyses. Assessment of the disagreement between these data sources, as measured by the incongruence length difference, reveals substantial conflict for the studies surveyed. In addition, the partitioned Bremer support was used to measure the degree of support provided by each data partition when analyzed together. Despite the significant incongruence found for nearly half the studies, the PBS indices suggest both types of data contribute positively to the combined analyses and that, when standardized by the number of phylogenetically informative characters, morphology data generally provide equal or greater support than do the molecular data. This result, combined with the fact that morphological characters generally exhibit higher consistency, indicates that this source of character information continues to be useful in systematics studies despite the increasing volume of available molecular data.

Animals↗
PubMed1998

Patterns of mitochondrial versus nuclear DNA sequence divergence among nymphalid butterflies: the utility of wingless as a source of characters for phylogenetic inference.

To investigate the utility of a region of wingless (wg) as a marker for molecular systematics, we compared wg sequences to mitochondrial COII sequences from twenty-two nymphalid butterfly taxa and one outgroup. Compositional characteristics of the two gene regions are compared, and their contributions to a cladogram inferred from the combined data set are assessed. Primarily due to its uniform base composition, wg appears to become saturated more slowly than mtDNA, although the two genes appear to be evolving at quite similar rates. We suggest that wg will be a useful source of characters for phylogenetic studies of butterflies, and perhaps other insect taxa, with divergence times up to 60 million years ago.

Animals↗
PubMed1997

A cladistic analysis of mitochondrial ribosomal DNA from the Bovidae.

There is a huge data base of genetic information for the domestic artiodactyl species Bos taurus (cow), Ovis aries (sheep), and Capra hircus (goat). However, the phylogenetic relationships of these economically critical taxa and their close relatives, family Bovidae, remain for the most part unresolved. In this report, we aligned new mitochondrial (mt) 12S and 16S ribosomal (r) DNA sequences from 26 bovid taxa with published sequences. Phylogenetic analyses of the more than 64 kilobases of mt rDNA from 57 taxa support a basal division in the Bovidae that separates Bos and its close relatives from Capra, Ovis, and their kin. As suggested by previous molecular and morphological studies, "antelopes" are a paraphyletic assemblage. Caprinae (sheep, goats, goat antelopes, and musk oxen) groups consistently with hippotragine and alcelaphine antelopes, while Bovini (cattle and buffaloes) clusters with tragelaphine and boselaphine antelopes. The traditional tribal subdivisions of Bovidae are supported in most cases, but there are exceptions within Caprinae and Antilopinae (gazelles and close relatives). The rDNA data consistently place the enigmatic genera Pelea, Pantholops, and Saiga, but the origin of Aepyceros, the impala, remains obscure. Combined phylogenetic analyses of the rDNA data with the skeletal characters of Gentry (1992) were used to assess the stability of the molecular results.

Animals↗
PubMed1997

Multiple sources of character information and the phylogeny of Hawaiian drosophilids.

Relationships among representatives of the five major Hawaiian Drosophila species groups were examined using data from eight different gene regions. A simultaneous analysis of these data resulted in a single most-parsimonious tree that (1) places the adiastola picture-winged subgroup as sister taxon to the other picture-winged subgroups, (2) unites the modified-tarsus species group with flies from the Antopocerus species group, and (3) places the white-tip scutellum species group as the most basal taxon. Because of the different gene sources used in this study, numerous process partitions can be erected within this data set. We examined the incongruence among these various partitions and the ramifications of these data for the taxonomic consensus, prior agreement, and simultaneous analysis approaches to phylogenetic reconstruction. Separate analyses and taxonomic consensus appear to be inadequate methods for dealing with the partitions in this study. Although detection of incongruence is possible and helps elucidate particular areas of disagreement among data sets, separation of partitions on the basis of incongruence is problematic for many reasons. First, analyzing all genes separately and then either presenting them all as possible hypotheses or taking their consensus provides virtually no information concerning the relationships among these flies. Second, despite some evidence of incongruence, there are no clear delineations among the various gene partitions that separate only heterogeneous data. Third, to the extent that problematic genes can be identified, these genes have nearly the same information content, within a combined analysis framework, as the remaining nonproblematic genes. Our data suggest that significant incongruence among data partitions may be isolated to specific relationships and the "false" signal creating this incongruence is most likely to be overcome by a simultaneous analysis. We present a new method, partitioned Bremer support, for examining the contribution of a particular data partition to the topological support of the simultaneous analysis tree.

Animals↗
PubMed1996

On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case.

Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic acid sequences are two different ways of character coding the information in a gene. Silent positions in the nucleotide sequence (first or third positions in codons that can accrue change without changing the identity of the amino acid that the triplet codes for) may accrue change relatively rapidly and become saturated, losing the pattern of historical divergence. On the other hand, non-silent nucleotide alterations and their accompanying amino acid changes may evolve too slowly to reveal relationships among closely related taxa. In general, the dynamics of sequence change in silent and non-silent positions in protein coding genes result in homoplasy and lack of resolution, respectively. We suggest that the combination of nucleic acid and the translated amino acid coded character states into the same data matrix for phylogenetic analysis addresses some of the problems caused by the rapid change of silent nucleotide positions and overall slow rate of change of non-silent nucleotide positions and slowly changing amino acid positions. One major theoretical problem with this approach is the apparent non-independence of the two sources of characters. However, there are at least three possible outcomes when comparing protein coding nucleic acid sequences with their translated amino acids in a phylogenetic context on a codon by codon basis. First, the two character sets for a codon may be entirely congruent with respect to the information they convey about the relationships of a certain set of taxa. Second, one character set may display no information concerning a phylogenetic hypothesis while the other character set may impact information to a hypothesis. These two possibilities are cases of non-independence, however, we argue that congruence in such cases can be thought of as increasing the weight of the particular phylogenetic hypothesis that is supported by those characters. In the third case, the two sources of character information for a particular codon may be entirely incongruent with respect to phylogenetic hypotheses concerning the taxa examined. In this last case the two character sets are independent in that information from neither can predict the character states of the other. Examples of these possibilities are discussed and the general applicability of combining these two sources of information for protein coding genes is presented using sequences from the homeobox region of 46 homeobox genes from Drosophila melanogaster to develop a hypothesis of genealogical relationship of these genes in this large multigene family.

Algorithms↗
PubMed1996

Crossroads, milestones and landmarks in insect development and evolution: implications for systematics.

Our understanding of insect development and evolution has increased greatly due to recent advances in the comparative developmental approach. Modern developmental biology techniques such as in situ hybridization and molecular analysis of developmentally important genes and gene families have greatly facilitated these advances. The role of the comparative developmental approach in insect systematics is explored in this paper and we suggest two important applications of the approach to insect systematics--character dissection and morphological landmarking. Existing morphological characters can be dissected into their genetic and molecular components in some cases and this will lead to more and richer character information in systematic studies. Character landmarking will he essential to systematic studies for clarifying structures such as shapes or convergences, which are previously hard to analyze anatomical regions. Both approaches will aid greatly in expanding our understanding of homology in particular, and insect development in general.

Animals↗
PubMed1995

Homologues of the engrailed gene from five molluscan classes.

We used the polymerase chain reaction (PCR) to amplify, clone, and sequence 10 engrailed homeodomains from 8 species in the five major molluscan classes, including the serially organized chiton (Polyplacophora) lineage. The Drosophila melanogaster gene engrailed (en) is one of several genes involved in embryonic segment polarity determination. Studies of engrailed sequence and expression in molluscs are of interest due to questions regarding the evolution and homology of segmentation in these taxa. Nucleotide and deduced amino acid sequence comparisons reflect evolutionary conservation within helices of the en homeodomain and ancient divergences in the region 3' to the homeodomain.

Animals↗