Genetics at the brink of extinction.
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Adaptation, Biological↗
Biomedical subjects
R DeSalle
Publications and source records attributed to R DeSalle.
The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae.
Forty-five new Homeotic Complex (HOM-C) homeobox sequences from six species of Drosophilidae (Drosophila heteroneura, D. adiastola, Zaprionus vittiger, Chymomyza amoena, Scaptodrosophila pattersoni and Hirtodrosophila pictiventris) were obtained using a PCR-cloning method. These new homeoboxes are from the labial, proboscipedia, Deformed, Sex combs reduced, fushi tarazu, Antennapedia, Ultrabithorax, abdominal-A and Abdominal-B genes. Phylogenetic signal in the homeobox sequences was assessed and several aspects of sequence evolution were examined. In particular, codon bias was examined and found to exist between the drosophilid species examined here and Anopheles gambiae outgroup sequences. In addition, different patterns of codon bias were detected in homeoboxes interrupted with introns when compared to homeoboxes that are uninterrupted.
Amino Acid Sequence↗
Characteristic attributes in cancer microarrays.
Rapid advances in genome sequencing and gene expression microarray technologies are providing unprecedented opportunities to identify specific genes involved in complex biological processes, such as development, signal transduction, and disease. The vast amount of data generated by these technologies has presented new challenges in bioinformatics. To help organize and interpret microarray data, new and efficient computational methods are needed to: (1) distinguish accurately between different biological or clinical categories (e.g., malignant vs. benign), and (2) identify specific genes that play a role in determining those categories. Here we present a novel and simple method that exhaustively scans microarray data for unambiguous gene expression patterns. Such patterns of data can be used as the basis for classification into biological or clinical categories. The method, termed the Characteristic Attribute Organization System (CAOS), is derived from fundamental precepts in systematic biology. In CAOS we define two types of characteristic attributes ('pure' and 'private') that may exist in gene expression microarray data. We also consider additional attributes ('compound') that are composed of expression states of more than one gene that are not characteristic on their own. CAOS was tested on three well-known cancer DNA microarray data sets for its ability to classify new microarray samples. We found CAOS to be a highly accurate and robust class prediction technique. In addition, CAOS identified specific genes, not emphasized in other analyses, that may be crucial to the biology of certain types of cancer. The success of CAOS in this study has significant implications for basic research and the future development of reliable methods for clinical diagnostic tools.
Acute Disease↗
Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila.
BACKGROUND: Polytene chromosome banding patterns have long been used by Drosophila evolutionists to infer degree of relatedness among taxa. Recently, nucleotide sequences have preempted this traditional method. We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utility in comparison to nucleotide sequences. RESULTS: A simultaneous analysis framework was used to examine the congruence of the chromosomal inversion data with more recent DNA sequence data in four Drosophila species groups - the melanogaster, virilis, repleta, and picture wing. Inversions and nucleotides were highly congruent with one another based on incongruence length difference and partitioned Bremer support values. Inversion phylogenies were less resolved because of fewer numbers of characters. Partitioned Bremer supports, corrected for the number of characters in each matrix, were higher for inversion matrices. CONCLUSIONS: Polytene chromosome data are highly congruent with DNA sequence data and, when placed in a simultaneous analysis framework, are shown to be more information rich than nucleotide data.
Animals↗
The identity of plant glutamate receptors.
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Arabidopsis↗
Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification.
Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB, PilT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis.
Acid Anhydride Hydrolases↗
A molecular phylogeny of Costaceae (Zingiberales).
The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gingers (Zingiberaceae), were investigated with a combination of two chloroplast loci (the trnL-F locus, including the trnL intron, the 3'trnL exon, and the trnL-F intergenic spacer, and the trnK locus, including the trnK intron and the matK coding region) and one nuclear locus (ITS1-5.8s-ITS2). The resulting parsimony analysis of selected taxa that demonstrate the range of floral morphological variation in the family shows that the Cadalvena-type [corrected] floral morphology is ancestral to the group and that both Tapeinochilos species and a Monocostus + Dimerocostus clade represent recent divergences. The genus Costus is broadly paraphyletic but Costus subgenus Eucostus K. Schum. represents a large monophyletic radiation that is poorly resolved. Within this clade, secondary analyses suggest that pollination syndrome, traditionally used for taxonomic and classification purposes within the genus Costus, is a relatively plastic trait of limited phylogenetic utility. This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography.
Chloroplasts↗
Genes for tight adherence of Actinobacillus actinomycetemcomitans: from plaque to plague to pond scum.
The Gram-negative periodontal pathogen Actinobacillus actinomycetemcomitans forms an extremely tenacious biofilm on solid surfaces such as glass, plastic and hydroxyapatite. This characteristic is likely to be important for colonization of the oral cavity and initiation of a potentially devastating form of periodontal disease. Genetic analysis has revealed a cluster of tad genes responsible for tight adherence to surfaces. Evidence indicates that the tad genes are part of a locus encoding a novel secretion system for the assembly and release of long, bundled Flp pili. Remarkably similar tad loci appear in the genomes of a wide variety of Gram-negative and Gram-positive bacteria, including many significant pathogens, and in Archaea. We propose that the tad loci are important for microbial colonization in a variety of environmental niches.
Aggregatibacter actinomycetemcomitans↗
Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives.
Endogenous retrovirus-like elements characterizable by a leucine tRNA primer (ERV-Ls) are reiterated genomic sequences known to be widespread in mammals, including humans. They may have arisen from an ancestral foamy virus-like element by successful germ line infection followed by copy number expansion. However, among mammals, only primates and rodents have thus far exhibited high copy number amplification and sequence diversification. Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa having good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing proboscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L sequences, and thus it was expected that uranotheres should as well. Here, we show that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lineages. Selection is the most parsimonious explanation for observed differences in ERV-L distribution and frequency, with relative success being reflected in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant elephantid samples).
Animals↗
Systematic analysis of DNA microarray data: ordering and interpreting patterns of gene expression.
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Classification↗
Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae).
A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprising three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most-parsimonious cladogram with relatively strong support at the majority of nodes. The phylogenetic utility of different classes of molecular data was also examined. In particular, using a number of different measures of utility in both a combined and separate analysis framework, we focused on the distinction between mitochondrial and nuclear genes and between faster-evolving characters and slower-evolving characters. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationships than are the mitochondrial genes. The nuclear genes exhibit less homoplasy, are less incongruent with one another and with the combined data, and contribute more support to the combined analysis topology than do the mitochondrial genes. Results from the second comparison, however, provide little evidence of a clear difference in utility. Despite indications of rapid divergence and saturation, faster-evolving characters in both the nuclear and mitochondrial data sets still provide substantial phylogenetic signal. In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions.
ATP-Binding Cassette Transporters↗
How the fruit fly changed (some of) its spots.
Recent results show that the establishment of wing melanization patterns in Drosophila depends on the veins. While several genes have been shown to play a role in melanization, changes in a single gene - the one encoding tyrosine hydroxylase - are sufficient to generate novel pigmentation patterns.
Animals↗
Phylogeny and character behavior in the family Lemuridae.
A phylogenetic analysis of the family Lemuridae was accomplished using multiple gene partitions and morphological characters. The results of the study suggest that several nodes in the lemurid phylogeny can be robustly resolved; however, the relationships of the species within the genus Eulemur are problematically nonrobust. The genus Varecia is strongly supported as the basal genus in the family. Hapalemur and Lemur catta are strongly supported as sister taxa and together are the sister group to the genus Eulemur. E. mongoz is the most basal species in the genus Eulemur. E. fulvus subspecies form a monophyletic group with three distinct lineages. E. coronatus is strongly supported as the sister taxon to E. macaco. The relationships of E. rubriventer, E. fulvus, and the E. macaco-E. coronatus pair are unresolved. Our combined molecular and morphological analysis demonstrates the lack of influence that morphology has on the simultaneous analysis tree when these two kinds of data are given equal weight. The effects of several extreme weighting schemes (removal of transitions and of third positions in protein-coding regions) and maximum-likelihood analysis were also explored. We suggest that these other forms of inference add little to resolving the problematic relationships of the species in the genus Eulemur.
Animals↗
Phylogenetic analysis of the repleta species group of the genus Drosophila using multiple sources of characters.
The species in the repleta group of the genus Drosophila have been placed into five subgroups-the mulleri, hydei, mercatorum, repleta, and fasciola subgroups. Each subgroup has been further subdivided into complexes and clusters. Extensive morphological and cytological analyses of the members of this species group have formed the foundation for the proposed relationships among the members of the repleta species group. Fifty-four taxa, including 46 taxa belonging to the repleta species group, were sequenced for fragments of four genes-16S ribosomal DNA (16S), cytochrome oxidase II (COII), and nitrogen dehydrogenase 1 (ND1) of the mitochondrial genome and a region of the hunchback (hb) nuclear gene. We also generated a partial data set of elongation factor 1-alpha (Ef1alpha) sequences for a subset of taxa. Our analysis used both DNA characters and chromosomal inversion data. The phylogenetic hypothesis we obtained supports many of the traditionally accepted clades within the mulleri subgroup, but the monophyly of taxonomic groups outside of this subgroup appears not to be supported. Phylogenetic analysis revealed one well-supported, highly resolved clade that consists of closely related members of the mulleri and buzzatii complexes. The remaining taxa, a wide assortment of taxonomic groups, ranging from members of other species groups to members of several subgroups and members of three species complexes from the mulleri subgroup are found in poorly supported arrangements at the base of the tree.
Animals↗
World-wide genetic differentiation of Eubalaena: questioning the number of right whale species.
Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis, multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales world-wide.
Animals↗
Transformationalism, taxism, and developmental biology in systematics.
Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the recent developmental data on systematic theory and practice. We examine the philosophical and practical aspects of the transformational approach and the relevance of this approach to recent molecular-based developmental data. We also examine the theoretical basis of the taxic approach to molecular developmental data and suggest that developmental data are perfectly amenable to the taxic approach. Two recent examples from the molecular developmental biology literature--the evolution of insect wings and the evolution of dorsal ventral inversion in vertebrates and invertebrates--are used to compare the taxic and transformational approaches. We conclude that the transformational approach is entirely appropriate for ontogenetic studies and furthermore can serve as an excellent source of hypotheses about the evolution of characters. However, the taxic approach is the ultimate arbiter of these hypotheses.
Animals↗
Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea.
The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particularly destructive form of periodontal disease in adolescents. This bacterium has also been isolated from a variety of other infections, notably endocarditis. Fresh clinical isolates of A. actinomycetemcomitans form tenacious biofilms, a property likely to be critical for colonization of teeth and other surfaces. Here we report the identification of a locus of seven genes required for nonspecific adherence of A. actinomycetemcomitans to surfaces. The recently developed transposon IS903phikan was used to isolate mutants of the rough clinical isolate CU1000 that are defective in tight adherence to surfaces (Tad(-)). Unlike wild-type cells, Tad(-) mutant cells adhere poorly to surfaces, fail to form large autoaggregates, and lack long, bundled fibrils. Nucleotide sequencing and genetic complementation analysis revealed a 6.7-kb region of the genome with seven adjacent genes (tadABCDEFG) required for tight adherence. The predicted TadA polypeptide is similar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localization but no obvious functions. We suggest that the tad genes are involved in secretion of factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of the bubonic plague bacillus Yersinia pestis and the human and animal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganisms indicates that they have important functions. We propose that tad-like genes have a significant role in microbial colonization.
Aggregatibacter actinomycetemcomitans↗
Gene family evolution and homology: genomics meets phylogenetics.
With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.
Animals↗