Steven A. Nadler

Bio: Steven A. Nadler is an academic researcher from University of California, Davis. The author has contributed to research in topics: Phylogenetic tree & Phylogenetics. The author has an hindex of 47, co-authored 114 publications receiving 6392 citations. Previous affiliations of Steven A. Nadler include University of California & National Autonomous University of Mexico.

Disparate rates of molecular evolution in cospeciating hosts and parasites

Abstract: DNA sequences for the gene encoding mitochondrial cytochrome oxidase I in a group of rodents (pocket gophers) and their ectoparasites (chewing lice) provide evidence for cospeciation and reveal different rates of molecular evolution in the hosts and their parasites. The overall rate of nucleotide substitution (both silent and replacement changes) is approximately three times higher in lice, and the rate of synonymous substitution (based on analysis of fourfold degenerate sites) is approximately an order of magnitude greater in lice. The difference in synonymous substitution rate between lice and gophers correlates with a difference of similar magnitude in generation times.

Phylogenetic trees support the coevolution of parasites and their hosts

Abstract: The close correspondence often observed between the taxonomy of parasites and their hosts has led to Fahrenholz's rule, which postulates that parasites and their hosts speciate in synchrony. This leads to the prediction that phylogenetic trees of parasites and their hosts should be topologically identical. We report here a test of this prediction which involves the construction of phylogenetic trees for rodents and their ectoparasites using protein electrophoretic data. We find a high degree of concordance in the branching patterns of the trees which suggests that there is a history of cospeciation in this host-parasite assemblage. In several cases where the branching patterns were identical in the host and parasite phylogenies, the branch lengths were also very similar which, given the assumptions of molecular clock theory, strongly suggests that the speciation of these hosts and ectoparasites was roughly contemporaneous and causally related.

Molecular and morphological characterisation of two reproductively isolated species with mirror-image anatomy ({Nematoda}: {Cephalobidae})

Abstract: Detailed descriptions are given of the amphimictic nematode strains PS1158, PS2052 and PS2160, which are unusual in that they only differ in predominant body handedness. Although these strains are morphologically identical in all other respects, published reproductive data and new DNA sequence data of the D2/D3 region of the large subunit rRNA gene show that they do represent two separate species. On the basis of comparison with type material, the left-handed strains PS1158 and PS2160 are identified as Acrobeloides bodenheimeri , and the right-handed strain PS2052 as A. camberenensis , which is re-instated as a valid species. A. bodenheimeri and its relatives exhibit various types of diagnostic and taxonomic problems at species level, and it is shown that D2/D3 sequence data provide an important new diagnostic tool for addressing these problems. Phylogenetic analysis shows that two right-handed parthenogenetic strains identified as A. maximus represent a third species which is more closely related to A. camberenensis than to A. bodenheimeri . Caracterisation morphologique et moleculaire de deux especes intersteriles de chiralite contraire (Nematoda: Cephalobidae) - Une description detaillee est donnee des souches amphimictiques de nematodes PS1158, PS2052 et PS2160, souches inhabituelles car differant par la chiralite du corps. Bien que ces souches soient morphologiquement identiques sous tout autre rapport, les resultats publies de tests de croisement et de nouvelles donnees concernant la sequence d'ADN de la region D2/D3 du gene de la grosse sous-unite d'ARN ribosomal montrent qu'elles representent en fait deux especes distinctes. Se fondant sur une comparaison avec le materiel type, les souches sinistres PS1158 et PS2160 sont identifiees comme Acrobeloides bodenheimeri et la souche dextre PS2052 comme A. camberenensis , ainsi retabli comme espece valide. A. bodenheimeri et les especes proches posent differents problemes diagnostiques et taxinomiques au niveau specifique, et nous montrons que les donnees de sequence D2/D3 fournissent un nouvel outil diagnostique important pour aborder ces problemes. L'analyse phylogenetique montre que deux souches parthenogenetiques dextres identifiees comme A. maximus representent en fait une troisieme espece, plus proche de A. camberenensis que de A. bodenheimeri .

Phylogeny of the Ascaridoidea (Nematoda: Ascaridida) based on three genes and morphology: hypotheses of structural and sequence evolution.

Abstract: Ascaridoid nematodes parasitize the gastrointestinal tract of vertebrate definitive hosts and are represented by more than 50 described genera. We used 582 nucleotides (83% of the coding sequence) of the mitochondrial gene cytochrome oxidase subunit 2, in combination with published small- and large-subunit nuclear rDNA sequences (2,557 characters) and morphological data (20 characters), to produce a phylogenetic hypothesis for representatives of this superfamily. This combined evidence phylogeny strongly supported clades that, with 1 exception, were consistent with Fagerholm's 1991 classification. Parsimony mapping of character states on the combined evidence tree was used to develop hypotheses for the evolution of morphological, life history, and amino acid characters. This analysis of character evolution revealed that certain key features that have been used by previous workers for developing taxonomic and evolutionary hypotheses represent plesiomorphic states. Cytochrome oxidase subunit 2 nucleotides show a strong compositional bias to A+T and a substitution bias to thymine. These biases are most apparent at third positions of codons and 4-fold degenerate sites, which is consistent with the nonrandom substitution pattern of A+T pressure. Despite nucleotide bias, cytochrome oxidase amino acid sequences show conservation and retention of critical functional residues, as inferred from comparisons to other organisms.

Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology.

Abstract: Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments

Abstract: Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.

Genetic Data Analysis

Abstract: LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.