Ronald W. DeBry

Improving Interpretation of the Decay Index for DNA Sequence Data

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Peracarid monophyly and interordinal phylogeny inferred from nuclear small-subunit ribosomal DNA sequences (Crustacea: Malacostraca: Peracarida)

ABSTRACT Peracarids are a large group of malacostracan crustaceans whose systematics and phylogeny are uncertain. The present phylogenetic study of peracarids is, to our knowledge, the first that includes full-length nuclear (n) small-subunit (SSU) ribosomal DNA (rDNA) sequences for representatives of every peracarid order. Sequence length varied substantially (1807–2746 base pairs), and two variable regions (V4 and V7) contained long expansion segments. Variable regions also exhibited significantly greater heterogeneity in nucleotide frequencies than did core regions. Maximum-parsimony, maximum-likelihood, Bayesian, and distance phylogenetic estimates indicated a monophyletic Peracarida that excluded the Mysida and included the Thermosbaenacea. This peracarid clade received strong support under Bayesian, maximum-parsimony, and distance analyses, but not maximum likelihood. Further, the thermosbaenacean lineage does not occupy a basal position relative to other peracarids, as suggested by many morphology-based phylogenies. The phylogenetic position of the Mysida within the Malacostraca remains uncertain, but a sister-group relationship between Mysida and Lophogastrida (i.e., a monophyletic Mysidacea) was consistently rejected, a result that also differs from those of most morphology-based phylogenies. High Bayesian clade-credibility support was obtained for an (Isopoda + Tanaidacea + Cumacea) clade and a (Lophogastrida + [Spelaeogriphacea + Amphipoda]) clade. Within the peracarid clade, internal branches were considerably shorter than terminal ones, so relationships among some peracarid lineages were equivocal. Data partitions corresponding to stem and loop regions in a secondary-structure model for nSSU rRNA had congruent phylogenetic signal but differed in nucleotide composition and evolutionary model. Maximum parsimony and Bayesian phylogenetic estimates based on the loop partition generally shared more nodes in trees inferred from combined data than did those based on stems, even though the stem partition had roughly twice as many characters.

Identifying Conflicting Signal in a Multigene Analysis Reveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mammalia)

Homoplasy among morphological characters has hindered inference of higher level rodent phylogeny for over 100 years. Initial molecular studies, based primarily on single genes, likewise produced little resolution of the deep relationships among rodent families. Two recent molecular studies (Huchon et al., 2002, Mol. Biol. Evol. 19:1053-1065; Adkins et al., 2003, Mol. Phylogenet. Evol. 26:409-420), using larger samples from the nuclear genome, have produced phylogenies that are generally concordant with each other, but many of the deep superfamilial nodes were still lacking substantial statistical support. Data are presented here for a total of approximately 3,600 base pairs from portions of three different nuclear protein-coding genes, CB1, IRBP, and RAG2, from 19 rodents and three outgroups. Separate analyses, with data partitioned according to both genes and codon position, produced conflicting results. Trees obtained from all partitions of CB1 and RAG2 and those obtained from the first- plus second-position sites of IRBP were generally concordant with each other and the trees from the two recent studies, whereas trees obtained from the third-position sites of IRBP were not. Although the IRBP third-position sites represent only 1/9 of the total data set, combined analyses using either parsimony or likelihood resulted in trees in agreement with the IRBP third-position sites and in disagreement with the remaining 8/9 of the sites from this data set and the two recent multigene studies. In contrast, maximum-likelihood analysis using a site-specific rates model did recover a tree that is highly congruent with the trees in the two recent studies. If the IRBP third-position sites are removed from the current data set, then combined likelihood analyses obtain a tree that is highly congruent with those of the two recent studies. This analysis also provides, for the first time in a study of rodent phylogeny, robust statistical support for every bipartition, with just one exception. This tree divides rodents into two major clades. The first contains Myodonta (Muroidea plus Dipodidae) and the only unresolved trichotomy, from which descend Geomyoidea, Pedetidae, and Castoridae. On the other side of the root is a clade containing Sciuroidea plus Gliridae, and Hystricognathi. Some uncertainty remains on the placement of the root. Trees on which the Hystricognathi are the basal sister group to Myodonta, Geomyoidea, Pedetidae, and Castoridae are also found within a Bayesian 95% credible set, as estimated by Metropolis-coupled Markov chain Monte Carlo sampling.

NUCLEAR INTRON SEQUENCES FOR PHYLOGENETICS OF CLOSELY RELATED MAMMALS: AN EXAMPLE USING THE PHYLOGENY OF MUS

Abstract DNA sequence data from 2 nuclear introns (mitochondrial malate dehydrogenase intron 7 and acid phosphatase type V intron 2) were collected for 9 taxonomic units of rodents, 8 of which were in the genus Mus. Data were used to infer phylogenetic history of the 9 taxa, which was then compared with a consensus phylogeny taken from previous literature. In general, the nuclear intron data provided strong support (bootstrap proportions > 80) for relationships accepted in the consensus tree. The intron data disagreed with previous mitochondrial data in that 2 M. m. domesticus sequences were paraphyletic with respect to M. m. castaneus and M. m. musculus. This paraphyly, if real, likely reflects the longer lineage-sorting time of the nuclear genome compared with the mitochondrial genome. Introns seem to provide an attractive source of nuclear DNA sequence data for phylogenetic analysis, but mitochondrial data are likely to be superior for very recent divergences.

Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

ABSTRACT The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.

The Systematic Component of Phylogenetic Error as a Function of Taxonomic Sampling Under Parsimony

The effect of taxonomic sampling on phylogenetic accuracy under parsimony is examined by simulating nucleotide sequence evolution. Random error is minimized by using very large numbers of simulated characters. This allows estimation of the consistency behavior of parsimony, even for trees with up to 100 taxa. Data were simulated on 8 distinct 100-taxon model trees and analyzed as stratified subsets containing either 25 or 50 taxa, in addition to the full 100-taxon data set. Overall accuracy decreased in a majority of cases when taxa were added. However, the magnitude of change in the cases in which accuracy increased was larger than the magnitude of change in the cases in which accuracy decreased, so, on average, overall accuracy increased as more taxa were included. A stratified sampling scheme was used to assess accuracy for an initial subsample of 25 taxa. The 25-taxon analyses were compared to 50- and 100-taxon analyses that were pruned to include only the original 25 taxa. On average, accuracy for the 25 taxa was improved by taxon addition, but there was considerable variation in the degree of improvement among the model trees and across different rates of substitution.

mtDNA-based identification of Lucilia cuprina (Wiedemann) and Lucilia sericata (Meigen) (Diptera: Calliphoridae) in the continental United States.

Existing data suggest that the forensically important dipteran species Lucilia cuprina (Wiedemann) and Lucilia sericata (Meigen) may be particularly difficult to discriminate using DNA sequence data. L. cuprina is paraphyletic with respect to L. sericata in mtDNA phylogenies, with some L. cuprina having mtDNA haplotypes that are very similar to those of L. sericata. We examine this problem by providing the first DNA data for L. cuprina from North America, including portions of both the mitochondrial COI gene and the nuclear 28S rRNA gene. With the new data, L. cuprina remains monophyletic for 28S but paraphyletic with respect to L. sericata for COI. However, we find that all flies that are identified as L. cuprina by morphology and have L. sericata-like mtDNA form a distinctly monophyletic mtDNA clade. This clade may possibly have originated by hybridization between L. cuprina and L. sericata, but its wide geographic distribution strongly suggests a singular origin as opposed to repeated incidents of hybridization. The phylogenetic results strongly support the hypothesis that L. cuprina and L. sericata can be discriminated using mtDNA sequence data. We find that a fragment of COI spanning approximately 1200 base pairs is sufficient to discriminate between the two species with greater than 95% bootstrap support.

Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae)

In an effort to improve our knowledge of the phylogenetic relationships among species and genera of the subfamily Sarcophaginae, we analysed data from three mitochondrial gene fragments. Sequence data for portions of the genes cytochrome oxidase I (COI), cytochrome oxidase II (COII) and dehydrogenase subunit 4 (ND4) were obtained from 43 species of Sarcophagidae representing 15 genera. We used a Bayesian approach to simultaneously choose how best to partition the data and which substitution model to apply to each partition. Phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods. Our results are consistent with monophyly of the subfamily Sarcophaginae (posterior probability 1; bootstrap support 93%), as well as with monophyly of several genera within the Sarcophaginae (including Sarcophaga s.l.; posterior probability 1; bootstrap support 97%). We found support for a sister‐group relationship between Ravinia Robineau‐Desvoidy and Oxysarcodexia Townsend, which has been hypothesised by past authors on the basis of morphological similarities, although this was supported only in the Bayesian analyses (posterior probability 0. 81–0. 98), and for some novel supra‐generic clades. Contrary to a recent morphological hypothesis, we do not find Helicobia Coquillett to be nested within Sarcophaga Meigen; our data suggest, but do not strongly support, a hypothesis that Peckia Robineau‐Desvoidy is the sister group to Sarcophaga.

Maximum Likelihood Analysis of Gene-Based and Structure-Based Process Partitions, Using Mammalian Mitochondrial Genomes

Aligned protein-coding genes from 19 completely sequenced mammalian mitochondrial genomes were examined by parsimony and maximum likelihood analyses. Particular attention is given to a comparison between gene-based and structure-based data partitions. Because actual structures are not known for most of the mitochondrially encoded proteins, three different surrogate partitioning schemes were examined, each based on the identity of the consensus amino acid at a specific homologous position. One of the amino-acid-based partitioning schemes gave the highest likelihood, but that scheme was based on concordance with a well-corroborated phylogeny from an earlier parsimony analysis. The gene-based partitioning scheme gave a significantly higher likelihood compared to the only structure-based scheme examined that could be generated without prior assumptions about the phylogeny. Two contrasting phylogenetic inferences were supported by the analyses. Both unpartitioned analyses and analyses in which all partitions were constrained to have identical patterns of branch lengths supported ((Artiodactyla, Cetacea) (Perissodactyla, Carnivora)), whereas all analyses with that constraint relaxed supported (((Artiodactyla, Cetacea) Carnivora) Perissodactyla).

The Nocturnal Ovipositing Behavior of Carrion Flies in Cincinnati, Ohio

Abstract:  The behavioral patterns of nocturnal oviposition represent a window of time that potentially has a large impact on postmortem interval estimations. We investigated the behavioral patterns of carrion flies at night by exposing euthanized rats between sunset and sunrise to see if carrion flies oviposited upon the carrion over two consecutive summers. We investigated urban and rural locations, in both lit and unlit conditions with n = 125. We found that nocturnal ovipositing did not occur in the Cincinnati metropolitan area. We conclude that nocturnal oviposition is an unlikely event in the Cincinnati metropolitan area.