Robert DeSalle

Historical Mammal Extinction on Christmas Island (Indian Ocean) Correlates with Introduced Infectious Disease

It is now widely accepted that novel infectious disease can be a leading cause of serious population decline and even outright extinction in some invertebrate and vertebrate groups (e.g., amphibians). In the case of mammals, however, there are still no well-corroborated instances of such diseases having caused or significantly contributed to the complete collapse of species. A case in point is the extinction of the endemic Christmas Island rat (Rattus macleari): although it has been argued that its disappearance ca. AD 1900 may have been partly or wholly caused by a pathogenic trypanosome carried by fleas hosted on recently-introduced black rats (Rattus rattus), no decisive evidence for this scenario has ever been adduced. Using ancient DNA methods on samples from museum specimens of these rodents collected during the extinction window (AD 1888–1908), we were able to resolve unambiguously sequence evidence of murid trypanosomes in both endemic and invasive rats. Importantly, endemic rats collected prior to the introduction of black rats were devoid of trypanosome signal. Hybridization between endemic and black rats was also previously hypothesized, but we found no evidence of this in examined specimens, and conclude that hybridization cannot account for the disappearance of the endemic species. This is the first molecular evidence for a pathogen emerging in a naïve mammal species immediately prior to its final collapse.

OrthologID: automation of genome-scale ortholog identification within a parsimony framework

MOTIVATIONnThe determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.nnnRESULTSnWe have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.nnnAVAILABILITYnhttp://nypg.bio.nyu.edu/orthologid/

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.

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.

Using molecular and ecological data to diagnose endangered populations of the puritan tiger beetle Cicindela puritana

Populations of the puritan tiger beetle Cicindela puritana in the eastern United States were found to be highly threatened at the Connecticut River, whereas several large populations on the western shore and newly discovered populations on the eastern shore of the Chesapeake Bay appeared to be less endangered. We assessed if the disjunct C. puritana subgroups are genetically distinct and therefore should be treated as separate units for conservation purposes. A total of 13 individuals from the Connecticut River and 27 individuals from the Chesapeake Bay were each analysed by sequencing of up to 837 base pairs of mitochondrial DNA per individual. Five different haplotypes could be distinguished. In a phylogenetic analysis of these DNA sequences that included four related Cicindela species as out‐groups, haplotypes from the Chesapeake Bay represent a distinct clade. The conservation status of these populations was evaluated using a phylogenetic approach based on cladistic analysis and the framework of the phylogenetic species concept. According to this analysis, beetles from the Connecticut River and the Chesapeake Bay have to be considered as independent units. Populations from the eastern and western shore of Chesapeake Bay are not split in more than one unit using the same criteria, although they exhibited some degree of genetic subdivision. The results from the mtDNA analysis were corroborated by ecological parameters in that the Chesapeake Bay populations can be distinguished from all congeners by their different tat association.

An effective method for isolating DNA from historical specimens of baleen.

DNA was isolated from an early twentieth century museum specimen of northern right whale baleen. A system of stringent controls and a novel set of cetacean specific primers eliminated contamination from external sources and ensured the authenticity of the results. Sequence analysis revealed that there were informative nucleotide positions between the museum specimen and extant members of the population and closely related species. The results indicate that museum specimens of baleen can be used to assess historical genetic population structure of the great whales.

Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis

The Hawaiian Drosophilidae are comprised of an estimated 1000 species, all arising from a single common ancestor in the last 25 million years. This group, because of its species diversity, marked sexual dimorphism and complex mating behavior, host plant specificity, and the well-known chronology of the Hawaiian Archipelago, is an excellent model system for evolutionary studies. Here we present a phylogeny of this group based on ~2.6 kb of mitochondrial DNA sequence. Our taxon sampling is the most extensive to date, with nearly 200 species representing all species groups and most subgroups from the larger clades. Our results suggest that the picture wing and modified mouthpart species, long believed to be derived within this radiation, may actually occupy a basal position in the phylogeny. The haleakale species group, in contrast, is strongly supported as sister to the AMC clade. We use the phylogenetic results to examine the evolution of two important ecological characters, the host family and type of substrate used for oviposition and larval development. Although both host and substrate transitions are common in the group, oviposition substrate is more conserved among species groups than host plant family. While the ancestral host plant family is equivocally reconstructed, our results suggest that the ancestor of this group may have used rotting bark as a primary oviposition substrate.

Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii and A. stellatus.

Two species, the Siberian sturgeon, Acipenser baerii, and stellate sturgeon, A. stellatus, were studied using mitochondrial DNA (mtDNA) (D‐loop, cytochrome b (cyt‐b) and ND5/6 genes) sequencing to determine whether traditionally defined subspecies correspond to taxonomic entities and conservation management units. Initially, several mtDNA regions for each taxon (A. baerii: 737 bp D‐loop, 750 bp ND5, 200 bp ND6, and 790 bp cyt‐b;A. stellatus: 737 bp D‐loop and 600 bp ND5) were examined. The D‐loop was the most variable region and was sequenced for 35 A. baerii and 82 A. stellatus individuals. No fixed, diagnostic differences were found between any of the subspecies. Geographical structuring of haplotypes was observed within A. baerii, and gene flow estimates suggest isolation of the A. baerii baicalensis subspecies and the Yenisie and Lena River populations. No intraspecific subdivisioning was found within the genetic data for A. stellatus. The use of the phylogenetic criterion (fixed diagnostic differences) for identifying conservation units is compared to the rationale and results of other methods. Overall, morphologically and geographically based subspecies designations within Acipenseridae may not directly correspond to the biological entities appropriate for management and should not be used for conservation programmes without genetic support.

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 embyonic 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.

Description of Freshwater Bacterial Assemblages from the Upper Paraná River Floodpulse System, Brazil

Bacteria were identified from a large, seasonally flooded river (Paraná River, Brazil) and two floodplain habitats that were part of the same river system yet very different in nature: clearwater Garças Lagoon and the highly humic waters of Patos Lagoon. Bacterioplankton were collected during mid-summer (Jan. 2002) from water samples (2xa0l) filtered first through a 1.2-μm filter then a 0.2-μm membrane filter representing the particle-attached and free-living sub-communities, respectively. DNA was extracted from filters and purified and a 16S rRNA clone library established for each habitat. Over 300 clones were sequenced and checked for similarity to existing 16S sequences in GenBank using the BLAST algorithm with default parameters. Further classification of clones was done using a species “backbone” attachment followed by parsimony analysis. The majority (85%) of sequences, referred to here as operational taxonomic units (OTUs), were most similar to uncultured bacterium 16S sequences. OTUs from each Proteobacteria sub-phylum (α, β, γ, δ, ɛ) were present in the Upper Paraná River system, as well as members of the Bacteroidetes. The microbial assemblage from Patos Lagoon was least like other samples in that it had no Firmicutes present and was dominated by Actinobacteria. Verrucomicrobia OTUs were only found in the free-living assemblage. This study documents the presence of globally distributed phyla in Upper Paraná River and taxa unique to habitat and particle attachment.