Biological identifications through DNA barcodes: the case of the Crustacea

The ability of a 650 base pair section of the mitochondrial cytochrome c oxidase I (COI) gene to provide species-level identifications has been demonstrated for large taxonomic assemblages of animals such as insects, birds, and fishes, but not for the subphylum Crustacea, one of the most diverse groups of arthropods. In this study, we test the ability of COI to provide identifications in this group, examining two disparate levels in the taxonomic hierarchy — orders and species. The first phase of our study involved the development of a sequence profile for 23 dominant crustacean orders, based upon the analysis of 150 species, each belonging to a different family. The COI amino acid data placed these taxa into cohesive assemblages whose membership coincided with currently accepted boundaries at the order, superorder, and subclass levels. Species-level resolution was subsequently examined in an assemblage of Decapoda and in representatives of the genera Daphnia (Cladocera) and Gammarus (Amphipoda). These studies revealed that levels of nucleotide sequence divergence were from 19 to 48 times greater between congeneric species than between individuals of a species. We conclude that sequence variation in the COI barcode region will be very effective for discriminating species of Crustacea.

A new Puumala hantavirus subtype in rodents associated with an outbreak of Nephropathia epidemica in South-East Germany in 2004

A micro-epidemic of hantavirus infections occurred in Lower Bavaria, South-East Germany, starting in April 2004. While only three cases were registered from 2001 to 2003, a dramatically increased number of clinically apparent human hantavirus infections (n=38) was observed in 2004, plus seven additional cases by June 2005. To determine the reservoir responsible for the infections, a total of 43 rodents were trapped in Lower Bavaria. Serological and genetic investigations revealed that Puumala virus (PUUV) is dominant in the local population of bank voles. Partial PUUV S segment nucleotide sequences originating from bank voles at four different trapping sites in Lower Bavaria showed a low divergence (up to 3·1%). This is contrasted by a nucleotide sequence divergence of 14–16% to PUUV strains detected in Belgium, France, Slovakia or North-Western Germany. PUUV sequences from bank voles in Lower Bavaria represent a new PUUV subtype which seems to be responsible for the observed increase of human hantavirus infections in 2004–2005.

Strong Selective Pressure for Evolution of an Epstein-Barr Virus LMP2B Homologue in the Rhesus Lymphocryptovirus

ABSTRACT Latent membrane protein 2B (LMP2B) is expressed during latent Epstein-Barr virus (EBV) infection, but little is known about its role. The goal of this study was to determine whether an LMP2B homologue is conserved in the rhesus monkey lymphocryptovirus (LCV). Both rhesus LCV LMP2A and LMP2B genes were cloned and sequenced. The rhesus LCV LMP2B gene is positionally conserved, and the EBNA-2 responsiveness and the bidirectional nature of the LMP1-LMP2B promoter have also been functionally conserved. However, this region of the genome encoding the LMP1, LMP1-LMP2B promoter, and LMP2B first exon demonstrates the most dramatic nucleotide sequence divergence between human and nonhuman LCV observed to date. Evolution of the rhesus LCV LMP2B promoter and transcript despite the dynamic nature of this genomic region reflects strong selective pressure for a yet-to-be-identified LMP2B function.

Genetic Comparison Between Pacific Herring (Clupea pallasi) and a Norwegian Fjord Stock of Atlantic Herring (Clupea harengus)

Genetic studies on populations of Atlantic herring (Clupea harengus L.) in Norwegian seawaters have revealed a number of genetically distinct fjord populations. One population in Balsfjord in northern Norway was nearly fixed for several alleles that were very rare in the Atlanto-Scandian herring stock. A comparison with a sample of Pacific herring (Clupea pallasi) from British Columbia demonstrated that these alleles were identical to the more common alleles in this species. Genetic distance estimates based on six polymorphic loci demonstrated that Balsfjord herring were more similar to Pacific herring. Balsfjord and Pacific herring were also similar in vertebrae number and spawning behaviour. Restriction fragment analyses of mitochondrial DNA using five restriction enzymes revealed distinct clones that separated different herring groups. Nucleotide sequence divergence among groups was small.