Abstract The northeastern Atlantic spiny spider crab occurs from the British Islands to Senegal, where it is an important fishery resource. From morphological characters this crab has recently been proposed as a distinct species, Maja brachydactyla, although for commercial purposes it is still considered the same species as its Mediterranean congener M. squinado. We have studied variation at two mitochondrial genes in several crab populations from the Atlantic (putatively M. brachydactyla) and Mediterranean (M. squinado and M. crispata) basins, in order to clarify the taxonomic status of this crab in the northeastern Atlantic and Mediterranean regions. Phylogenetic analysis revealed that each of these three taxa forms a distinct and well-defined clade. While the divergence within each taxon was 0% for 16S and 0-0.3% for COI, divergence between taxa was 0.6-2.5% for 16S and 5.3-8.7% for COI; values that are in the range of the differences observed between other crustacean species. These results confirm the genetic distinctiveness of each taxa and support their designation as different species. Therefore, the Atlantic spider crab should be referred as M. brachydactyla, a fact that should be taken into account for conservation and commercial purposes.
Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (approximately 5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate, robust and extensible subtyping procedures is clear.
Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".
Abstract Equalization of parental contributions is one of the most simple and widely recognized methods to maintain genetic diversity in conservation programs, as it halves the rate of increase in inbreeding and genetic drift. It has, however, the negative side effect of implying a reduced intensity of natural selection so that deleterious genes are less efficiently removed from the population with possible negative consequences on the reproductive capacity of the individuals. Theoretical results suggest that the lower fitness resulting from equalization of family sizes relative to that for free contribution schemes is expected to be substantial only for relatively large population sizes and after many generations. We present a long-term experiment with Drosophila melanogaster, comparing the fitness performance of lines maintained with equalization of contributions (EC) and others maintained with no management (NM), allowing for free matings and contributions from parents. Two (five) replicates of size N = 100 (20) individuals of each type of line were maintained for 38 generations. As expected, EC lines retained higher gene diversity and allelic richness for four microsatellite markers and a higher heritability for sternopleural bristle number. Measures of life-history traits, such as egg-to-adult viability, mating success, and global fitness declined with generations, but no significant differences were observed between EC and NM lines. Our results, therefore, provide no evidence to suggest that equalization of family sizes entails a disadvantage on the reproductive capacity of conserved populations in comparison with no management procedures, even after long periods of captivity.