pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Felid sex identification based on noninvasive genetic samples

We developed two tests for sex identification of felids using y‐chromosome deletions in the zinc‐finger and amelogenin regions. These tests provide positive results for both males and females, while reducing the need to co‐amplify microsatellites to test for DNA quality in hair and scat samples. Furthermore, the y‐chromosome deletions are absent in a wide‐range of prey species; thus, when these tests are used on scat samples, potential contamination caused by prey DNA incidentally extracted, is minimized.     

CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein.     

Cellulose-microfibril-orienting mechanisms in plant cells walls

A brief review is given of the changing views over the years, as knowledge of wall structure has developed, concerning the mechanism whereby cellulose chains may be oriented. This leads to an examination of current concepts, particularly those concerning microtubules. It is shown that none of the mechanisms suggested whereby microtubules might cause orientation of cellulose microfibrils is consistent with the known range of molecular architectures found in plant cell walls. It is further concluded that any mechanism which necessitates an indissoluble link between the plasmalemma and the cellulose-synthesising complex at the tip of a microfibril is unacceptable. A new proposal is presented in which it is speculated that both microtubules and microfibrils are oriented by a mechanism separate from both. It is shown that if two vectors are contemplated, one parallel to cell length and one at right angles, and a sensor exists on the plasmalemma surface which responds to changes in the vectors, then all known wall structures may be explained. The possible nature of the vectors and the sensor are considered.     

Metazoan parasites of Engraulis ringens as tools for stock discrimination along the Chilean coast

The value of the metazoan parasites of the anchoveta Engraulis ringens as biological tags for stock discrimination is assessed. Three hundred and fifty-nine specimens, obtained from six landing ports in northern and central Chile (Arica, Antofagasta, Caldera, Coquimbo, Valparaiso and Talcahuano) covering a latitudinal gradient of c . 18°, were analysed. Six metazoan parasite species (three ectoparasites and three endoparasites) were obtained. A correspondence analysis suggested that anchoveta from northern and central Chile are comprised of two stocks. Identification of stocks was largely based on qualitative differences (absence in southern localities of the monogenean Pseudanthocotyloides heterocotyle , a parasite proper of engraulids, and the copepod Caligus sp.) and quantitative differences in the prevalence of infection for the remaining species. Inertia and mass value for the correspondence analysis supported the hypothesis of two stocks.     

Spatial organization and conformational peculiarities of the callatostatin family of neuropeptides.

The structures and conformational peculiarities of five members of the callatostatin family of neuropeptides, i.e. Leu- and Met-callatostatins, ranging in size from 8 to 16 amino acid residues have been investigated by a theoretical conformational analysis method. A comparative analysis of the conformational flexibilities of Met-callatostatin with those of the hydroxylated analogues, [Hyp2]- and [Hyp3]-Met-callatostatin has been carried out. Helically packed C-terminal pentapeptide in the structure of all investigated Leu-callatostatins are shown to be possible. The reason for the great number low-energy conformers for the callatostatin N-terminus is discussed.     

Host plant growth characteristics as determinants of abundance and phenology in jumping plant-lice on downy willow

1. Salix lapponum host plants at an upper altitudinal site differed significantly in size, structural density, phenology, growth performance, and spatial isolation from those growing at a lower site. 2. Plant differences were paralleled by significant differences in psyllid population density and phenology parameters, with psyllid population density, percentage of catkins occupied, and phenological development relatively lower or retarded at the upper site. Population densities at the upper site, nevertheless, remained high. 3. Plant measurements were good predictors of insect density, often explaining up to 73% of the variance in abundance among plants at a given site. 4. Sets of four plant characters identified by best subsets regression were better predictors of psyllid density and development than single factors, although differences were often not great and the combinations of characters selected by multiple regression sometimes differed from the best single predictors. 5. Best single predictors of psyllid density on catkins were measurements of plant size, particularly height, length, and basal stem diameter. Shoot density and catkin phenology were occasionally important but plant isolation and prior growth performance were less important. 6. By contrast with density, age structure of the psyllid population was predicted best from plant phenological measurements, notably catkin phenology.     

Microgeographic genetic structure and intraspecific parasitism in the ant Leptothorax nylanderi

1. Genetic colony structure of the small central European ant Leptothorax nylanderi is affected strongly by ecological constraints such as nest site availability and intraspecific social parasitism. 2. Although L. nylanderi is generally monogynous and monandrous, more than a quarter of all nests collected in a dense population near Würzburg, Germany, contained several matrilines. As shown by microsatellite analysis, the average nest‐mate relatedness in these nests was 0.20. Genetically heterogeneous nests arise from nest take‐over by alien colonies or founding queens, a result of severe competition for nest sites. 3. In summer, more than one‐third of all colonies inhabited several nest sites at a time. Polydomy appears to be rather limited, with two or three nests belonging to a single polydomous colony. 4. Queens appear to dominate male production; only a small fraction (8%) of males was definitively not progeny of the queen present but might have been worker progeny or offspring of another queen. 5. Strong evidence for heterozygote deficiency was found and a total of nine diploid males was discovered in two colonies. These findings suggest deviation from random mating through small, localised nuptial flights.