Distribution maps

Abstract

There are two groups of Pellia peroxidase isozyme phenotypes, one composed of P. epiphylla, P. neesiana and P. borealis, the other of P. endiviifolia from Europe, P. endiviifolia from Japan and P. megaspora. The phenotypes within the second group differ supporting the suggestion that there are three taxa present.     

Ecological vegetation maps

On ecological vegetation maps, the distribution of vegetation is related to one or more features of the environment. Tolerance, competition, map scales and the environment are discussed with regard to their bearing on the geographical distribution of phytocenoses and their portrayal on maps. There are two types of ecological vegetation maps: those relating the vegetation to one environmental quality, and those with two or more such qualities. The interpretation of ecological vegetation maps is relatively simple when plant communities are related to a single quality of the biotope and difficult but usually more useful when related to several qualities. Perfection is not possible but can be approached asymptotically.     

CEPH maps.

There are CEPH genetic maps on each homologous human chromosome pair. Genotypes for these maps have been generated in 88 laboratories that receive DNA from a reference panel of large nuclear pedigrees/families supplied by the Centre d'Etude du Polymorphisme Humain. These maps serve as useful tools for the localization of both disease genes and other genes of interest.     

Self-organizing semantic maps

Self-organized formation of topographic maps for abstract data, such as words, is demonstrated in this work. The semantic relationships in the data are reflected by their relative distances in the map. Two different simulations, both based on a neural network model that implements the algorithm of the selforganizing feature maps, are given. For both, an essential, new ingredient is the inclusion of the contexts, in which each symbol appears, into the input data. This enables the network to detect the logical similarity between words from the statistics of their contexts. In the first demonstration, the context simply consists of a set of attribute values that occur in conjunction with the words. In the second demonstration, the context is defined by the sequences in which the words occur, without consideration of any associated attributes. Simple verbal statements consisting of nouns, verbs, and adverbs have been analyzed in this way. Such phrases or clauses involve some of the abstractions that appear in thinking, namely, the most common categories, into which the words are then automatically grouped in both of our simulations. We also argue that a similar process may be at work in the brain.On leave from: Institut für Physik, Technische Universität München, James-Franck-Strasse, D-8046 Garching, FRG     

AFLP maps of Petunia hybrida: building maps when markers cluster

AFLP mapping in Petunia hybrida was undertaken with the intention of building a high-density genetic map suitable for applications such as map-based gene cloning. In total five maps were constructed from two mapping populations, with placement of more than 800 markers. Despite the large number of markers the resulting map is roughly ten-fold smaller than those of other plant species, including the closely related tomato. Low levels of recombination are reflected in clusters of tightly linked markers, both AFLPs and RFLPs, in all the maps. Clustering patterns vary between mapping populations, however, such that loci tightly linked in one population may be separable in another. Combined with earlier reports of aberrant meiotic pairing and recombination, our results suggest that, for species like petunia, map-based cloning may be more complex than in model species such as arabidopsis and tomato.     

Correlation between thermal stability maps and genetic maps of double-stranded DNAs

The positional correlation of boundaries of cooperatively melting regions with boundaries of genes and with cleavage sites of restriction enzymes are statistically examined for phiX174, G4, fd, SV40, BKV, and polyoma DNAs. A statistically significant correlation does exist in the case of gene boundaries, but none is detected for cleavage sites.     

Brazilian vegetation on maps

The development and current status of mapping the vegetation of Brazil is discussed. This includes the manner of portraying the vegetation on maps, especially with regard to physiognomy and structure, the floristic composition and ecological relations. A slow beginning has given way to a rapid though uneven development. Recent government efforts tend to correct this.     

Counting on comparative maps

Comparative maps record the history of chromosome rearrangements that have occurred during the evolution of plants and animals. Effective use of these maps in genetic and evolutionary studies relies on quantitative analyses of the patterns of segment conservation. We review the analytical methods that have been developed for characterizing these maps and evaluate their application to existing comparative maps mainly for plants and animals.     

Unfolding large-scale maps.

This is an account of the development and use of genetic maps, from humble beginnings at the hands of Thomas Hunt Morgan, to the sophistication of genome sequencing. The review charters the emergence of molecular marker maps exploiting DNA polymorphism, the renaissance of cytogenetics through the use of fluorescence in situ hybridisation, and the discovery and isolation of genes by map-based cloning. The historical significance of sequencing of DNA prefaces a section describing the sequencing of genomes, the ascendancy of particular model organisms, and the utility and limitations of comparative genomic and functional genomic approaches to further our understanding of the control of biological processes. Emphasis is given throughout the treatise as to how the structure and biological behaviour of the DNA molecule underpin the technological development and biological applications of maps.     

Landmark maps for honeybees

Experiments by Fabre (1915), Thorpe (1950), Chmurzynski (1964), and most recently Gould (1986) suggest that insects have maps of their terrain which enable them to find their way directly to a goal when they are displaced several hundred metres from it. This paper discusses what might constitute an insect's map in terms of a two-part computational model. The first part describes how an insect reaches a goal when the insect is sufficiently close that it can see some of the landmarks which are visible from the goal. The second part considers the problem of navigating when there is no similarity between the view from the release-site and the view from the goal.We start from a model designed to explain how a bee might return to a goal using a two-dimensional snapshot of the landscape seen from the goal (Collett and Cartwright 1983). To guide its return, the model bee continuously compares its snapshot with its current retinal image and moves so as to reduce the discrepancy between the two. Bees can only be guided in the right direction by the difference between current retinal image and snapshot when there is some resemblance between the two. In a realistically cluttered world, snapshot and retinal image become very dis-similar only a short distance from the goal.To increase the distance from which a model bee can return, the bee takes two snapshots at the goal. The first snapshot excludes landmarks near to the goal and the second snapshot includes them. With close landmarks filtered from both snapshot and retinal image, the match between the two deteriorates gradually as the bee moves away from the goal. A model bee using a filtered snapshot and image finds its way back to the neighbourhood of the goal from a relatively long distance (Fig. 2). The bee then switches to the second snapshot and is guided to the precise spot by its memory of the close landmarks.For longer range guidance, the model bee is equipped with an album of snapshots, each taken at a different location within the terrain. Linked to each snapshot is a vector encoding the distance and direction from the place where the snapshot was taken to the hive. When the bee is displaced to a new position, it selects the snapshot which best matches its current image and follows the associated home-vector back to the hive (Fig. 3). Such a hive-centred map can also be used to devise novel routes to places other than the hive. For instance, a bee can reach a foraging site from anywhere in its terrain by adding the home-vector recalled at the starting position to a vector specifying the distance and direction of the foraging site from the hive. The sum of these two vectors defines a direct trajectory to the foraging site.     

Building chromosome-wide LD maps

SUMMARY: BMapBuilder builds maps of pairwise linkage disequilibrium (LD) in either two or three dimensions. The optimized resolution allows for graphical display of LD for single nucleotide polymorphisms (SNPs) in a whole chromosome. AVAILABILITY: The program is coded in Java, which runs on all relevant operating systems, including Windows, Mac and Unix/Linux, and is available from http://bios.ugr.es/BMapBuilder.     

Depositing electron microscopy maps

A meeting was held at the European Bioinformatics Institute (EBI) in Hinxton, United Kingdom to discuss recent progress in the development of EMD, a database for maps determined by electron microscopy that is now integrated with MSD, the macromolecular structure database at EBI. This meeting of representatives of many of the major image processing groups in electron microscopy also discussed possible software developments that would ease the documentation and deposition of such datasets. The meeting concluded with a strong endorsement of map deposition in electron microscopy and its linkage with the family of archival databases in biomedical research.     

Construction of restriction maps

A computer program is described, which constructs maps of restrictionendonuclease cleavage sites in linear or circular DNA molecules,given the fragment lengths in single and double digestions withtwo enzymes. The algorithm is based upon a partition methodand a very simple rule to chain fragments. The program is writtenin Prolog II. Received on July 28, 1987; accepted on December 31, 1987     

Comparison of wheat physical maps with barley linkage maps for group 7 chromosomes

Comparative genetic maps among the Triticeae or Gramineae provide the possibility for combining the genetics, mapping information and molecular-marker resources between different species. Dense genetic linkage maps of wheat and barley, which have a common array of molecular markers, along with deletion-based chromosome maps of Triticum aestivum L. will facilitate the construction of an integrated molecular marker-based map for the Triticeae. A set of 21 cDNA and genomic DNA clones, which had previously been used to map barley chromosome 1 (7H), were used to physically map wheat chromosomes 7A, 7B and 7D. A comparative map was constructed to estimate the degree of linkage conservation and synteny of chromosome segments between the group 7 chromosomes of the two species. The results reveal extensive homoeologies between these chromosomes, and the first evidence for an interstitial inversion on the short arm of a barley chromosome compared to the wheat homoeologue has been obtained. In a cytogenetically-based physical map of group 7 chromosomes that contain restriction-fragment-length polymorphic DNA (RFLP) and random amplified polymorphic DNA (RAPD) markers, the marker density in the most distal third of the chromosome arms was two-times higher than in the proximal region. The recombination rate in the distal third of each arm appears to be 8–15 times greater than in the proximal third of each arm where recombination of wheat chromosomes is suppressed.     

Guidelines for genotyping in genomewide linkage studies: single-nucleotide-polymorphism maps versus microsatellite maps

Genomewide linkage scans have traditionally employed panels of microsatellite markers spaced at intervals of approximately 10 cM across the genome. However, there is a growing realization that a map of closely spaced single-nucleotide polymorphisms (SNPs) may offer equal or superior power to detect linkage, compared with low-density microsatellite maps. We performed a series of simulations to calculate the information content associated with microsatellite and SNP maps across a range of different marker densities and heterozygosities for sib pairs (with and without parental genotypes), sib trios, and sib quads. In the case of microsatellite markers, we varied density across 11 levels (1 marker every 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cM) and marker heterozygosity across 6 levels (2, 3, 4, 5, 10, or 20 equally frequent alleles), whereas, in the case of SNPs, we varied marker density across 4 levels (1 marker every 0.1, 0.2, 0.5, or 1 cM) and minor-allele frequency across 7 levels (0.5, 0.4, 0.3, 0.2, 0.1, 0.05, and 0.01). When parental genotypes were available, a map consisting of microsatellites spaced every 2 cM or a relatively sparse map of SNPs (i.e., at least 1 SNP/cM) was sufficient to extract most of the inheritance information from the map (>95% in most cases). However, when parental genotypes were unavailable, it was important to use as dense a map of markers as possible to extract the greatest amount of inheritance information. It is important to note that the information content associated with a traditional map of microsatellite markers (i.e., 1 marker every ~10 cM) was significantly lower than the information content associated with a dense map of SNPs or microsatellites. These results strongly suggest that previous linkage studies that employed sparse microsatellite maps could benefit substantially from reanalysis by use of a denser map of markers.