A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

Planning an adaptive numerical classification

Summary While numerical methods of classification seek to strictly formalise one part of the classificatory process, a human classifier uses a variety of different approaches to obtain a satisfactory organisation of data. In this paper some means of increasing the flexibility of numerical methods are discussed, in particular the possible uses of the taxonomic hierarchy. It is first necessary to show that higher taxonomic units contain ecologically interesting information. Then, using a two parameter classification method a means of progressing from higher to lower taxonomic units, during analysis and in a data dependent manner, is outlined. A similar procedure is possible with nested samples. However, since the value of a classification resides in its ecological interpretation, an automatic classification requires some means of ascribing meanings to classes. While such a semantic analysis seems theoretically possible, its practical attainment presents considerable difficulties.Contribution to the Symposium on Plant species and plant communities, held at Nijmegen, 11–12 November 1976, on the occasion of the 60th birthday of Professor Victor Westhoff.     

Book reviews

Editing of community data matrices is complementary to analyzing data by multivariate techniques of classification and ordination in the overall task of data analysis. A computer program, DATAEDIT, is described that can perform numerous editing functions, including data transformation, deletion of certain species or samples, deletion of rare species, deletion of outliers, separation of disjunet sample groups, reordering of the species or samples of a data matrix, and the formation of composite samples or of sample subsets. DATAEDIT can use the information in a nonhierarchical or hierarchical classification, and includes its own internal routine for reciprocal averaging ordination.We appreciate valuable suggestions from the late Robert H. Whittaker, and from Philip Dixon, David Hieks, Laura Huenneke, Linda Olsvig-whittaker, and Mark Wilson. Mark O. Hill kindly supplied a fast subroutine for reciprocal averaging.     

Réflexions critiques sur l'écologieet la systématique des Lingules actuelles et fossiles

New topics on ecology and systematics of recent and fossil Lingulids lead to an obvious revision of our knowledges on this zoological group. At first, the recent species need systematics and taxonomy on the bases of new described specific criteria (as, morphology of deltidial areas, muscle disposition); the results are briefly indicated. But, in fossil species, disorder and disparity of used characteristics are emphasized.The general conceiving on ecology of Lingulids are reviewed and discussed, especially on bathymetry and salinity; sediment and oxygenation conditions; taphocoenosis and lingulid «communities. On recent species, all these points are also studied, especially some ecological requirements (salinity, bathymetry, grain size), and mechanism of burrowing ability, burrow living positions in the sediments, as shell preservations after death and fossilization, to facilitate the paleobiotope interpretations. Recent animals are euryhalin, surviving at salinities from about 13 to 42‰; they could be considered as well adapted to waters with strong salinity fluctuations. They show preference to fine sand bottoms (lowest particle size about 40–60 μm). Their bathymetric distribution occurs between 0 and about 500 m (Lingula especially between 5–50 m; Glottidia 15–70 m). The isotherms 8–10°C seem to restrict their geographical and bathymetric distribution.Therefore, some post-palaeozoic lingulid bedsare studied or redescribed on the bases of the above discussed characteristics, and new interpretations on the environmental situation are given (Trias of Vosges Mountains; Oligocene from Japan; Eocene of London Basin). More caution must be used in study of fossil Lingulids that are not especially animals living in infralittoral bottoms with low salinity and deficient oxygenation, as generally accepted.     

Alleviation of Both Water and Nutrient Limitations is Necessary to Accelerate Ecological Restoration of Waste Rock Tips

Hard rock quarries are commonly located close to national parks and special areas of conservation and are generally regarded as visually intrusive. Consequently, restoration strategies that effectively accelerate natural plant regeneration processes are required. Slate waste tips present extreme conditions for plant establishment with multiple potential limiting factors (e.g., lack of organic matter, nutrients, and poor water retention). In this study, we investigated ecological strategies to accelerate natural regeneration at the largest slate quarry in Europe. A field experiment was conducted to assess ecosystem restoration using a contrasting set of native woody species. Treatments included amendments of waste tips with: polyacrylamide gel to increase water‐holding capacity; mineral fertilizer to increase nutrient supply; and two treatments that increased both (organic waste or boulder clay addition). Ecosystem recovery was evaluated through above‐ and below‐ground productivity (plant and microbial, respectively) and soil analyses. Neither increasing nutrient supply (with mineral fertilizer) nor water‐holding capacity (with polyacrylamide gel) was sufficient, alone, to improve plant establishment. However, both boulder clay and organic waste amendment significantly enhanced plant growth. There was a marked positive interaction in the effects on tree growth of the amendment with organic waste and boulder clay. Large interactions occurred between tree species and substrate amendments. The growth of N₂‐fixing species was strongly favored over non‐fixers where there was no addition of material increasing soil nitrogen supply, whereas the growth advantage of pioneer species over non‐pioneers was greatest with fertilizer, organic waste, or clay additions. Organic waste addition had the greatest positive impact on soil processes.     

Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)

? Premise of the study: Microsatellite markers were developed for the population genetic analyses of the neotropical tree Dipteryx alata (Fabaceae). ? Methods and Results: Microsatellites were developed from a genomic shotgun library. Polymorphism at each microsatellite loci was analyzed based on 94 individuals from three populations. Eight loci amplified successfully and presented one to 10 alleles, and expected heterozygosities ranged from 0.097 to 0.862. Four loci also amplified in Pterodon emarginatus and presented similar polymorphism. ? Conclusion: The eight microsatellite primer pairs are potentially suitable for population genetic studies and successfully amplified in another Fabaceae species.     

Poplar genomics is getting popular: the impact of the poplar genome project on tree research

Trees, due to their long life-span, have characteristics that distinguish them from annual, herbaceous plants. It is likely that many of these properties are based on a tree-specific genetic foundation. The U.S. Department of Energy initiated a genome-sequencing project for Populus, a model perennial plant. Through international collaboration and input to the sequencing effort, the annotated whole genome sequence of Populus trichocarpa will be released to the public in early 2004. This genomic resource will, for the first time, allow comparison between a perennial and an annual plant on a whole genome basis and therefore provide clues for molecular research on tree-specific questions like dormancy, development of a secondary cambium, juvenile-mature phase change, or long-term host-pest interactions. The approximately 520 Mbp of annotated genomic sequence will complement and expand the knowledge provided so far by the 125,000 ESTs from poplar that are available in public databases. This article introduces the international poplar research programmes and points out the significance of the poplar genome project for plant research.