Molecular prospecting for cryptic species of nematodes: mitochondrial DNA versus internal transcribed spacer

DNA sequence divergence at internal transcribed spacer regions (ITS-1 and ITS-2) was compared with divergence at mitochondrial cox1 or nad4 loci in pairs of congeneric nematode species. Mitochondrial sequences accumulate substitutions much more quickly than internal transcribed spacer, the difference being most striking in the most closely related species pairs. Thus, mitochondrial DNA may be the best choice for applications in which one is using sequence data on small numbers of individuals to search for potential cryptic species. On the other hand, internal transcribed spacer remains an excellent tool for DNA diagnostics (quickly distinguishing between known species) owing to its lower level of intraspecific polymorphism.     

Estimating the number of species in a stochastic abundance model

Consider a stochastic abundance model in which the species arrive in the sample according to independent Poisson processes, where the abundance parameters of the processes follow a gamma distribution. We propose a new estimator of the number of species for this model. The estimator takes the form of the number of duplicated species (i.e., species represented by two or more individuals) divided by an estimated duplication fraction. The duplication fraction is estimated from all frequencies including singleton information. The new estimator is closely related to the sample coverage estimator presented by Chao and Lee (1992, Journal of the American Statistical Association 87, 210-217). We illustrate the procedure using the Malayan butterfly data discussed by Fisher, Corbet, and Williams (1943, Journal of Animal Ecology 12, 42-58) and a 1989 Christmas Bird Count dataset collected in Florida, U.S.A. Simulation studies show that this estimator compares well with maximum likelihood estimators (i.e., empirical Bayes estimators from the Bayesian viewpoint) for which an iterative numerical procedure is needed and may be infeasible.     

Thirteen years of wetland vegetation succession following a permanent drawdown,Myrkdalen Lake,Norway

Myrkdalen Lake in Western Norway was subjected to a 1.4 mdrawdown in June 1987. Plant establishment and vegetation succession on theexposed sediments of a fluvial delta plain was monitored through 2000. Theinvestigated area extended from the original Equisetumfluviatile zone to the new lake edge. The substrate was homogeneousand consisted mainly of minerogenous fluvial sediments. Vegetation data weresampled within continuous quadrats along transects perpendicular to the shore,and they dropped 93 cm in elevation. Detrended CorrespondenceAnalysis and Canonical Correspondence Analysis confirmed that time sincedrawdown and elevation of the quadrats appeared to be ofnearly equal importance in explaining succession. Plant establishment was rapidon the exposed sediments due to a seed bank and to rapid invasion of plants.Thesuccession includes both floristic change as a function of time and a spatialseparation in relation to the water level. The species succession was marked bya growth form progression: mosses and annuals non-clonal perennialsclonal perennials. After one month, the annual Subulariaaquatica and small acrocarpous mosses dominated the site. Dominancethen shifted to Deschampsia cespitosa, Juncus filiformis, Blasiapusilla and Polytrichum commune. Subsequentlythere was an increase of Carex vesicaria in the lower zoneand Calamagrostis purpurea in the upper zone,while Phalaris arundinacea was common over most of theelevational gradient. Equisetum declined where it haddominated before drawdown, but it expanded gradually towards the new shoreline.The vegetation remained dynamic after 13 years and it is not considered to beinequilibrium with the new environmental gradient yet. However, annual changesmeasured by DCA scores have slowed and two vegetation zones have developed. Themajor vegetational differences along the elevational gradient can be explainedby the height of the mean June water limit. This example of species turnover inspace and time may be a model for other successions that occur along a stronggradient.     

Relationships among species inCarex sect.Phyllostachys (Cyperaceae) based on allozyme divergence

Allozyme variation was examined inCarex sect.Phyllostachys (Cyperaceae) to provide insight into phylogenetic relationships hypothesized in an earlier study and to determine the degree of genetic differentiation within and between taxa. Genetic identity values are concordant with the morphological differences found between species. The lowest values are found between species with the greatest morphological dissimilarity. Conversely, the highest values are associated with species pairs distinguished by relatively few morphological differences. Conspecific populations possess high genetic identities, although interpopulation differentiation has characterized the evolutionary history of some species. Geographic patterning is also evident within species, with geographically proximate populations often having the highest identity values. Phylogenetic trees produced using different cladistic methods were poorly supported and varied in their depiction of relationships among species. One cladogram produced using presence/absence allelic data is more or less congruent with a topology recovered from an earlier analysis utilizing molecular and morphological data. The wide- and narrow-scaled clades are maintained as are the sister species pairsC. backii/C. saximontana, C. basiantha/C. superata, andC. jamesii/C. juniperorum. Contrary to the finding of our previous study, however,C. willdenowii is aligned withC. jamesii/C. juniperorum.     

Monitoring microbial aeroflora using vegetable waste media: an ecological aspect

For isolation of aeromicroflora in ecologically different zones, a liquid vegetable waste, deproteinised leaf juice (DLJ) was used instead of usual media. DLJ samples from three different plants, cowpea (Vigna sinensis), turnip (Brassica campestris) and radish (Raphanus sativus), were used in order to determine their efficiency as potential growth media for different types of microbes. Four different ecological zones of West Bengal, India were selected to study the aeromicroflora. The zones were as follows: (i) densely populated and industrially polluted Calcutta (CAL); (ii) plateau region of western part of the state (WEST); (iii) Terai region of Northern Bengal (TER); (iv) sandy coastal zone of Midnapore district of Southern Bengal (SB). Each zone was subdivided into three subzones. The variation in population of fungi, bacteria and actinomycetes among these zones was studied. The relative abundance and species diversities of microbes were noted. The study indicates that pollution and ecological diversity both play important roles in controlling the above two factors.     

Prion's Progress: Patterns and Rates of Molecular Evolution in Relation to Spongiform Disease

Modification of the cellular prion protein has been correlated with the acquisition of several neurodegenerative diseases, including kuru, scrapie, bovine spongiform encephalopathy (BSE), and Creutzfeldt–Jakob disease (CJD). Sequence conservation and amino acid identity are known to influence the efficacy of interspecific transmission. We analyzed patterns of interspecific genetic variation with a view toward identifying features related to disease transmission. The reconstructed gene trees and amino acid tree were compared with the species tree, and all discordances observed were related to the species barrier of disease transmission. The rates of synonymous substitution, nonsynonymous substitution, and nucleotide content were determined for the protein-coding gene. Substitutions implicated in each of the prion diseases were found to occur in regions of the protein that are least variable across all species—opposite to the pattern of variability expected from interaction with an infectious pathogen. Amino acid residues related to the species barrier form a single cluster associated with the first alpha-helical domain of the protein. Residues related to sporadic and hereditary human prion disease form two separate clusters, associated with the second and third alpha-helical domains. Taken together, these results are consistent with the view that prion diseases arise from accidents in protein folding, rather than infection with an undiscovered virus-like particle. We speculate that the differences in disease phenotype between transmissable and hereditary forms could result from interactions between different parts of the protein during propagation. Received: 18 April 1997 / Accepted: 17 October 1997     

Hippopotamus incognitus nov. sp., un hippopotame (Mammalia,Artiodactyla) du Pléistocène d'Europe occidentale

The new species Hippopotamus incognitus is recognized for the first time in the Middle and Upper Pleistocene of Western Europe. It was confused either with the Lower Middle Pleistocene H. major or the recent H. amphibius. H. incognitus is quite different from H. major with a lesser size, a lower skull, more slender limb bones and lenghtened metapodials. The size is bigger, the cheek teeth more bulky and the proportions of the limb bones different than in H. amphibius. These three species correspond to three distinct phylogenetical lineages originating in the same african tetraprotodont Pleistocene stock.     

Plot shape effects on plant species diversity measurements

Abstract. Question: Do rectangular sample plots record more plant species than square plots as suggested by both empirical and theoretical studies? Location: Grasslands, shrublands and forests in the Mediterranean‐climate region of California, USA. Methods: We compared three 0.1‐ha sampling designs that differed in the shape and dispersion of 1‐m² and 100‐m² nested subplots. We duplicated an earlier study that compared the Whittaker sample design, which had square clustered subplots, with the modified Whittaker design, which had dispersed rectangular subplots. To sort out effects of dispersion from shape we used a third design that overlaid square subplots on the modified Whittaker design. Also, using data from published studies we extracted species richness values for 400‐m² subplots that were either square or 1:4 rectangles partially overlaid on each other from desert scrub in high and low rainfall years, chaparral, sage scrub, oak savanna and coniferous forests with and without fire. Results: We found that earlier empirical reports of more than 30% greater richness with rectangles were due to the confusion of shape effects with spatial effects, coupled with the use of cumulative number of species as the metric for comparison. Average species richness was not significantly different between square and 1:4 rectangular sample plots at either 1‐ or 100‐m². Pairwise comparisons showed no significant difference between square and rectangular samples in all but one vegetation type, and that one exhibited significantly greater richness with squares. Our three intensive study sites appear to exhibit some level of self‐similarity at the scale of 400 m², but, contrary to theoretical expectations, we could not detect plot shape effects on species richness at this scale. Conclusions: At the 0.1‐ha scale or lower there is no evidence that plot shape has predictable effects on number of species recorded from sample plots. We hypothesize that for the mediterranean‐climate vegetation types studied here, the primary reason that 1:4 rectangles do not sample greater species richness than squares is because species turnover varies along complex environmental gradients that are both parallel and perpendicular to the long axis of rectangular plots. Reports in the literature of much greater species richness recorded for highly elongated rectangular strips than for squares of the same area are not likely to be fair comparisons because of the dramatically different periphery/area ratio, which includes a much greater proportion of species that are using both above and below‐ground niche space outside the sample area.     

AGLAOTHAMNION WESTBROOKIAE SP. NOV. (RHODOPHYTA), A SPECIES PREVIOUSLY CONFUSED UNDER THE NAME CALLITHAMNION BYSSOIDES1

We propose the name Aglaothamnion westbrookiae sp. nov. for the alga referred to as Callithamnion byssoides Arnott ex Harvey in Hooker by Edwards and others from the eastern coast of North America. A. westbrookiae differs from the European A. byssoides (Arnott ex Harvey in Hooker) L'Hardy-Halos et Rueness (= C. byssoides, type locality Cornwall, England) by having fronds branched pinnately, not spirally as in A. byssoides. The gonimolobes in A. westbrookiae are rounded, not conical and lobed as in A. byssoides. The spermatangia are in dense hemispherical clusters whereas in A. byssoides the equivalent structure is elongated. The two taxa are sexually incompatible. Aglaothamnion westbrookiae also differs in morphological features and is not interfertile with A. pseudobyssoides from France. We suggest that A. westbrookiae and A. feldmanniae Halos from Europe are similar in most features, including the involucral branches subtending carposporophytes. However, cross-ability tests demonstrated that they are not interfertile, and differences in vegetative structure suggest that they should be treated as two different species.     

The role of seed rain in determining the assembly of a cliff community

Abstract. Cliff-face communities of the Niagara Escarpment in Ontario, Canada, are dominated by long-lived Thuja occidentalis and a consistent assemblage of other plants. Our objective was to determine whether seed rain plays a role in determining why these species are dominant. Seed rain was collected from the cliff face and from the surrounding plateau-and talus communities at two sites over a 2-yr period in order to compare these three adjacent, but different communities. Multivariate Discriminant Analysis first separated the two sites: primarily due to the importance of Betula papyrifera at one site. The three community types were also separated, although there was still substantial overlap. There was a predictable array of species associated with each community although the seed rain on the cliff faces differed slightly. When characterized by univariate ANOVAs, seed rain in the cliff faces and plateaus had a lower species richness and lower total seed density than the talus sites. Seeds of two of the 11 species analysed individually showed an influence of habitat type on their number. Seed morphology did not influence patterns of seed rain. Finally, there was no correlation between the seed rain and above-ground vegetation in any of the communities. We conclude that the seed rain patterns that exist do not act to filter the plants that form the mature vegetation of cliffs.