Scale and species numbers

One of the main tasks confronting community ecologists is to explain why a particular site harbours a certain number of species. The site might range from a drop of water to the whole Earth, and the species might be drawn from a very restricted taxon or include all living organisms. The common problem, however, is to understand the relative importance of speciation and extinction and, more locally, of immigration and loss. Speciation is the ultimate motor driving biodiversity and ecologists need to know the factors influencing rates of speciation, and whether there is a feedback, positive or negative, between species numbers and the generation of new taxa. However, the relative importance of speciation and other factors determining species numbers varies crucially across different scales of enquiry. Here, we explore some of these issues as we move from a macro- to microscale perspective, focusing on a limited number of studies that we believe make important advances in the field.     

Comparison of species ordinations resulting from alternative indices of interspecific association and different numbers of included species

Summary Several measures of interspecific association are compared. Dispersion and covariance are limited in value because they respond to the commonness of the species compared. Correlation is not so limited but it responds to discrepancies in commonness among the species. The practical result of these relationships between commonness and association is that only the most common species can occupy periferal positions in a species ordination. Rare species are relegated to positions near the center not on the basis of their phytosociological pattern but simply because of their rarity. Both Cole's index of association and the tetrachoric correlation overcome the problem imposed by the relationship between ordination position and species commonness and they both produce very similar results. The effect of differing numbers of species on the ordination configuration is examined using both Pearson's correlation and Cole's index. The basic pattern of the ordination is set with the first few species when Cole's index is used, however, since rare species are given more weight in the analysis with this index, the addition of several very rare species can change the configuration of the ordination.Nomenclature of species is given in Table 1.Research supported by the Eastern Deciduous Forest Biome Project, US-IBP, funded by the National Science Foundation under Interagency Agreement AG-199, BMS69-01147 A09 with the Energy Research and Development Administration — Oak Ridge National Laboratory. Research also supported by the U.S. Energy Research and Development Administration under contract with the Union Carbide Corporation. Contribution No. 240 from the EDFB, US-IBP. Publication No. 790. Environmental Sciences Division, ORNL.     

A novel swine sex-linked marker and its application across different mammalian species

Transgenic Research - Advances in genome editing tools have reduced barriers to the creation of animal models. Due to their anatomical and physiological similarities to humans, there has been a...     

Variations in leaf respiration across different seasons for Mediterranean evergreen species

Leaf respiration (R _L) of evergreen species co-occurring in the Mediterranean maquis developing along the Latium coast was analyzed. The results on the whole showed that the considered evergreen species had the same R _L trend during the year, with the lowest rates [0.83 ± 0.43 μmol(CO₂) m^?2 s^?1, mean value of the considered species] in winter, in response to low air temperatures. Higher R _L were reached in spring [2.44 ± 1.00 μmol(CO₂) m^?2 s^?1, mean value] during the favorable period, and in summer [3.17 ± 0.89 μmol(CO₂) m^?2 s^?1] during drought. The results of the regression analysis showed that 42% of R _L variations depended on mean air temperature and 13% on total monthly rainfall. Among the considered species, C. incanus, was characterized by the highest R _L in drought [4.93 ± 0.27 μmol(CO₂) m^?2 s^?1], low leaf water potential at predawn (Ψ_pd= ?1.08 ± 0.18 MPa) and midday (Ψ_md = ?2.75 ± 0.11 MPa) and low relative water content at predawn (RWC_pd = 80.5 ± 3.4%) and midday (RWC_md = 67.1 ± 4.6%). Compared to C. incanus, the sclerophyllous species (Q. ilex, P. latifolia, P. lentiscus, A. unedo) and the liana (S. aspera), had lower R _L [2.72 ± 0.66 μmol(CO₂) m^?2 s^?1, mean value of the considered species], higher RWC_pd (91.8 ± 1.8%), RWC_md (82.4 ± 3.2%), Ψ_pd (?0.65 ± 0.28 MPa) and Ψ_md (?2.85 ± 1.20 MPa) in drought. The narrow-leaved species (E. multiflora, R. officinalis, and E. arborea) were in the middle. The coefficients, proportional to the respiration increase for each 10°C rise (Q₁₀), ranging from 1.49 (E. arborea) to 1.98 (A. unedo) were indicative of the different sensitivities of the considered species to air temperature variation.     

GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers

Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. To compare experiments that are performed on these different platforms, array probes and sequence tags need to be linked. An additional challenge is cross-referencing between species, to compare human profiles with those obtained in a mouse model, for example. We have developed the web-based search engine GeneHopper to link different expression resources based on UniGene clusters and HomoloGene orthologs databases of the National Center for Biotechnology Information (NCBI).     

Environmental filtering of species with different functional traits into plant assemblages across a tropical coniferous-broadleaved forest ecotone

Background and aims

Ecotones between coniferous and broadleaved forests in tropical regions are poorly understood. Our aim was to understand community assembly across the ecotones by integrating changes in both plant functional traits and environmental factors.

Methods

The coniferous, ecotone, and broadleaved zones along each of the 15 investigation transects were discerned and surveyed. We measured eight functional traits of 174 woody species and 10 environmental factors along transects across the ecotones. We assessed between-site differences by using ANOVA, and correlations between functional traits and the environmental factors by RDA ordination.

Results

With the variation of vegetation zones from coniferous through the ecotone to broadleaved, the functional traits of plants at the community level changed in accordance with the changes in soil and light regimes. The low soil nutrients and low soil water in the coniferous zone were the major constraints for most lowland rain forest species with acquisitive traits, while high soil nutrients, high soil water and low light in the broadleaved zone had strong filtering effects on the conifer and tropical monsoon rainforest species with conservative traits.

Conclusions

The soil and light conditions were the major determinants for the functional community structure of the vegetation types across the tropical coniferous and broadleaved forest ecotone.     

Phylogenetic relationships amongPinus species (Pinaceae) inferred from different numbers of 6PGDH loci

Electrophoretic examination of variousPinus species from both subgenera revealed that several taxa differ in the number of loci that control the enzyme system 6-phosphogluconate dehydrogenase (6PGDH). Based on inheritance analyses and published data, it was established that all species of subg.Pinus possess only two 6PGDH loci, whereas all stone pines of subg.Strobus exhibit four controlling loci. In order to trace the phylogenetic links at which one or two gene duplications occurred during pine evolution, several species of subsect.Strobi (sectionStrobus) and two species of sect.Parrya were additionally investigated. Based on conclusions about the uniqueness of gene duplications and the different numbers of 6PGDH loci, a phylogenetic tree of the pine taxa was constructed. This tree shows some new features not recognized in earlier studies and supports several novel assignments postulated in very recent pine classifications.     

Electrophoretic karyotypes and chromosome numbers in Candida species

The electrophoretic karyotypes of five Candida albicans isolates and of five other Candida species have been determined, using orthogonal field alternating gel electrophoresis (OFAGE). None of the C. albicans isolates had the same electrophoretic karyotype. By comparing all five strains, we arrived at a chromosome number of nine to ten, but since the organism is diploid, we cannot distinguish genetically different chromosomes from homologues which resolve. We determined minimal chromosome numbers of 9 for Candida stellatoidea, 10 for C. glabrata and 6 for C. guilliermondii.     

Tall fescue EST-SSR markers with transferability across several grass species

Tall fescue (Festuca arundinacea Schreb.) is a major cool season forage and turf grass in the temperate regions of the world. It is also a close relative of other important forage and turf grasses, including meadow fescue and the cultivated ryegrass species. Until now, no SSR markers have been developed from the tall fescue genome. We designed 157 EST-SSR primer pairs from tall fescue ESTs and tested them on 11 genotypes representing seven grass species. Nearly 92% of the primer pairs produced characteristic simple sequence repeat (SSR) bands in at least one species. A large proportion of the primer pairs produced clear reproducible bands in other grass species, with most success in the close taxonomic relatives of tall fescue. A high level of marker polymorphism was observed in the outcrossing species tall fescue and ryegrass (66%). The marker polymorphism in the self-pollinated species rice and wheat was low (43% and 38%, respectively). These SSR markers were useful in the evaluation of genetic relationships among the Festuca and Lolium species. Sequencing of selected PCR bands revealed that the nucleotide sequences of the forage grass genotypes were highly conserved. The two cereal species, particularly rice, had significantly different nucleotide sequences compared to the forage grasses. Our results indicate that the tall fescue EST-SSR markers are valuable genetic markers for the Festuca and Lolium genera. These are also potentially useful markers for comparative genomics among several grass species.Electronic Supplementary Material Supplementary material is available for this article at .     

Protein-protein interactions more conserved within species than across species

Experimental high-throughput studies of protein-protein interactions are beginning to provide enough data for comprehensive computational studies. Today, about ten large data sets, each with thousands of interacting pairs, coarsely sample the interactions in fly, human, worm, and yeast. Another about 55,000 pairs of interacting proteins have been identified by more careful, detailed biochemical experiments. Most interactions are experimentally observed in prokaryotes and simple eukaryotes; very few interactions are observed in higher eukaryotes such as mammals. It is commonly assumed that pathways in mammals can be inferred through homology to model organisms, e.g. the experimental observation that two yeast proteins interact is transferred to infer that the two corresponding proteins in human also interact. Two pairs for which the interaction is conserved are often described as interologs. The goal of this investigation was a large-scale comprehensive analysis of such inferences, i.e. of the evolutionary conservation of interologs. Here, we introduced a novel score for measuring the overlap between protein-protein interaction data sets. This measure appeared to reflect the overall quality of the data and was the basis for our two surprising results from our large-scale analysis. Firstly, homology-based inferences of physical protein-protein interactions appeared far less successful than expected. In fact, such inferences were accurate only for extremely high levels of sequence similarity. Secondly, and most surprisingly, the identification of interacting partners through sequence similarity was significantly more reliable for protein pairs within the same organism than for pairs between species. Our analysis underlined that the discrepancies between different datasets are large, even when using the same type of experiment on the same organism. This reality considerably constrains the power of homology-based transfer of interactions. In particular, the experimental probing of interactions in distant model organisms has to be undertaken with some caution. More comprehensive images of protein-protein networks will require the combination of many high-throughput methods, including in silico inferences and predictions. http://www.rostlab.org/results/2006/ppi_homology/     

In vitro responses in Passiflora species with different chromosome numbers,ploidy levels and nuclear 2C values: revisiting and providing new insights

Plant Cell, Tissue and Organ Culture (PCTOC) - Tissue culture in Passiflora has emerged as a strategy to propagate species with agronomic relevance, which is the main focus of most in vitro...     

Amphibian species richness across environmental gradients

Large‐scale field patterns are a fundamental source of inferences on processes responsible for variation in species richness among habitats. We examined species richness of larval amphibian communities in 37 ponds over seven years on the Univ. of Michigan's E. S. George Reserve. Ordination of the community incidence matrix indicated a strong major axis of variation in species associations that was correlated with pond hydroperiod, surface area and forest canopy cover. Communities were significantly nested with those species found in ponds with high canopy cover, small area and short hydroperiod being nested subsets of those found in ponds with contrasting characteristics. Presence of fish had strong negative effects on species richness; relaxation of this effect also was apparent when fish were extirpated from ponds by drought. We employed a model selection analysis to identify the most appropriate statistical model for predicting the long‐term average species richness of these ponds from local abiotic and biotic (predator and competitor density) factors. A model including only the abiotic factors was overwhelmingly superior for the anurans; hierarchical partitioning indicated that area and canopy cover alone accounted for over 70% of the independent effects of predictor variables. The global model including both abiotic and biotic factors was the best supported model for the caudates, and correspondingly hierarchical partitioning suggested that area, hydroperiod, invertebrate predators and caudate biomass all accounted for 9–16% of the independent effects. Overall, biotic factors accounted for much less of the variation in species richness than abiotic factors. The patterns in larger, open‐canopy ponds provided little evidence of competitive effects on species richness, though there were patterns consistent with competitive effects in small, closed‐canopy ponds. The unusual temporal and spatial extent of these data enabled us to critically evaluate ideas regarding patterns in larval amphibian communities, and the effects of area, disturbance (hydroperiod) and productivity (canopy cover) on species richness of these communities. These results have important implications to the conservation of amphibian species richness in freshwater wetlands, which are among the most threatened ecosystems worldwide.