Microsatellites: consensus and controversy

Microsatellite DNA loci have recently been adopted for many biological applications. Comparative studies across a wide range of species has revealed many details of their mutational properties and evolutionary life cycles. Experience shows that a full understanding of these processes is essential to ensure the effective use of microsatellites as analytical tools. In this article, we review the controversies that have arisen as biologists have taken up this new technology and the emerging consensus that has resulted from their debates. We point to the need for comparative DNA sequencing studies to produce input data for a new generation of theoretical models of microsatellite behaviour. We conclude by presenting our own conceptual model, ‘Snakes and Ladders’, as an aid to theory development.     

Marine nutrient contributions to freshwater apex predators

Recent investigations into the nutrient cycling of coastal ecosystems have suggested that migratory or anadromous fish could be important vectors of marine nutrients. Anadromous fish have assimilated marine nutrients that would contribute to the nutrient budgets of freshwater systems by excretion, gamete release, or the decay of post-reproductive carcasses. However, the extent to which freshwater predators utilize marine material is not well understood. In systems where anadromous fish temporarily constitute a major portion of the fish community, they may contribute substantially to the diet of piscivorous fish and other predators. Here we show the contribution of anadromous blueback herring, shad, and alewife (Alosa) to diets of large, non-indigenous piscivorous catfish (Ictalurus furcatus) using δ³⁴S and δ¹³C. The spawning anadromous Alosa, captured in tidal freshwater, had enriched δ³⁴S and δ¹³C values compared to resident, native freshwater species. As a result of consuming the anadromous Alosa, the I. furcatus isotope signature shifted towards the marine signal. The isotope analysis revealed that anadromous fish contribute substantially to the diet of most captured I. furcatus. The percentage of anadromous Alosa carbon and sulfur that was incorporated into I. furcatus (≥38 cm total length) ranged from 0 to 84% and 10 to 69%, and had means (±SD) of 42 (±24) and 43 (±16)%, respectively. Although the δ¹⁵N signal of marine-derived biomass is enriched by approximately 3‰ relative to terrestrial or freshwater biomass, it was not as useful as δ³⁴S and δ¹³C for nutrient source owing to trophic fractionation. This study demonstrates that anadromous fish may be a significant source of nutrients to tidal freshwater apex predators. Received: 19 March 1999 / Accepted: 26 October 1999     

Variants in the interleukin-1 alpha and beta genes,and the risk for periodontal disease in dogs

Elevated levels of interleukin-1 (IL-1) have been shown to amplify the inflammatory response against periodontopathogenic bacteria. In humans, polymorphisms in the IL1A and IL1B genes are the most well-studied genetic polymorphisms associated with periodontal disease (PD). In contrast to human, there is a lack of knowledge on the genetic basis of canine PD. A case–control study was conducted in which a molecular analysis of dog IL1A and IL1B genes was performed. Of the eight genetic variants identified, seven in IL1A gene and one in IL1B gene, IL1A/1_g.388A >C and IL1A/1_g.521T >A showed statistically significant differences between groups (adjusted OR (95% CI): 0.15 (0.03–0.76), P= 0.022; 5.76 (1.03–32.1), P= 0.046, respectively). It suggests that in the studied population the IL1A/1_g.388C allele is associated with a decreased PD risk, whereas the IL1A/1_g.521A allele can confer an increased risk. Additionally, the IL1A/2_g.515G >T variation resulted in a change of amino acid, i.e. glycine to valine. In silico analysis suggests that this change can alter protein structure and function, predicting it to be deleterious or damaging. This work suggests that IL1 genetic variants may be important in PD susceptibility in canines.     

Testing the quick meal hypothesis: The effect of pulp on hoarding and seed predation of Hymenaea courbaril by red‐rumped agoutis (Dasyprocta leporina)

Abstract: Red‐rumped agoutis (Dasyprocta leporina) are important seed dispersers/predators of Neotropical large‐seeded plants. Several species of seeds cached by agoutis have an edible reward, in contrast to temperate rodent‐dispersed diaspores. The quick meal hypothesis states that the presence of a reward such as edible pulp will enhance the efficiency of rodents as seed disperses by satiating the animal and, consequently, reducing seed predation and enhancing hoarding. In this study, this hypothesis was tested using as the reference system the pulp and seeds of Hymenaea courbaril. Seeds with and without pulp were offered to agoutis and the behaviour of each individual was recorded. Since the probability of predation and hoarding were complementary, we used the probability of predation. The proportion of agoutis that preyed on at least one seed was similar for seeds with (42.8% of individuals) and without (40.0% of individuals) pulp. In agoutis that preyed upon at least one seed, the probability that they killed a seed did not differ between seeds with (0.17 ± 0.03) and without (0.20 ± 0.08) pulp. Hence, these results do not support the ‘quick meal hypothesis’.     

Extrafloral nectaries as a deterrent mechanism against seed predators in the chemically protected weed Crotalaria pallida (Leguminosae)

Abstract In several plants, extrafloral nectaries (EFN) are located close to the reproductive structures, suggesting that ants may act as a defence against specialized seed predators that overcome chemical defences. Alternatively, ants may also deter herbivores in a generalized manner, thereby protecting the whole plant. In this work, we examined the relationship between the chemically protected weed Crotalaria pallida Ait. (Leguminosae) that bears EFN, its specialized seed predator, the larvae of the arctiid moth Utetheisa ornatrix L. (Arctiidae) and ants. We tested two hypotheses related to the type of deterrence caused by ants. The Seed Predator Deterrence Hypothesis predicts that ant deterrence is directed primarily towards herbivores that destroy seeds and other reproductive structures, without attacking herbivores on vegetative structures. The General Deterrence Hypothesis states that ants are general in their effects, equally deterring herbivores in vegetative and reproductive structures. Our results supported the predictions of the Seed Predator Deterrence Hypothesis, namely, that (i) ant activity on EFN was related to the vulnerability of reproductive structures to attack by U. ornatrix; (ii) ant patrolling was restricted almost entirely to racemes; (iii) ants removed termites used as baits more frequently on racemes than on leaves; and (iv) U. ornatrix larvae were often expulsed from the racemes. These results indicate that EFN can act as another deterrent mechanism in chemically protected plants by promoting the expulsion of specialist seed predators.     

Prediction of indirect interactions in proteins

Background  

Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. by changes in protein conformation and mobility, whereas direct interactions occur in close proximity of the protein's amino acids and the ligand. Molecular recognition is traditionally studied using three-dimensional methods, but with such techniques it is difficult to predict the effects caused by mutational changes of amino acids located far away from the ligand-binding site. We recently developed an approach, proteochemometrics, to the study of molecular recognition that models the chemical effects involved in the recognition of ligands by proteins using statistical sampling and mathematical modelling.     

REINTERPRETATION OF A CONULARIID-LIKE FOSSIL FROM THE VENDIAN OF RUSSIA

Abstract:  Vendoconularia triradiata Ivantsov and Fedonkin, recently described from Vendian (latest Proterozoic) strata of Russia, has been interpreted as a six-sided conulariid cnidarian. However, comparison of published illustrations of V .  triradiata with Palaeozoic conulariids suggests that certain key features of the anatomy of V .  triradiata should be reinterpreted. Specifically, features previously homologized with the corners of conulariid thecae may actually be homologous to the conulariid midlines. Under this new interpretation, the corners of the Vendoconularia theca were sulcate, and the midline of each face was non-sulcate and flanked by a pair of low internal carinae. This alternative set of hypotheses of homology makes the argument for a conulariid affinity for Vendoconularia stronger.