An automated method for modeling proteins on known templates using distance geometry.

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.     

Spatial components of foraging behavior in an African Ponerine ant,Paltothyreus tarsatus

Colonies of the African stink ant Paltothyreus tarsatuslocated in the forest have nests with shorter horizontal galleries and a smaller total foraging surface than colonies located in open areas. Each solitary worker specializes on the same central or peripheral hunting zone but she does not specialize on a particular sector during group-retrieving. The search for prey is characterized by a wandering walk with spatial parameters varying in two ways. Capture of a termite releases a path characterized by sinuosity and a decrease in speed of movement. In contrast, a failure in the course of an attempted capture releases an increase in both sinuosity and speed of movement corresponding to a socalled reserve behavior. Each worker shortens her retrieving trip in comparison with her search trip and the straightness of the homing paths depends on the size and shape of the prey. Our data show that behavioral flexibility at the individual level in P. tarsatusis important in determining spatial foraging strategy at the colony level.     

Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)

Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine the relative roles of dispersal vs. vicariance in disjunctions. We studied the phylogeographic pattern of the monotypic Conandron ramondioides (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum, and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus Conandron. The sharp phylogenetic separation, ecological niche divergence among these three groups, and the great number of private alleles in all populations sampled indicated a considerable time of independent evolution, and suggests the need for a taxonomic survey to detect potentially overlooked taxa.     

Constraints on prey size selection by the three-spined stickleback: energy requirements and the capacity and fullness of the gut

An experiment was designed to study how gut fullness and encounter with 5-mm Asellus aquaticus influenced acceptance or rejection of less profitable 8-mm Asellus . 45-mm sticklebacks were found to always accept 5-mm prey whereas 8-mm prey were accepted with an initial probability of about 0.9. This probability decreased as the gut filled. Fish of differing sizes and sex had similar daily energy intakes per unit body size, however the acceptance of 8-mm prey was related to fish size. Whenever a fish orientated to a prey it was followed by pursuit and manipulation independently of prey size. The decision to accept or reject prey occurred after one manipulation, a criterion that was more variable for the larger prey. For one feeding session per day the total energy intake was almost constant despite the changing combination of prey sizes eaten. The fish ate prey with long handling times if the energetic contents of the stomach had not reached 450 J. Calculations were made of how many of each millimetre prey size group would satisfy the 450 J demand and how long the estimated number would take to handle. This showed that the best option is to consume 5-mm prey if given the choice.     

GENETIC AND SOCIAL INHERITANCE OF BODY AND EGG SIZE IN THE BARNACLE GOOSE (BRANTA LEUCOPSIS)

We present heritability estimates for final size of body traits and egg size as well as phenotypic and genetic correlations between body and egg traits in a recently established population of the barnacle goose (Branta leucopsis) in the Baltic area. Body traits as well as egg size were heritable and, hence, could respond evolutionarily to phenotypic selection. Genetic correlations between body size traits were significantly positive and of similar magnitude or higher than the corresponding phenotypic correlations. Heritability estimates for tarsus length obtained from full-sib analyses were higher than those obtained from midoffspring-midparent regressions, and this indicates common environment effects on siblings. Heritabilities for tarsus length obtained from midoffspring-mother regressions were significantly higher than estimates from midoffspring-father regressions. The results suggest that this discrepancy is not caused by maternal effects through egg size, nor by extra-pair fertilizations, but by a socially inherited foraging site fidelity in females.     

Temporal Variation in the Relative Abundance of Fruit Bats (Megachiroptera: Pteropodidae) in Relation to the Availability of Food in a Lowland Malaysian Rain Forest

The aims of this study were to investigate the diet and relative abundance of fruit bats in a lowland Malaysian rain forest and to test the hypothesis that the local assemblage structure of fruit bats varies significantly over time in relation to the availability of food. In total, 352 fruit bats of eight species were captured during 72,306 m² mist‐net hours of sampling between February 1996 and September 1999. Three species of fruit bats (Balionycteris maculita, Chironax melanocephalus, and Cynopterus brachyotis) that fed on a wide range of “steady state” and “big bang” food resources were captured continuously throughout the study period, with no significant variation in capture rates over time. In contrast, five species that fed exclusively or almost exclusively on “big bang” food resources were sampled intermittently, with significant temporal variation in the capture rates of two species (Cynopterus horsfieldi and Megaerops ecaudatus). Significant variation in the capture rates of the remaining three species (Dyacopterus spadiceus, Eonycteris spelaea, and Rousettus amplexicaudatus) could not be detected due to small sample sizes. Since ephemeral “big bang” food resources were only sporadically available within the study area and were associated with large canopy trees and strangler figs, these results suggest that food abundance, or the availability of specific food items, may be important factors limiting local fruit bat species diversity in old‐growth Paleotropical rain forest. Thus, only three fruit bat species were locally resident within the forest throughout the study period. Therefore, further studies on the ranging behavior and habitat requirements of Malaysian fruit bats are required to assess the adequacy of existing reserves and protected areas.     

Terrestrial bird community patterns on the coralline islands of the Dahlak Archipelago, Red Sea, Eritrea

Aim This study aims to explain the patterns of species richness and nestedness of a terrestrial bird community in a poorly studied region. Location Twenty‐six islands in the Dahlak Archipelago, Southern Red Sea, Eritrea. Methods The islands and five mainland areas were censused in summer 1999 and winter 2001. To study the importance of island size, isolation from the mainland and inter‐island distance, I used constrained null models for the nestedness temperature calculator and a cluster analysis. Results Species richness depended on island area and isolation from the mainland. Nestedness was detected, even when passive sampling was accounted for. The nested rank of islands was correlated with area and species richness, but not with isolation. Idiosyncrasies appeared among species‐poor and species‐rich islands, and among common and rare species. Cluster analysis showed differences among species‐rich islands, close similarity among species‐poor and idiosyncratic islands, and that the compositional similarity among islands decreased with increasing inter‐island distance. Thus, faunas of species‐poor, smaller islands were more likely to be subsets of faunas of species‐rich, larger islands if the distance between the islands was short. Main conclusions Species richness and nestedness were related to island area, and nestedness also to inter‐island distances but not to isolation from the mainland. Thus, nestedness and species richness are not affected in the same way by area and distance. Moreover, idiosyncrasies may have been the outcome of species distributions among islands being influenced also by non‐nested distributions of habitats, inter–specific interactions, and differences in species distributions across the mainland. Idiosyncrasies in nested patterns may be as important as the nested pattern itself for conservation – and conservation strategies based on nestedness and strong area effects (e.g. protection of only larger islands) may fail to preserve idiosyncratic species/habitats.     

Foraging strategies in orb-spinning spiders: Ambient light and silk decorations in Argiope aetherea Walckenaer (Araneae: Araneoidea)

Abstract Many species of orb-spinning spiders construct silk decorations within the structure of the orb-web. The evolutionary significance of these decorations is poorly understood, but the silk decorations of many species reflect UV light, suggesting that they may function to attract insects. In these species, relatively more silk decoration may be required under dimmer light conditions in order to maintain a constant UV-reflecting signal, and hence level of insect attraction. We investigated experimentally whether the orb-spinning spider Argiope aetherea adjusts the amount of silk decoration added to the web according to light conditions. Consistent with the prey-attracting function, we found that spiders adjusted the quantity of silk decoration to their webs, adding more silk decoration when the web was located in dim light rather than bright light.     

Mating strategies based on foraging ability: an experiment with grasshoppers

Female mate choice and the benefits of this behavior are criticalaspects of Darwinian sexual selection, but they are seldom documentedbecause it is difficult to identify the male trait(s) that femalesmay be seeking. We conducted experiments with grasshoppers (Melanoplussangutnipes: Orthoptera, Acrididae) to examine this behavior.Males that feed more intensively and select a diet mix thatpermits greater food intake (food intake per body mass per time)in laboratory trials were preferentially selected by females.These better foraging males on average provide greater paternalinvestment (greater spermatophore mass) to the female, whichincreases her reproductive rate (eggs produced per body massper time). However, paternal investment may not entirely explainfemale choice of better foraging males, because these maleswere still selected even if they had their food intake restrictedor had been allowed to recently mate, which reduces spermatophoreproduction. Furthermore, males change their mating strategyin response to female choice and the foraging abilities of surroundingmales. Poorer foraging males attempt forcible copulation ratherthan displaying and allowing female choice. A male will facultativelyswitch between these strategies depending on the foraging abilitiesof the surrounding males. While females attempt to reject forciblecopulation, forcible copulation reduces the frequency with whichfemales successfully copulate with better foraging males. Therefore,males that are less "attractive" to females adopt alternativemating strategies to counter female choice which would excludethem from mating.[Behav Ecol 7: 438–444 (1996)]     

Intra- and inter-specific variations in Lens revealed by RAPD markers

Randomly amplified polymorphic DNA (RAPD) markers were used to estimate intra- and interspecific variations in the genus Lens (lentil). Twenty cultivars of L. culinaris ssp. culinaris, including 11 microsperma (small-seeded) and nine macrosperma (large-seeded) types, and 16 wild relatives (four accessions each of L. culinaris ssp. orientalis, L. odemensis, L. nigricans and L. ervoides), were evaluated for genetic variability using a set of 40 random 10-mer primers. Fifty reproducibly scorable DNA bands were observed from ten of the primers, 90% of which were polymorphic. Genetic distances between each of the accessions were calculated from simple matching coefficients. A dendrogram showing genetic relationships between them was constructed by an unweighted pair-group method with arithmetical averages (UPGMA). This study revealed that (1) expect for L. ervoides, the level of intraspecific variation in cultivated lentil is lower than that in wild species, (2) L. culinaris ssp. orientalis is the most likely candidate for a progenitor of the cultivated species, and (3) microsperma and macrosperma cultivars were indistinguishable by the RAPD markers identified here.