Predicting species distribution: offering more than simple habitat models

In the last two decades, interest in species distribution models (SDMs) of plants and animals has grown dramatically. Recent advances in SDMs allow us to potentially forecast anthropogenic effects on patterns of biodiversity at different spatial scales. However, some limitations still preclude the use of SDMs in many theoretical and practical applications. Here, we provide an overview of recent advances in this field, discuss the ecological principles and assumptions underpinning SDMs, and highlight critical limitations and decisions inherent in the construction and evaluation of SDMs. Particular emphasis is given to the use of SDMs for the assessment of climate change impacts and conservation management issues. We suggest new avenues for incorporating species migration, population dynamics, biotic interactions and community ecology into SDMs at multiple spatial scales. Addressing all these issues requires a better integration of SDMs with ecological theory.     

Psychophysical discrimination with more than two stimuli

A generalization is suggested of H. D. Landahl's theory of psychophysical discrimination by considering instead of two cross-inhibiting parallel chains of neural pathways,n such chains. The probabilities of then possible different reactions are in such a case expressed by (n−1) ple integrals. Forn=3 the method is illustrated by evaluating the probability of a reaction to the weakest of the three stimuli.     

Note on psychophysical discrimination with more than two stimuli

H. D. Landahl's well-known theory of psychophysical discrimination between two stimuli (Psychometrica,3, 107–125, 1938) is generalized to the case ofn mutually inhibiting stimuli, such that all the corresponding reactions are mutually incompatible so that only one response at most can occur at a time. It is shown that while in the two-stimulus case a “no-response” situation does not necessarily need to occur, in the case ofn stimuli andn responses a “no-response” situation always occurs with finite probability. Therefore, there is a probabilityP _i of the occurrence of each responsei as well as a probabilityP _e of no response, with . The probabilitiesP _i andP _e are expressed in terms of the intensities of then stimuliS _i and in terms of then distribution functions of the fluctuations at then corresponding connections. The expressions are in the form of sums ofn-tuple integrals of the products of the distribution functions, the limits of integration being determined by the intensities of then stimuli.     

Time,space and ecology: why some clades have more species than others

Aim We seek biotic and abiotic explanations for differences in lineage sizes of Afromontane sedges (Cyperaceae, Carex) and buttercups (Ranunculaceae, Ranunculus). Location Mountains of sub‐Saharan Africa and Madagascar. Methods We investigated differences in the species richness and diversification rates of 18 lineages of the pan‐temperate plant groups Carex and Ranunculus, established by long‐distance dispersal on African sky islands. We built generalized linear models to test the individual and the cumulative power of biotic and abiotic factors for predicting variation in the size of lineages. Tested variables were: ages of the lineages, their geographic distributions, number of mountain systems occupied, isolation/distance from ancestral areas, elevation range, number of vegetation zones and habitat types in which lineages are found, light requirement and water availability for each lineage, and the sum of the habitat factors, representing habitat heterogeneity. Habitat conservatism was measured by the overlap in habitats among the species within each lineage. Diversification rate changes were investigated using ‘laser’ in R. Results The number of Carex and Ranunculus lineages on the African mountains accumulated gradually through time. The size of these lineages could best be explained by a model combining age and distribution together with a measure of environmental heterogeneity (either elevation and water availability or habitat heterogeneity). Extensive overlap in environmental characteristics and distribution ranges among the species indicates a relatively high degree of conservatism of these characters. Main conclusions Lineages that are species‐rich are those that have the ability and time to occupy many mountain regions and a wide range of habitats. If allopatric or ecological speciation plays a role, then secondary dispersal and/or niche expansion soon obscures the patterns that may have existed at the point of speciation.     

Dynamics of proteins in crystals: comparison of experiment with simple models

The dynamic behavior of proteins in crystals is examined by comparing theory and experiments. The Gaussian network model (GNM) and a simplified version of the crystallographic translation libration screw (TLS) model are used to calculate mean square fluctuations of C(alpha) atoms for a set of 113 proteins whose structures have been determined by x-ray crystallography. Correlation coefficients between the theoretical estimations and experiment are calculated and compared. The GNM method gives better correlation with experimental data than the rigid-body libration model and has the added benefit of being able to calculate correlations between the fluctuations of pairs of atoms. By incorporating the effect of neighboring molecules in the crystal the correlation is further improved.     

Brain infarction correlates more closely with acrolein than with reactive oxygen species

Although it is thought that the major factor responsible for cell damage is reactive oxygen species (ROS), our recent studies have shown that acrolein is more toxic than ROS. Thus, the relative importance of acrolein and ROS in cell damage during brain infarction was compared using photochemically induced thrombosis model mice. The levels of acrolein-conjugated albumin, and of 4-hydroxynonenal (HNE)-conjugated albumin and 8-OHdG were evaluated as indicators of damage produced by acrolein and ROS, respectively. The increase in acrolein-conjugated albumin was much greater than the increase in HNE-conjugated albumin or 8-OHdG, suggesting that acrolein is more strongly involved in cell damage than ROS during brain infarction. It was also shown that infarction led more readily to RNA damage than to DNA or phospholipid damage. As a consequence, polyamines were released from RNA, and acrolein was produced from polyamines, especially from spermine by spermine oxidase. Production of acrolein from spermine by spermine oxidase was clarified using spermine synthase-deficient Gy mice and transglutaminase 2-knockout mice, in which spermine content is negligible or spermidine/spermine N¹-acetyltransferase activity is elevated.     

Stochastic resonance in two simple compare-and-fire models

Two neural models are analysed and shown to exhibit the stochastic resonance effect. Namely, they respond to an underthreshold sinusoidal signal with an output signal whose signal-to-noise ratio (SNR) firstly increases then decreases as the intensity of noise affecting the system increases. The resonance curves are determined, analytically for the first and simplest model and by a synthetic method for the second one, and the respective resonant behaviours are illustrated and interpreted.     

Evidence for more than two metallothionein isoforms in primates

Two isoforms of metallothionein (MT) have in general been identified in mammalian cells. We have analyzed Cd2+-induced MTs of primate origin and demonstrated the presence of more than two isoforms. Four low molecular weight Cd2+-binding proteins were separated from Cd2+-exposed HeLa cells by gel filtration and ion-exchange chromatography and identified as MTs by amino acid analysis. These were carboxymethylated and analyzed by electrophoresis under denaturing conditions. Three of these proteins were found to be distinct molecules. We also analyzed hepatic MTs from Cd2+-exposed rhesus monkeys, which have previously been partially separated. In this case, five distinct isomers were detected.     

Variation in the outcome of competition between two aphid species on pecan: plants matter more than predators

The relative importance of resource-mediated competition versus apparent competition was studied in two native aphids, Monellia caryella , and Melanocallis caryaefoliae, on pecan, Carya illinoensis . We compared reproduction and body size of the two aphid species when they were caged on pecan leaves as single or mixed species, and when green lacewing larvae ( Chrysoperla comanche or Chyrsopa nigricornis ) were present or absent. The experiment was repeated two times on mature compound leaves in the field in the autumn of 1997 and summer of 1998 and once in a greenhouse, on young seedlings with simple leaves.
Our results suggest that interspecific competition was variable and asymmetric; in both the Summer 98 experiment and the greenhouse experiment, reproduction of M. caryaefoliae was significantly reduced in the mixed species treatments relative to the single species treatment, while M. caryella reproduction was significantly reduced only in the Summer 98 experiment. No evidence of an effect of competition on reproduction was found in the Autumn 97 experiment. M. caryella body size was reduced in one of the mixed species treatments in the Autumn 97 experiment. Body size of both aphid species was reduced in the mixed species treatments of the greenhouse experiment.
The introduction of green lacewing larvae reduced the reproduction of aphids in two of the three experiments in comparison to controls. However, a significant interaction between aphid and predator treatment ( M. caryella in the greenhouse experiment) was found in only one experiment. Variation in the outcome of competition was more likely to be due to aspects of plant quality, including leaf age and previous aphid feeding.     

Sequence similarity is more relevant than species specificity in probabilistic backtranslation

Background  

Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons. The common approach to overcome this difficulty is based on imitation of codon usage within the target species.     

Mixture models for gene expression experiments with two species

Cross-species research in drug development is novel and challenging. A bivariate mixture model utilizing information across two species was proposed to solve the fundamental problem of identifying differentially expressed genes in microarray experiments in order to potentially improve the understanding of translation between preclinical and clinical studies for drug development. The proposed approach models the joint distribution of treatment effects estimated from independent linear models. The mixture model posits up to nine components, four of which include groups in which genes are differentially expressed in both species. A comprehensive simulation to evaluate the model performance and one application on a real world data set, a mouse and human type II diabetes experiment, suggest that the proposed model, though highly structured, can handle various configurations of differential gene expression and is practically useful on identifying differentially expressed genes, especially when the magnitude of differential expression due to different treatment intervention is weak. In the mouse and human application, the proposed mixture model was able to eliminate unimportant genes and identify a list of genes that were differentially expressed in both species and could be potential gene targets for drug development.     

Cost of reproduction as reduced growth in genotypes of two congeneric species with contrasting life histories

Summary We examined the effect of reproduction on growth in 33 genotypes of Plantago major and 14 genotypes of P. rugelii. These two herbaceous perennials have contrasting life histories; P. major reproduces at a smaller size, and allocates a larger proportion of its biomass to reproduction, than P. rugelii. The effect of reproduction on frowth was determined experimentally using photoperiod manipulations to control level of reproduction. The difference in growth between reproductive treatments was divided by the difference in capsule weight to produce a measure of reproductive cost per g of capsule for genotypes of the two species. In both species there was substantial variation among genotypes in the effect of reproduction on growth. Much of this variation could be correlated with differences among genotypes in the extent of reproductive investment and plant size. Cost in terms of reduction in growth per g of capsule increased with reproductive investment in P. rugelii, and with plant size in P. major. We suggest the differences between species in timing and extent of reproduction are related to the differences between species in effect of reproduction on growth. Plantago rugelii may reproduce to a lesser extent than P. major because cost per g of capsule in terms of reduced vegetative biomass, increases with reproductive output in the former species, but not in the latter. Similarly, P. major may reproduce earlier than P. rugelii because cost per g of capsule increases with plant size in P. major, but not in P. rugelii.     

Evolution of recombination in host-parasite systems. Multilocus models

Evolution of the recombination system caused by antagonistic species interactions (host and parasite, for example) was studied. The genetic structure of host population as well as that of parasite is explicitly present in our models. The selection intensity depends on host's resistance and parasite's virulence, both controlled by polygenic systems. The rec-system dynamics was numerically studied using the genetic operators method. It is shown that high-recombination alleles of the rec-modificator can have a short-term selective advantage in both interacting populations simultaneously.     

Dynamics of biomass partitioning in two competing meadow plant species

The optimal allocation theory predicts that growth is allocated between the shoot and the roots so that the uptake of the most limiting resource is increased. Allocation is dynamic due to resource depletion, interaction with competitors, and the allometry of growth. We assessed the effects of intra- and inter-specific competition on growth and resource allocation of the meadow species Ranunculus acris and Agrostis capillaris, grown in environments with high (+) or low (−) availability of light (L) and nutrients (N). We took samples twice a week over the 7 weeks experiment, to follow the changes in root-to-shoot ratios in plants of different sizes, and carried out a larger scale harvest at the end of the experiment. Of all the tested factors, availability of nutrients had the largest effect on the growth rate and shoot-to-root allocation in both species, although both competition and light had significant effects as well. The highest root-to-shoot ratios were measured from the L+N− treatment, and the lowest from the L−N+ treatment, as predicted by the optimal allocation theory. Competition changed resource allocation, but not always toward acquiring the resource that is most limiting to growth. We thus conclude that the greatest variation in shoot-to-root allocation was due to the resource availability and the effects of competition were small, probably due to low density of plants in the experiment.     

Detection of heteromerization of more than two proteins by sequential BRET-FRET

Identification of higher-order oligomers in the plasma membrane is essential to decode the properties of molecular networks controlling intercellular communication. We combined bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) in a technique called sequential BRET-FRET (SRET) that permits identification of heteromers formed by three different proteins. In SRET, the oxidation of a Renilla luciferase (Rluc) substrate by an Rluc fusion protein triggers acceptor excitation of a second fusion protein by BRET and subsequent FRET to a third fusion protein. We describe two variations of SRET that use different Rluc substrates with appropriately paired acceptor fluorescent proteins. Using SRET, we identified complexes of cannabinoid CB(1), dopamine D(2) and adenosine A(2A) receptors in living cells. SRET is an invaluable technique to identify heteromeric complexes of more than two neurotransmitter receptors, which will allow us to better understand how signals are integrated at the molecular level.     

Comparing the genetic population structure of two species of arctic lemmings: more local differentiation in Lemmus trimucronatus than in Dicrostonyx groenlandicus

Collared and brown lemmings ( Dicrostonyx groenlandicus and Lemmus trimucronatus ) are two largely sympatric and ecologically comparable species of arctic microtine rodents, differing however in some respects which allow us to hypothesise differences in the genetic structure of their populations. Collared lemmings are particularly well adapted to life at high latitude, they occasionally emerge to the surface of the snow and may disperse over larger distances than brown lemmings – possibly even over snow and ice. This should result in more local differentiation among populations of brown lemmings than among populations of collared lemmings. We compared the genetic population structure between the two lemming species in a fragmented landscape with small islands in the central Canadian Arctic using four microsatellite loci and partial mitochondrial control region sequences. Both types of genetic markers showed higher differentiation ( F _ST values) among local populations for brown lemmings than for collared lemmings. We discuss to what extent the observed genetic differences may be explained by differences in dispersal rates in addition to differences in average effective population size.     

Community dynamic models of two dioecious tree species

The effects of dioecy on community dynamics were examined by using transition matrix models for two dioecious tree species, one a superior competitor with a narrow dispersal range and the other an inferior competitor with a wide dispersal range. The models are based on tree-by-tree replacements in each identical microsite occupied by either male or female canopy trees of the superior competitor and canopy trees of the inferior competitor. Coexistence of the two species is possible not only because of a trade-off between competitive and dispersal abilities but also because of the existence of a competitor gap, which the superior competitor cannot occupy. The competitor gap is created under the male trees of the superior competitor. The inferior competitor occupies the competitor gap because of its wide dispersal range. The relative abundance of the two species depends on the dispersal ability and sex ratios of the superior competitor. The decreasing dispersal ability and the female abundance of the superior competitor increase the competitor gap, which allows the regeneration of the inferior competitor.An erratum to this article can be found at