Land-cover data improve bioclimatic models for anurans and turtles at a regional scale

Aim We investigated whether accounting for land cover could improve bioclimatic models for eight species of anurans and three species of turtles at a regional scale. We then tested whether accounting for spatial autocorrelation could significantly improve bioclimatic models after statistically controlling for the effects of land cover. Location Nova Scotia, eastern Canada. Methods Species distribution data were taken from a recent (1999–2003) herpetofaunal atlas. Generalized linear models were used to relate the presence or absence of each species to climate and land‐cover variables at a 10‐km resolution. We then accounted for spatial autocorrelation using an autocovariate or third‐order trend surface of the geographical coordinates of each grid square. Finally, variance partitioning was used to explore the independent and joint contributions of climate, land cover and spatial autocorrelation. Results The inclusion of land cover significantly increased the explanatory power of bioclimatic models for 10 of the 11 species. Furthermore, including land cover significantly increased predictive performance for eight of the 11 species. Accounting for spatial autocorrelation improved model fit for rare species but generally did not improve prediction success. Variance partitioning demonstrated that this lack of improvement was a result of the high correlation between climate and trend‐surface variables. Main conclusions The results of this study suggest that accounting for the effects of land cover can significantly improve the explanatory and predictive power of bioclimatic models for anurans and turtles at a regional scale. We argue that the integration of climate and land‐cover data is likely to produce more accurate spatial predictions of contemporary herpetofaunal diversity. However, the use of land‐cover simulations in climate‐induced range‐shift projections introduces additional uncertainty into the predictions of bioclimatic models. Further research is therefore needed to determine whether accounting for the effects of land cover in range‐shift projections is merited.     

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

We derive an analytic expression for site-specific stationary distributions of amino acids from the structurally constrained neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter, measuring the limit of divergent evolutionary changes at a given site, can be predicted from a site-specific topological property, the principal eigenvector of the contact matrix of the native conformation of the protein. These analytic results, obtained without free parameters, are compared with simulations of the SCN model and with the site-specific amino acid distributions obtained from the Protein Data Bank. These results also provide new insights into how the topology of a protein fold influences its designability, i.e., the number of sequences compatible with that fold. The dependence of the effective temperature on the principal eigenvector decreases for longer proteins, as a possible consequence of the fact that selection for thermodynamic stability becomes weaker in this case.     

Representing Statistical Distributions for Uncertain Parameters in LCA. Relationships between mathematical forms,their representation in EcoSpold,and their representation in CMLCA (7 pp)

Introduction Statistical information for LCA is increasingly becoming available in databases. At the same time, processing of statistical information is increasingly becoming easier by software for LCA. A practical problem is that there is no unique unambiguous representation for statistical distributions.- Representations. This paper discusses the most frequently encountered statistical distributions, their representation in mathematical statistics, EcoSpold and CMLCA, and the relationships between these representations.- The distributions. Four statistical distributions are discussed: uniform, triangular, normal and lognormal.- Software and examples. An easy to use software tool is available for supporting the conversion steps. Its use is illustrated with a simple example.Discussion This paper shows which ambiguities exist for specifying statistical distributions, and which complications can arise when uncertainty information is transferred from a database to an LCA program. This calls for a more extensive standardization of the vocabulary and symbols to express such information. We invite suppliers of software and databases to provide their parameter representations in a clear and unambiguous way and hope that a future revision of the ISO/TS 14048 document will standardize representation and terminology for statistical information.     

With a Machete Through the Jungle: Some Thoughts on Community Diversity

This short communication includes comments on a single sentence cited from a recent paper by C. Ricotta. I discuss shortly the relationship between diversity and classification as well as the possibility of expressing diversity for continuous variables.Asimple example shows that the notion of diversity can be expanded to situations without an underlying classification. I suggest an evenness formula based on absolute deviations from the perfectly even distribution. If expressed for species data and multiplied by number of species in the community, this becomes an easily interpretable diversity measure. It is stressed that conventional diversity formulae cannot be informative on community structure, but there is a solution.     

Persistent random motion: Uncovering cell migration dynamics

In this paper we study analytically the stick-slip models recently introduced to explain the stochastic migration of free cells. We show that persistent motion of cells of many different types is compatible with stochastic reorientation models which admit an analytical mesoscopic treatment. This is proved by examining and discussing experimental data compiled from different sources in the literature, and by fitting some of these results too. We are able to explain many of the ‘apparently complex’ migration patterns obtained recently from cell tracking data, like power-law dependences in the mean square displacement or non-Gaussian behavior for the kurtosis and the velocity distributions, which depart from the predictions of the classical Ornstein-Uhlenbeck process.     

The shade avoidance syndrome: A non-Markovian stochastic growth model

Plants at high population density compete for light, showing a series of physiological responses known as the shade avoidance syndrome. These responses are controlled by the synthesis of the hormone auxin, which is regulated by two signals, an environmental one and an internal one. Considering that the auxin signal induces plant growth after a time lag, this work shows that plant growth can be modelled in terms of an energy-like function extremization, provided that the Markov property is not applied. The simulated height distributions are bimodal and right skewed, as in real community of plants. In the case of isolated plants, theoretical growth dynamics and speed correctly fit Arabidopsis thaliana experimental data reported in literature. Moreover, the growth dynamics of this model is shown to be consistent with the biomass production function of an independent model. These results suggest that memory effects play a non-negligible role in plant growth processes.     

Patterns in body mass distributions: sifting among alternative hypotheses

Understanding how animals interact with their environment is critical for evaluating, mitigating and coping with anthropogenic alteration of Earth's biosphere. Researchers have attempted to understand some aspects of these interactions by examining patterns in animal body mass distributions. Energetic, phylogenetic, biogeographical, textural discontinuity and community interaction hypotheses have been advanced to explain observed patterns. Energetic and textural discontinuity hypotheses focus upon the allometry of resource use. The community interaction hypothesis contends that biotic interactions within assemblages of species are of primary importance. Biogeographical and phylogenetic hypotheses focus on the role of constraints on the organization of communities. This paper examines and organizes these various propositions about species body mass distributions and discusses the multiple competing hypotheses, how their predictions vary, and possible methods by which the hypotheses can be distinguished and tested. Each of the hypotheses is partial, and explains some elements of pattern in body mass distributions. The scale of appropriate application, relevance and interpretation varies among the hypotheses, and the mechanisms underlying observed patterns are likely to be multicausal and vary with scale.     

New ages for Middle and Later Stone Age deposits at Mumba rockshelter, Tanzania: optically stimulated luminescence dating of quartz and feldspar grains

The archaeological deposits at Mumba rockshelter, northern Tanzania, have been excavated for more than 70 years, starting with Margit and Ludwig Köhl-Larsen in the 1930s. The assemblages of Middle Stone Age (MSA) and Later Stone Age (LSA) artefacts collected from this site constitute the type sequences for these cultural phases in East Africa. Despite its archaeological importance, however, the chronology of the site is poorly constrained, despite the application since the 1980s of several dating methods (radiocarbon, uranium-series and amino acid racemisation) to a variety of materials recovered from the deposits. Here, we review these previous chronologies for Mumba and report new ages obtained from optically stimulated luminescence (OSL) and infrared stimulated luminescence (IRSL) measurements on single grains of quartz and multi-grain aliquots of potassium (K) feldspar from the MSA and LSA deposits. Measurements of single grains of quartz allowed the rejection of unrepresentative grains and the application of appropriate statistical models to obtain the most reliable age estimates, while measurements of K-feldspars allowed the chronology to be extended to older deposits. The seven quartz ages and four K-feldspar ages provide improved temporal constraints on the archaeological sequence at Mumba. The deposits associated with the latest Kisele Industry (Bed VI-A) and the earliest Mumba Industry (Bed V) are dated to 63.4 ± 5.7 and 56.9 ± 4.8 ka (thousands of years ago), respectively, thus constraining the time of transition between these two archaeological phases to ∼60 ka. An age of 49.1 ± 4.3 ka has been obtained for the latest deposits associated with the Mumba Industry, which show no evidence for post-depositional mixing and contain ostrich eggshell (OES) beads and abundant microlithics. The Nasera Industry deposits (Bed III) contain large quantities of OES beads and date to 36.8 ± 3.4 ka. We compare the luminescence ages with the previous chronologies for Mumba, and briefly discuss how the revised chronology fits in the context of existing archaeological records and palaeoclimatic reconstructions for East Africa.     

Population heterogeneity and color stimulus heterogeneity in agent-based color categorization

Investigating the interactions between universal and culturally specific influences on color categorization across individuals and cultures has proven to be a challenge for human color categorization and naming research. The present article simulates the evolution of color lexicons to evaluate the role of two realistic constraints found in the human phenomenon: (i) heterogeneous observer populations and (ii) heterogeneous color stimuli. Such constraints, idealized and implemented as agent categorization and communication games, produce interesting and unexpected consequences for stable categorization solutions evolved and shared by agent populations. We find that the presence of a small fraction of color deficient agents in a population, or the presence of a “region of increased salience” in the color stimulus space, break rotational symmetry in population categorization solutions, and confine color category boundaries to a subset of available locations. Further, these heterogeneities, each in a different, predictable, way, might lead to a change of category number and size. In addition, the concurrent presence of both types of heterogeneity gives rise to novel constrained solutions which optimize the success rate of categorization and communication games. Implications of these agent-based results for psychological theories of color categorization and the evolution of color naming systems in human societies are discussed.