The geometric theory of adaptive evolution: trade-off and invasion plots

The purpose of this paper is to take an entirely geometrical path to determine the evolutionary properties of ecological systems subject to trade-offs. In particular we classify evolutionary singularities in a geometrical fashion. To achieve this, we study trade-off and invasion plots (TIPs) which show graphically the outcome of evolution from the relationship between three curves. The first invasion boundary (curve) has one strain as resident and the other strain as putative invader and the second has the roles of the strains reversed. The parameter values for one strain are used as the origin with those of the second strain varying. The third curve represents the trade-off. All three curves pass through the origin or tip of the TIP. We show that at this point the invasion boundaries are tangential. At a singular TIP, in which the origin is an evolutionary singularity, the invasion boundaries and trade-off curve are all tangential. The curvature of the trade-off curve determines the region in which it enters the singular TIP. Each of these regions has particular evolutionary properties (EUS, CS, SPR and MI). Thus we determine by direct geometric argument conditions for each of these properties in terms of the relative curvatures of the trade-off curve and invasion boundaries. We show that these conditions are equivalent to the standard partial derivative conditions of adaptive dynamics. The significance of our results is that we can determine whether the singular strategy is an attractor, branching point, repellor, etc. simply by observing in which region the trade-off curve enters the singular TIP. In particular we find that, if and only if the TIP has a region of mutual invadability, is it possible for the singular strategy to be a branching point. We illustrate the theory with an example and point the way forward.     

Phenological responses of plants to climate change in an urban environment

Global climate change is likely to alter the phenological patterns of plants due to the controlling effects of climate on plant ontogeny, especially in an urbanized environment. We studied relationships between various phenophases (i.e., seasonal biological events) and interannual variations of air temperature in three woody plant species (Prunus davidiana, Hibiscus syriacus, and Cercis chinensis) in the Beijing Metropolis, China, based on phenological data for the period 1962–2004 and meteorological data for the period 1951–2004. Analysis of phenology and climate data indicated significant changes in spring and autumn phenophases and temperatures. Changes in phenophases were observed for all the three species, consistent with patterns of rising air temperatures in the Beijing Metropolis. The changing phenology in the three plant species was reflected mainly as advances of the spring phenophases and delays in the autumn phenophases, but with strong variations among species and phenophases in response to different temperature indices. Most phenophases (both spring and autumn phenophases) had significant relationships with temperatures of the preceding months. There existed large inter- and intra-specific variations, however, in the responses of phenology to climate change. It is clear that the urban heat island effect from 1978 onwards is a dominant cause of the observed phenological changes. Differences in phenological responses to climate change may cause uncertain ecological consequences, with implications for ecosystem stability and function in urban environments.     

Areas of endemism of arthropods in the Atlantic Forest (Brazil): an approach based on a metaconsensus criterion using endemicity analysis

An analysis of endemicity (NDM/VNDM) based on 6541 records from 791 species of arthropods was conducted aiming to delimitate areas of endemism (AEs) in the Atlantic Forest (Brazil). Nine analyses were run employing different analytical parameters of grid size and data extrapolation of species distribution, and their effects on the results were observed. The present study is the first to employ an analysis of sensitivity with UPGMA (unweighted pair group method with arithmatic mean) as a metaconsensus criterion to compare and select AEs resulting from analyses of endemicity with different analytical parameters. In total, 724 AEs grouped into 313 consensus areas were identified. With the metaconsensus criterion, 29 groups of areas were defined, most of them coinciding with the areas obtained in other studies, which confirms that the metaconsus criterion is a clear and objective method for comparing and selecting AEs. The results of the present imply that species of arthorpods respond differently to events and, moreover, that the geographical/climate features usually employed to explain distributional patterns of other taxa do not uniformly affect all species included in the study. The AEs identified in the present study represent a major advance in the search for quantitative distribution patterns in the Atlantic Rainforest, contributing to studies of historical biogeography and other approaches related to the conservation.     

A new selection criterion for yield in wheat

Summary The mortality of young tillers to an extent of 36.5% under optimum cultural conditions was recorded in a field experiment. Attention is drawn to the necessity of minimising this loss and to diverting it towards productive tillers by applying selection pressure. Future yield advances may be achieved by selecting genotypes which tiller moderately in the vegetative phase, most of which survive to produce grains. The character association of each variety under consideration was studied for the suitability towards this objective. A modified selection procedure is suggested which may be advantageously applied to achieve this objective. The proposed new methodology may also be effectively applied to such other cereal crops as barley, triticale and oats.     

The solution conformation of sialyl-α(2→6)-lactose studied by modern NMR techniques and Monte Carlo simulations

Summary We present a comprehensive strategy for detailed characterization of the solution conformations of oligosaccharides by NMR spectroscopy and force-field calculations. Our experimental strategy generates a number of interglycosidic spatial constraints that is sufficiently large to allow us to determine glycosidic linkage conformations with a precision heretofore unachievable. In addition to the commonly used {¹H,¹H} NOE contacts between aliphatic protons, our constraints are: (a) homonuclear NOEs of hydroxyl protons in H₂O to other protons in the oligosaccharide, (b) heteronuclear {¹H,¹³C} NOEs, (c) isotope effects of O¹H/O²H hydroxyl groups on¹³C chemical shifts, and (d) long-range heteronuclear scalar coupling across glycosidic bonds.We have used this approach to study the trisaccharide sialyl-(26)-lactose in aqueous solution. The experimentally determined geometrical constraints were compared to results obtained from force-field calculations based on Metropolis Monte Carlo simulations. The molecule was found to exist in 2 families of conformers. The preferred conformations of the (26)-linkage of the trisaccharide are best described by an equilibrium of 2 conformers with angles at –60° or 180° and of the 3 staggered rotamers of the angle with a predominantgt conformer. Three intramolecular hydrogen bonds, involving the hydroxyl protons on C8 and C7 of the sialic acid residue and on C3 of the reducing-end glucose residue, contribute significantly to the conformational stability of the trisaccharide in aqueous solution. Supplementary material available from the corresponding author: Table containing values for the dihedral angles , , , , and for bond angles , for the six lowest-energy conformations of sialyl-(26)-lactose (1 page).     

IMa2p – parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model

IMa2 and related programs are used to study the divergence of closely related species and of populations within species. These methods are based on the sampling of genealogies using MCMC, and they can proceed quite slowly for larger data sets. We describe a parallel implementation, called IMa2p, that provides a nearly linear increase in genealogy sampling rate with the number of processors in use. IMa2p is written in OpenMPI and C++, and scales well for demographic analyses of a large number of loci and populations, which are difficult to study using the serial version of the program.     

ANCESTRAL CHARACTER ESTIMATION UNDER THE THRESHOLD MODEL FROM QUANTITATIVE GENETICS

Evolutionary biology is a study of life's history on Earth. In researching this history, biologists are often interested in attempting to reconstruct phenotypes for the long extinct ancestors of living species. Various methods have been developed to do this on a phylogeny from the data for extant taxa. In the present article, I introduce a new approach for ancestral character estimation for discretely valued traits. This approach is based on the threshold model from evolutionary quantitative genetics. Under the threshold model, the value exhibited by an individual or species for a discrete character is determined by an underlying, unobserved continuous trait called “liability.” In this new method for ancestral state reconstruction, I use Bayesian Markov chain Monte Carlo (MCMC) to sample the liabilities of ancestral and tip species, and the relative positions of two or more thresholds, from their joint posterior probability distribution. Using data simulated under the model, I find that the method has very good performance in ancestral character estimation. Use of the threshold model for ancestral state reconstruction relies on a priori specification of the order of the discrete character states along the liability axis. I test the use of a Bayesian MCMC information theoretic criterion based approach to choose among different hypothesized orderings for the discrete character. Finally, I apply the method to the evolution of feeding mode in centrarchid fishes.     

Searching Optimal Designs in the Presence of Serially Correlated Errors

Based on simple updating formulaé, a computer algorithm for searching optimal designs when the errors are believed to be serially correlated in the one-dimensional situation is described. The performance of the designs found by the algorithm is compared with the optimal designs available in the literature.