Nachtrag zuEquisetum maximum

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Nachtrag zuEquisetum maximum

Ohne Zusammenfassung     

Improved parameterized complexity of the maximum agreement subtree and maximum compatible tree problems

Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively, maximum compatible tree problem (MCT), consists of finding a largest subset of taxa such that all input trees restricted to these taxa are isomorphic, respectively compatible. These problems have several applications in phylogenetics such as the computation of a consensus of phylogenies obtained from different data sets, the identification of species subjected to horizontal gene transfers and, more recently, the inference of supertrees, e.g., Trees Of Life. We provide two linear time algorithms to check the isomorphism, respectively, compatibility, of a set of trees or otherwise identify a conflict between the trees with respect to the relative location of a small subset of taxa. Then, we use these algorithms as subroutines to solve MAST and MCT on rooted or unrooted trees of unbounded degree. More precisely, we give exact fixed-parameter tractable algorithms, whose running time is uniformly polynomial when the number of taxa on which the trees disagree is bounded. The improves on a known result for MAST and proves fixed-parameter tractability for MCT.     

Prediction of one repetition maximum strength from multiple repetition maximum testing and anthropometry

The purpose of this study was to quantify the decrease in the load lifted from 1 to 5, 10, and 20 repetitions to failure for the flat barbell bench press (chest press; CP) and plate-loaded leg press (LP). Furthermore, we developed prediction equations for 1 repetition maximum (RM) strength from the multiple RM tests, including anthropometric data, gender, age, and resistance training volume. Seventy subjects (34 men, 36 women), 18-69 years of age, completed 1, 5, 10, and 20RM testing for each of the CPs and LPs. Regression analyses of mean data revealed a nonlinear decrease in load with increasing repetition number (CP: linear S(y.x) = 2.6 kg, nonlinear S(y.x) = 0.2 kg; LP: linear S(y.x) = 11.0 kg, nonlinear S(y.x) = 2.6 kg, respectively). Multiple regression analyses revealed that the 5RM data produced the greatest prediction accuracy, with R(2) data for 5, 10, and 20RM conditions being LP: 0.974, 0.933, 0.915; CP: 0.993, 0.976, and 0.955, respectively. The regression prediction equations for 1RM strength from 5RM data were LP: 1RM = 1.0970 x (5RM weight [kg]) + 14.2546, S(y.x) = 16.16 kg, R(2) = 0.974; CP: 1RM = 1.1307 x (5RM weight) + 0.6999, S(y.x) = 2.98 kg, R(2) = 0.993. Dynamic muscular strength (1RM) can be accurately estimated from multiple repetition testing. Data reveal that no more than 10 repetitions should be used in linear equations to estimate 1RM for the LP and CP actions.     

Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics

Using a four-taxon example under a simple model of evolution, we show that the methods of maximum likelihood and maximum posterior probability (which is a Bayesian method of inference) may not arrive at the same optimal tree topology. Some patterns that are separately uninformative under the maximum likelihood method are separately informative under the Bayesian method. We also show that this difference has impact on the bootstrap frequencies and the posterior probabilities of topologies, which therefore are not necessarily approximately equal. Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434, 1996) stated that bootstrap frequencies can, under certain circumstances, be interpreted as posterior probabilities. This is true only if one includes a non-informative prior distribution of the possible data patterns, and most often the prior distributions are instead specified in terms of topology and branch lengths. [Bayesian inference; maximum likelihood method; Phylogeny; support.].     

Inconsistency of maximum parsimony revisited

Felsenstein (1978, Syst. Zool. 27:401-410) showed that the method of maximum parsimony can be inconsistent, i.e., lead to an incorrect result with an infinite amount of data. The situation in which this inconsistency occurs is often called the "Felsenstein zone," the phenomenon also known as "long-branch attraction." Felsenstein derived a sufficient inconsistency condition from a model for four taxa with only two different parameters for the probability of change on the five branches connecting the four taxa. In the present paper, his approach is used to derive the inconsistency condition of maximum parsimony from the most general model for four taxa, i.e., with five different parameters for the probabilities of change on the five branches and, for the first time, for characters with k states (k = 2, 3, 4, 5, 6, ...) This is used to determine the factors that can cause the inconsistency of maximum parsimony. It is shown that the probability of change on all five branches and the number of character states play a role in causing inconsistency.     

Haplotype inference by maximum parsimony

MOTIVATION: Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via experimental methods is both time-consuming and expensive, haplotype inference methods that infer haplotypes based on genotype samples become attractive alternatives. RESULTS: (1) We design and implement an algorithm for an important computational model of haplotype inference that has been suggested before in several places. The model finds a set of minimum number of haplotypes that explains the genotype samples. (2) Strong supports of this computational model are given based on the computational results on both real data and simulation data. (3) We also did some comparative study to show the strength and weakness of this computational model using our program. AVAILABILITY: The software HAPAR is free for non-commercial uses. Available upon request (lwang@cs.cityu.edu.hk).     

Links between maximum likelihood and maximum parsimony under a simple model of site substitution

Stochastic models of nucleotide substitution are playing an increasingly important role in phylogenetic reconstruction through such methods as maximum likelihood. Here, we examine the behaviour of a simple substitution model, and establish some links between the methods of maximum parsimony and maximum likelihood under this model.     

Efficient maximum likelihood pedigree reconstruction

A simple and efficient algorithm is presented for finding a maximum likelihood pedigree using microsatellite (STR) genotype information on a complete sample of related individuals. The computational complexity of the algorithm is at worst (O(n³2ⁿ)), where n is the number of individuals. Thus it is possible to exhaustively search the space of all pedigrees of up to thirty individuals for one that maximizes the likelihood. A priori age and sex information can be used if available, but is not essential. The algorithm is applied in a simulation study, and to some real data on humans.     

Pregnancy reduces critical thermal maximum,but not voluntary thermal maximum,in a viviparous skink

Journal of Comparative Physiology B - Upper thermal limits are commonly measured in ectotherms; however, the effects of life-history stages, and in particular pregnancy in viviparous species, are...     

Factors limiting maximum cold-induced heat production

A previous study indicated that respiratory and cardiovascular functions are not limiting factors for maximum thermogenesis in acute cold exposure. The present study investigated the other two possibilities: 1) exhaustion of cellular oxidative capability, and 2) substrate-related functions, as limiting factors. Unanesthetized male rats were exposed to HeO₂ (20.94% oxygen, balance helium) at ?10°C, which elicited maximum thermogenesis and mild hypothermia. To alter the endogenous substrate profile, each rat was either fed or not fed the night before the experiment (self-control). The data do not indicate that exhaustion of cellular oxidative capability is the limiting factor for maximum thermogenesis. In the fed state, the maximum rate of thermogenesis and total heat production were significantly greater (p < .05) than those found in the non-fed state, resulting in significantly less (p < .05) depression of body temperature at end of cold exposure. It is suggested that substrate availability may act as a limiting factor for effective expression of maximum thermogenesis in acute cold exposure.     

Phytoplankton competition in deep biomass maximum

Resource competition in heterogeneous environments is still an unresolved problem of theoretical ecology. In this article, I analyze competition between two phytoplankton species in a deep water column, where the distributions of main resources (light and a limiting nutrient) have opposing gradients and co-limitation by both resources causes a deep biomass maximum. Assuming that the species have a trade-off in resource requirements and the water column is weakly mixed, I apply the invasion threshold analysis (Ryabov and Blasius, Ecol Lett 14:220–228, 2011) to determine relations between environmental conditions and phytoplankton composition. Although species deplete resources in the interior of the water column, the resource levels at the bottom and surface remain high. As a result, the slope of resources gradients becomes a new crucial factor which, rather than the local resource values, determines the outcome of competition. The value of resource gradients nonlinearly depend on the density of consumers. This leads to complex relationships between environmental parameters and species composition. In particular, it is shown that an increase of both the incident light intensity or bottom nutrient concentrations favors the best light competitors, while an increase of the turbulent mixing or background turbidity favors the best nutrient competitors. These results might be important for prediction of species composition in deep ocean.     

Equisetum heleocharis,maximum undAthyrium alpestre

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