The comparative analysis of statistics,based on the likelihood ratio criterion,in the automated annotation problem

Background  

This paper discusses the problem of automated annotation. It is a continuation of the previous work on the A⁴-algorithm (Adaptive algorithm of automated annotation) developed by Leontovich and others.     

Accelerated likelihood surface exploration: the likelihood ratchet

The existence of multiple likelihood maxima necessitates algorithms that explore a large part of the tree space. However, because of computational constraints, stepwise addition-based tree-searching methods do not allow for this exploration in reasonable time. Here, I present an algorithm that increases the speed at which the likelihood landscape can be explored. The iterative algorithm combines the computational speed of distance-based tree construction methods to arrive at approximations of the global optimum with the accuracy of optimality criterion based branch-swapping methods to improve on the result of the starting tree. The algorithm moves between local optima by iteratively perturbing the tree landscape through a process of reweighting randomly drawn samples of the underlying sequence data set. Tests on simulated and real data sets demonstrated that the optimal solution obtained using stepwise addition-based heuristic searches was found faster using the algorithm presented here. Tests on a previously published data set that established the presence of tree islands under maximum likelihood demonstrated that the algorithm identifies the same tree islands in a shorter amount of time than that needed using stepwise addition. The algorithm can be readily applied using standard software for phylogenetic inference.     

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001).     

Pattern analysis of long arm grain count as a criterion of homology in eight cases of Bp-

Summary The variation in grain count between regions of the long arms of the B group chromosomes is examined. The longer, later-labelling pair (4 s) show a different pattern of labelling to the shorter, earlier-labelling pair (5 s). It is concluded that pattern analysis may be a better criterion of homology than either length measurement or total grain count.     

Ancestors and homology

Current issues concerning the nature of ancestry and homology are discussed with reference to the evolutionary origin of the tetrapod limb. Homologies are argued to be complex conjectural inferences dependant upon a pre-existing phylogenetic analysisand a theoretical model of the evolutionary development of ontogenetic information. Ancestral conditions are inferred primarily from character (synapomorphy/homology) distributions within phylogeny, because of the deficiencies of palaeontological data. Recent analyses of tetrapod limb ontogeny, and the diverse, earliest morphologies known from the fossil record, are inconsistent with typological concepts such as fixed ancestral patterns or bauplans, emphasising the incompatibility of these with evolutionary continuity. The evolutionary origin of the tetrapod limb is also examined in the light of its recent discussion in developmental genetics. While this field promises to reveal more of the fundamental ontogenetic content of homology (identity), at present it is concerned mostly with the abstraction of a new set of types, rather than investigating diversity and change.     

When is homology not homology?

Although genes have specific phenotypic consequences in a given species, this functional relationship can clearly change during the course of evolution. Many cases of evolutionary dissociations between homologous genes and homologous morphological features are now known. These dissociations have interesting and important implications for understanding the genetic basis for evolutionary change in morphology.