Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model

Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein-Uhlenbeck processes. We focused on identifying where, how, and why these methods break down so that users can apply them with greater understanding of their strengths and weaknesses. Our analysis identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled. Interestingly, we find that model-selection power can be high even in regions that were previously thought to be difficult, such as when tree size is small. On the other hand, we find that model parameters are in many circumstances difficult to estimate accurately, indicating a relative paucity of information in the data relative to these parameters. Nevertheless, we note that accurate model selection is often possible when parameters are only weakly identified. Our results have implications for more sophisticated methods inasmuch as the latter are generalizations of the case we study.Comment: 38 pages, in press at Systematic Biolog

Algorithm of OMA for large-scale orthology inference

Since the publication of our article (Roth, Gonnet, and Dessimoz: BMC Bioinformatics 2008 9: 518), we have noticed several errors, which we correct in the following

Horticultural Availability and Homeowner Preferences Drive Plant Diversity and Composition in Urban Yards

Understanding the factors that influence biodiversity in urban areas is important for informing management efforts aimed at enhancing the ecosystem services in urban settings and curbing the spread of invasive introduced species. We determined the ecological and socioeconomic factors that influence patterns of plant richness, phylogenetic diversity, and composition in 133 private household yards in the Minneapolis‐Saint Paul Metropolitan area, Minnesota, USA. We compared the composition of spontaneously occurring plant species and those planted by homeowners with composition in natural areas (at the Cedar Creek Ecosystem Science Reserve) and in the horticulture pool of species available from commercial growers. Yard area and fertilizer frequency influenced species richness of the spontaneous species but expressed homeowner values did not. In contrast, the criteria that homeowners articulated as important in their management decisions, including aesthetics, wildlife, neatness and food provision, significantly predicted cultivated species richness. Strikingly, the composition of plant species that people cultivated in their yards resembled the taxonomic and phylogenetic composition of species available commercially. In contrast, the taxonomic and phylogenetic composition of spontaneous species showed high similarity to natural areas. The large fraction of introduced species that homeowners planted was a likely consequence of what was available for them to purchase. The study links the composition and diversity of yard flora to their natural and anthropogenic sources and sheds light on the human factors and values that influence the plant diversity in residential areas of a major urban system. Enhanced understanding of the influences of the sources of plants, both native and introduced, that enter urban systems and the human factors and values that influence their diversity is critical to identifying the levers to manage urban biodiversity and ecosystem services

Phase transition and landscape statistics of the number partitioning problem

The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in which almost all instances have no solution, is investigated by examining the energy landscape of this classic optimization problem. This is achieved by coding the information about the minimum energy paths connecting pairs of minima into a tree structure, termed a barrier tree, the leaves and internal nodes of which represent, respectively, the minima and the lowest energy saddles connecting those minima. Here we apply several measures of shape (balance and symmetry) as well as of branch lengths (barrier heights) to the barrier trees that result from the landscape of the NPP, aiming at identifying traces of the easy/hard transition. We find that it is not possible to tell the easy regime from the hard one by visual inspection of the trees or by measuring the barrier heights. Only the {\it difficulty} measure, given by the maximum value of the ratio between the barrier height and the energy surplus of local minima, succeeded in detecting traces of the phase transition in the tree. In adddition, we show that the barrier trees associated with the NPP are very similar to random trees, contrasting dramatically with trees associated with the $p$ spin-glass and random energy models. We also examine critically a recent conjecture on the equivalence between the NPP and a truncated random energy model

Statistical properties of neutral evolution

Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the requirement that the native state remains thermodynamically stable, and compare them to the ones of Kimura's model of neutral evolution. Our study is based on the Structurally Constrained Neutral (SCN) model which we recently proposed. We show that, in the SCN model, the substitution rate decreases as longer time intervals are considered, and fluctuates strongly from one branch of the evolutionary tree to another, leading to a non-Poissonian statistics for the substitution process. Such strong fluctuations are also due to the fact that neutral substitution rates for individual residues are strongly correlated for most residue pairs. Interestingly, structurally conserved residues, characterized by a much below average substitution rate, are also much less correlated to other residues and evolve in a much more regular way. Our results could improve methods aimed at distinguishing between neutral and adaptive substitutions as well as methods for computing the expected number of substitutions occurred since the divergence of two protein sequences.Comment: 17 pages, 11 figure

Variation in limb loading magnitude and timing in tetrapods

Comparative analyses of locomotion in tetrapods reveal two patterns of stride cycle variability. Tachymetabolic tetrapods (birds and mammals) have lower inter-cycle variation in stride duration than bradymetabolic tetrapods (amphibians, lizards, turtles, and crocodilians). This pattern has been linked to the fact that birds and mammals share enlarged cerebella, relatively enlarged and heavily myelinated Ia afferents, and γ-motoneurons to their muscle spindles. Tachymetabolic tetrapod lineages also both possess an encapsulated Golgi tendon morphology, thought to provide more spatially precise information on muscle tension. The functional consequence of this derived Golgi tendon morphology has never been tested. We hypothesized that one advantage of precise information on muscle tension would be lower and more predictable limb bone stresses, achieved in tachymetabolic tetrapods by having less variable substrate reaction forces than bradymetabolic tetrapods. To test this hypothesis, we analyzed hindlimb substrate reaction forces during locomotion of 55 tetrapod species in a phylogenetic comparative framework. Variation in species-means of limb loading magnitude and timing confirm that, for most of the variables analyzed, variance in hindlimb loading and timing is significantly lower in species with encapsulated versus unencapsulated Golgi tendon organs. These findings suggest that maintaining predictable limb loading provides a selective advantage for birds and mammals by allowing for energy-savings during locomotion, lower limb bone safety factors, and quicker recovery from perturbations. The importance of variation in other biomechanical variables in explaining these patterns, such as posture, effective mechanical advantage, and center-of-mass mechanics, remains to be clarified

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction

We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at