Correlates of substitution rate variation in mammalian protein-coding sequences

BACKGROUND: Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear loci, and for synonymous and non-synonymous sites. We use phylogenetic comparative methods, refined to take into account the special nature of substitution rate data. Particular attention is paid to the widespread correlations between the components of mammalian life history, which can complicate the interpretation of results. RESULTS: We find that mitochondrial synonymous substitution rates, estimated from the 9 longest mitochondrial genes, show strong negative correlations with body mass and with maximum recorded lifespan. But lifespan is the sole variable to remain after multiple regression and model simplification. Nuclear synonymous substitution rates, estimated from 6 genes, show strong negative correlations with body mass and generation time, and a strong positive correlation with fecundity. In contrast to the mitochondrial results, the same trends are evident in rates of nonsynonymous substitution. CONCLUSION: A substantial proportion of variation in mammalian substitution rates can be explained by aspects of their life history, implying that molecular and life history evolution are closely interlinked in this group. The strength and consistency of the nuclear body mass effect suggests that molecular dating studies may have been systematically misled, but also that methods could be improved by incorporating the finding as a priori information. Mitochondrial synonymous rates also show the body mass effect, but for apparently quite different reasons, and the strength of the relationship with maximum lifespan provides support for the hypothesis that mtDNA damage is causally linked to aging

The single morpheme -ed/-en of the English past/passive

All English regular verbs and about half its irregular verbs have the same form for the finite past tense and the past participle. The finite past tense is different from the participle only for a closed class of about 100 irregular verbs. These latter can be analyzed by a lexical device of wide-ranging applicability called Alternative Realization. All other Past forms of Vs, finite and non-finite, can then be derived from a single morpheme -ed which appears in two contexts: one when V is finite and one when it is selected by a semantically empty stative verb, have or be. There is also a third use of -ed to form passive participles, in both verbal and adjectival passives.The paper presents a formalized system of selection features for lexical items including but going beyond classical subcategorization. This system permits formulating a single full lexical entry for the suffix -ed that covers all its uses. The final version of this entry exemplifies how to specify Alternative Realization, uninterpretability of categories and disjunctive contexts, and independently justifies each of these notations

Conformal Realization of the Neutrino Option

It was recently proposed that the electroweak hierarchy problem is absent if the generation of the Higgs potential stems exclusively from quantum effects of heavy right-handed neutrinos which can also generate active neutrino masses via the type-I seesaw mechanism. Hence, in this framework dubbed the "neutrino option", the tree-level scalar potential is assumed to vanish at high energies. Such a scenario therefore lends itself particularly well to be embedded in a classically scale-invariant theory. In this paper we perform a survey of models featuring conformal symmetry at the high scale. We find that the minimal framework compatible with the "neutrino option" requires the Standard Model to be extended by two real scalar singlet fields in addition to right-handed neutrinos. The spontaneous breaking of scale invariance, which induces the dynamical generation of Majorana masses for the right-handed neutrinos, is triggered by renormalization group effects. We identify the parameter space of the model for which a phenomenologically viable Higgs potential and neutrino masses are generated, and for which all coupling constants remain in the perturbative regime up to the Planck scale.Comment: 18 pages, 4 figures, matches version published in PR

Correlates of substitution rate variation in mammalian protein-coding sequences

<p>Abstract</p> <p>Background</p> <p>Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear loci, and for synonymous and non-synonymous sites. We use phylogenetic comparative methods, refined to take into account the special nature of substitution rate data. Particular attention is paid to the widespread correlations between the components of mammalian life history, which can complicate the interpretation of results.</p> <p>Results</p> <p>We find that mitochondrial synonymous substitution rates, estimated from the 9 longest mitochondrial genes, show strong negative correlations with body mass and with maximum recorded lifespan. But lifespan is the sole variable to remain after multiple regression and model simplification. Nuclear synonymous substitution rates, estimated from 6 genes, show strong negative correlations with body mass and generation time, and a strong positive correlation with fecundity. In contrast to the mitochondrial results, the same trends are evident in rates of nonsynonymous substitution.</p> <p>Conclusion</p> <p>A substantial proportion of variation in mammalian substitution rates can be explained by aspects of their life history, implying that molecular and life history evolution are closely interlinked in this group. The strength and consistency of the nuclear body mass effect suggests that molecular dating studies may have been systematically misled, but also that methods could be improved by incorporating the finding as <it>a priori </it>information. Mitochondrial synonymous rates also show the body mass effect, but for apparently quite different reasons, and the strength of the relationship with maximum lifespan provides support for the hypothesis that mtDNA damage is causally linked to aging.</p

The Supertree Tool Kit

<p>Abstract</p> <p>Background</p> <p>Large phylogenies are crucial for many areas of biological research. One method of creating such large phylogenies is the supertree method, but creating supertrees containing thousands of taxa, and hence providing a comprehensive phylogeny, requires hundred or even thousands of source input trees. Managing and processing these data in a systematic and error-free manner is challenging and will become even more so as supertrees contain ever increasing numbers of taxa. Protocols for processing input source phylogenies have been proposed to ensure data quality, but no robust software implementations of these protocols as yet exist.</p> <p>Findings</p> <p>The aim of the Supertree Tool Kit (STK) is to aid in the collection, storage and processing of input source trees for use in supertree analysis. It is therefore invaluable when creating supertrees containing thousands of taxa and hundreds of source trees. The STK is a Perl module with executable scripts to carry out various steps in the processing protocols. In order to aid processing we have added meta-data, via XML, to each tree which contains information such as the bibliographic source information for the tree and how the data were derived, for instance the character data used to carry out the original analysis. These data are essential parts of previously proposed protocols.</p> <p>Conclusions</p> <p>The STK is a bioinformatics tool designed to make it easier to process source phylogenies for inclusion in supertree analysis from hundreds or thousands of input source trees, whilst reducing potential errors and enabling easy sharing of such datasets. It has been successfully used to create the largest known supertree to date containing over 5000 taxa from over 700 source phylogenies.</p

Colony size predicts division of labour in Attine ants

Division of labour is central to the ecological success of eusocial insects, yet the evolutionary factors driving increases in complexity in division of labour are little known. The size–complexity hypothesis proposes that, as larger colonies evolve, both non-reproductive and reproductive division of labour become more complex as workers and queens act to maximize inclusive fitness. Using a statistically robust phylogenetic comparative analysis of social and environmental traits of species within the ant tribe Attini, we show that colony size is positively related to both non-reproductive (worker size variation) and reproductive (queen–worker dimorphism) division of labour. The results also suggested that colony size acts on non-reproductive and reproductive division of labour in different ways. Environmental factors, including measures of variation in temperature and precipitation, had no significant effects on any division of labour measure or colony size. Overall, these results support the size–complexity hypothesis for the evolution of social complexity and division of labour in eusocial insects. Determining the evolutionary drivers of colony size may help contribute to our understanding of the evolution of social complexity

Colony size predicts division of labour in Attine ants

Division of labour is central to the ecological success of eusocial insects, yet the evolutionary factors driving increases in complexity in division of labour are little known. The size–complexity hypothesis proposes that, as larger colonies evolve, both non-reproductive and reproductive division of labour become more complex as workers and queens act to maximize inclusive fitness. Using a statistically robust phylogenetic comparative analysis of social and environmental traits of species within the ant tribe Attini, we show that colony size is positively related to both non-reproductive (worker size variation) and reproductive (queen–worker dimorphism) division of labour. The results also suggested that colony size acts on non-reproductive and reproductive division of labour in different ways. Environmental factors, including measures of variation in temperature and precipitation, had no significant effects on any division of labour measure or colony size. Overall, these results support the size–complexity hypothesis for the evolution of social complexity and division of labour in eusocial insects. Determining the evolutionary drivers of colony size may help contribute to our understanding of the evolution of social complexity

Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$ and without degree-2 nodes -- called the "species tree". One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g. DNA sequences originating from some species in $X$), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The so-obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping -- but not identical -- sets of labels, is called "supertree". In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed-parameter tractable in the number of input trees $k$, by using their expressibility in Monadic Second Order Logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on $k$ of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time $2^{O(k^2)} \cdot n$, where $n$ is the total size of the input.Comment: 18 pages, 1 figur

Reconstructing pedigrees: some identifiability questions for a recombination-mutation model

Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R (recombinations without mutations) and Model RM (recombinations with mutations). For these models, we ask an identifiability question: is it possible to construct a pedigree from the joint probability distribution of extant sequences? We present partial identifiability results for general pedigrees: we show that when the crossover probabilities are sufficiently small, certain spanning subgraph sequences can be counted from the joint distribution of extant sequences. We demonstrate how pedigrees that earlier seemed difficult to distinguish are distinguished by counting their spanning subgraph sequences.Comment: 40 pages, 9 figure