The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

<p>Abstract</p> <p>Background</p> <p>During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.</p> <p>Results</p> <p>A phylogenetic analysis of cytochrome <it>b </it>third-codon position confirms that the mitochondrial DNA mutation rate is quite variable in birds, passerines being the fastest evolving order. On average, mitochondrial DNA evolves slower in birds than in mammals of similar body size. This result is in agreement with the longevity hypothesis, and contradicts the hypothesis of a metabolic rate-dependent mutation rate. Birds show no footprint of adaptive selection on cytochrome <it>b </it>evolutionary patterns, but no link between direct estimates of population size and cytochrome <it>b </it>diversity. The mutation rate is the best predictor we have of within-species mitochondrial diversity in birds. It partly explains the differences in mitochondrial DNA diversity patterns observed between mammals and birds, previously interpreted as reflecting Hill-Robertson interferences with the W chromosome.</p> <p>Conclusion</p> <p>Mitochondrial DNA diversity patterns in birds are strongly influenced by the wide, unexpected variation of mutation rate across species. From a fundamental point of view, these results are strongly consistent with a relationship between species maximal longevity and mitochondrial mutation rate, in agreement with the mitochondrial theory of ageing. Form an applied point of view, this study reinforces and extends the message of caution previously expressed for mammals: mitochondrial data tell nothing about species population sizes, and strongly depart the molecular clock assumption.</p

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

BACKGROUND: A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. RESULTS: We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. CONCLUSION: Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

Background: Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially) large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of genetree conflicts in this tribe. Results: We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF) approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-lik

Evolutionary forces affecting base composition in coding sequences of plant genomes

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Balancing selection in self-fertilizing populations

International audienceSelf-fertilization commonly occurs in hermaphroditic species, either occasionally or as the main reproductive mode. It strongly affects the genetic functioning of a population by increasing homozygozity and genetic drift and reducing the effectiveness of recombination. Balancing selection is a form of selection that maintains polymorphism, which has been extensively studied in outcrossing species. Yet, despite recent developments, the analysis of balancing selection in partially selfing species is limited to specific cases and a general treatment is still lacking. In particular, it is unclear whether selfing globally reduced the efficacy of balancing selection as in the well-known case of overdominance. I provide a unifying framework, quantify how selfing affects the maintenance of polymorphism and the efficacy of the different form of balancing selection, and show that they can be classified into two main categories: overdominance-like selection (including true overdominance, selection variable in space and time, and antagonistic selection), which is strongly affected by selfing, and negative frequency-dependent selection, which is barely affected by selfing, even at multiple loci. I also provide simple analytical results for all cases under the assumption of weak selection. This framework provides theoretical background to analyze the genomic signature of balancing selection in partially selfing species. It also sheds new light on the evolution of selfing species, including the evolution of selfing syndrome, the interaction with pathogens, and the evolutionary fate of selfing lineages

Dynamics of selfing evolution and its genomic consequences in Aegilops species (wheat relatives)

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Dynamics of selfing evolution and its genomic consequences in Aegilops species (wheat relatives)

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How Are Deleterious Mutations Purged? Drift Versus Nonrandom Mating

International audienceAccumulation of deleterious mutations has important consequencesfor the evolution of mating systems and the persistence of smallpopulations. It is well established that consanguineous mating canpurge a part of the mutation load and that lethal mutations canalso be purged in small populations. However, the efficiency ofpurging in natural populations, due to either consanguineousmating or to reduced population size, has been questioned.Consequences of consanguineous mating systems and small populationsize are often equated under 'inbreeding' because both increasehomozygosity, and selection is though to be more efficient againsthomozygous deleterious alleles. I show that two processes ofpurging that I call 'purging by drift' and 'purging by nonrandommating' have to be distinguished. Conditions under which the twoways of purging are effective are derived. Nonrandom mating canpurge deleterious mutations regardless of their dominance level,whereas only highly recessive mutations can be purged by drift.Both types of purging are limited by population size, and sharpthresholds separate domains where purging is either effective ornot. The limitations derived here on the efficiency of purging arecompatible with some experimental studies. Implications of theseresults for conservation and evolution of mating systems arediscussed