A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences

Through an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern-day species. We introduce a novel method for the analysis of variation in selection pressures within and between species, spatially along the genome and temporally between lineages. We model codon evolution explicitly using a joint population genetics-phylogenetics approach that we developed for the construction of multiallelic models with mutation, selection, and drift. Our approach has the advantage of performing direct inference on coding sequences, inferring ancestral states probabilistically, utilizing allele frequency information, and generalizing to multiple species. We use a Bayesian sliding window model for intragenic variation in selection coefficients that efficiently combines information across sites and captures spatial clustering within the genome. To demonstrate the utility of the method, we infer selective pressures acting in Drosophila melanogaster and D. simulans from polymorphism and divergence data for 100 X-linked coding regions.</p

Cross-country differences in unemployment : fiscal policy, unions, and household preferences in general equilibrium

We develop a five period overlapping generations model with individuals who differ by ability and with an imperfect labour market (union wage setting) for the individuals of lower ability. The model explains human capital formation, hours worked and unemployment within one coherent framework. Its predictions match the differences in the unemployment rate across 12 OECD countries remarkably well. A Shapley decomposition of these differences reveals an almost equal role for fiscal policy variables and union preferences. As to fiscal policy, differences in unemployment benefits play a much more important role than tax differences. Differences in households’ taste for leisure are unimportant

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Engineering & Performance of DuoTurbo: Microturbine with Counter-Rotating Runners

Considering the nuclear phase-out strategy of several European countries and the future tendency to promote renewable energies, the exploitation of small hydropower sites (<10 MW) becomes increasingly important. In this framework DuoTurbo Turbine, a new DuoTurbo-microturbine prototype for drinking water networks has been jointly developed by the HES-SO Valais//Wallis , the EPFL-Laboratory for Hydraulic Machines and industrial partners. The modular in- line “plug & play” technology requires low investment, reaching economic feasibility with an available power between 5 kW and 25 kW. One stage of the microturbine consists of two axial counter-rotating runners that form a compact independent unit. Each runner of the turbine holds its own rim generator, the DuoTurbo-configuration involving that each hydraulic runner is integral with each electrical rotor. The possibility of stacking several stages in series enables covering quite a wide range of hydraulic power and, thus, recovering a maximum of energy dissipated in release valves of water supply systems. The present work introduces the global concept of the implemented prototype of the DuoTurbo-microturbine, to target a maxim al injected power of 5 kW for a discharge of 9 l/ s and a head of 24.5 m per stage. The main features of the hydraulic, the mechanical, the electrical and the electronic design are presented. The hydraulic performance is, then, assessed using CFD simulations for the expected operating range. Finally, the performance measurements of the single-stage prototype installed in the hydraulic test rig of the HES-SO Valais//Wallis are presented

On Reconciling Single and Recurrent Hitchhiking Models

A major focus of modern population genetics involves using polymorphism data in order to identify regions impacted by recent positive selection (so-called genomic scans). Recently, methodology has been proposed not to identify individual loci, but rather to quantify genomic recurrent hitchhiking (RHH) parameters using this same type of polymorphism data. I here examine to what extent genomic scans for adaptively important loci may be informed by recently estimated RHH parameters (and vice versa). I find that published results are largely incompatible with one another, with approximately an order of magnitude more sweeps being empirically identified than would be predicted under RHH estimates. Results demonstrate that making this connection between SHH and RHH models is crucial for a more complete and accurate characterization of adaptive evolution

Genomic signatures of population decline in the malaria mosquito Anopheles gambiae

Population genomic features such as nucleotide diversity and linkage disequilibrium are expected to be strongly shaped by changes in population size, and might therefore be useful for monitoring the success of a control campaign. In the Kilifi district of Kenya, there has been a marked decline in the abundance of the malaria vector Anopheles gambiae subsequent to the rollout of insecticide-treated bed nets. To investigate whether this decline left a detectable population genomic signature, simulations were performed to compare the effect of population crashes on nucleotide diversity, Tajima's D, and linkage disequilibrium (as measured by the population recombination parameter ρ). Linkage disequilibrium and ρ were estimated for An. gambiae from Kilifi, and compared them to values for Anopheles arabiensis and Anopheles merus at the same location, and for An. gambiae in a location 200 km from Kilifi. In the first simulations ρ changed more rapidly after a population crash than the other statistics, and therefore is a more sensitive indicator of recent population decline. In the empirical data, linkage disequilibrium extends 100-1000 times further, and ρ is 100-1000 times smaller, for the Kilifi population of An. gambiae than for any of the other populations. There were also significant runs of homozygosity in many of the individual An. gambiae mosquitoes from Kilifi. These results support the hypothesis that the recent decline in An. gambiae was driven by the rollout of bed nets. Measuring population genomic parameters in a small sample of individuals before, during and after vector or pest control may be a valuable method of tracking the effectiveness of interventions

An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila

The recurrent fixation of newly arising, beneficial mutations in a species reduces levels of linked neutral variability. Models positing frequent weakly beneficial substitutions or, alternatively, rare, strongly selected substitutions predict similar average effects on linked neutral variability, if the product of the rate and strength of selection is held constant. We propose an approximate Bayesian (ABC) polymorphism-based estimator that can be used to distinguish between these models, and apply it to multi-locus data from Drosophila melanogaster. We investigate the extent to which inference about the strength of selection is sensitive to assumptions about the underlying distributions of the rates of substitution and recombination, the strength of selection, heterogeneity in mutation rate, as well as the population's demographic history. We show that assuming fixed values of selection parameters in estimation leads to overestimates of the strength of selection and underestimates of the rate. We estimate parameters for an African population of D. melanogaster (ŝ∼2E−03, ) and compare these to previous estimates. Finally, we show that surveying larger genomic regions is expected to lend much more discriminatory power to the approach. It will thus be of great interest to apply this method to emerging whole-genome polymorphism data sets in many taxa

How and Why Chromosome Inversions Evolve

Chromosome inversions are a major engine of genome evolution. New genomic and ecological data are beginning to reveal the evolutionary forces that drive the evolution of inversions