Estimation of the spontaneous mutation rate in Heliconius melpomene

This is the final published version. It first appeared at mbe.oxfordjournals.org/content/early/2014/11/03/molbev.msu302.abstract.We estimated the spontaneous mutation rate in Heliconius melpomene by genome sequencing of\ud a pair of parents and 30 of their offspring, based on the ratio of number of de novo heterozygotes\ud to the number of callable site-individuals. We detected nine new mutations, each one affecting a\ud single site in a single offspring. This yields an estimated mutation rate of 2.9 x 10-9 (95%\ud confidence interval, 1.3 x 10-9 - 5.5 x 10-9), which is similar to recent estimates in Drosophila\ud melanogaster, the only other insect species in which the mutation rate has been directly estimated.\ud We infer that recent effective population size of H. melpomene is about 2 million, a substantially\ud lower value than its census size, suggesting a role for natural selection reducing diversity. We\ud estimate that H. melpomene diverged from its M?llerian co-mimic H. erato about 6 MYA, a\ud somewhat later date than estimates based on a local molecular clock.CJ was funded by BBSRC [H01439X/1], JWD was funded by the Herchel Smith Fund and PDK and\ud RWN were funded by the BBSRC

Variation in Base-Substitution Mutation in Experimental and Natural Lineages of Caenorhabditis Nematodes

Variation among lineages in the mutation process has the potential to impact diverse biological processes ranging from susceptibilities to genetic disease to the mode and tempo of molecular evolution. The combination of high-throughput DNA sequencing (HTS) with mutation-accumulation (MA) experiments has provided a powerful approach to genome-wide mutation analysis, though insights into mutational variation have been limited by the vast evolutionary distances among the few species analyzed. We performed a HTS analysis of MA lines derived from four Caenorhabditis nematode natural genotypes: C. elegans N2 and PB306 and C. briggsae HK104 and PB800. Total mutation rates did not differ among the four sets of MA lines. A mutational bias toward G:C→A:T transitions and G:C→T:A transversions was observed in all four sets of MA lines. Chromosome-specific rates were mostly stable, though there was some evidence for a slightly elevated X chromosome mutation rate in PB306. Rates were homogeneous among functional coding sequence types and across autosomal cores, arms, and tips. Mutation spectra were similar among the four MA line sets but differed significantly when compared with patterns of natural base-substitution polymorphism for 13/14 comparisons performed. Our findings show that base-substitution mutation processes in these closely related animal lineages are mostly stable but differ from natural polymorphism patterns in these two species

Model-Independent νˉe\bar\nu_{e} Short-Baseline Oscillations from Reactor Spectral Ratios

We consider the ratio of the spectra measured in the DANSS neutrino experiment at 12.7 and 10.7~m from a nuclear reactor. These data give a new model-independent indication in favor of short-baseline $\bar\nu_{e}$ oscillations which reinforce the model-independent indication found in the late 2016 in the NEOS experiment. The combined analysis of the NEOS and DANSS spectral ratios in the framework of 3+1 active-sterile neutrino mixing favor short-baseline $\bar\nu_{e}$ oscillations with a statistical significance of $3.7\sigma$. The two mixing parameters $\sin^{2}2\vartheta_{ee}$ and $\Delta{m}^{2}_{41}$ are constrained at $2\sigma$ in a narrow-$\Delta{m}^{2}_{41}$ island at $\Delta{m}^2_{41} \simeq 1.3 \, \text{eV}^2$, with $\sin^{2}2\vartheta_{ee} = 0.049 \pm 0.023$ ($2\sigma$). We discuss the implications of the model-independent NEOS+DANSS analysis for the reactor and Gallium anomalies. The NEOS+DANSS model-independent determination of short-baseline $\bar\nu_{e}$ oscillations allows us to analyze the reactor rates without assumptions on the values of the main reactor antineutrino fluxes and the data of the Gallium source experiments with free detector efficiencies. The corrections to the reactor neutrino fluxes and the Gallium detector efficiencies are obtained from the fit of the data. In particular, we confirm the indication in favor of the need for a recalculation of the $^{235}\text{U}$ reactor antineutrino flux found in previous studies assuming the absence of neutrino oscillations.Comment: 10 pages; analysis improved by taking into account the uncertainties of the reactor fission fraction

Indication for the disappearance of reactor electron antineutrinos in the Double Chooz experiment

The Double Chooz Experiment presents an indication of reactor electron antineutrino disappearance consistent with neutrino oscillations. A ratio of 0.944 $\pm$ 0.016 (stat) $\pm$ 0.040 (syst) observed to predicted events was obtained in 101 days of running at the Chooz Nuclear Power Plant in France, with two 4.25 GW$_{th}$ reactors. The results were obtained from a single 10 m$^3$ fiducial volume detector located 1050 m from the two reactor cores. The reactor antineutrino flux prediction used the Bugey4 measurement as an anchor point. The deficit can be interpreted as an indication of a non-zero value of the still unmeasured neutrino mixing parameter \sang. Analyzing both the rate of the prompt positrons and their energy spectrum we find \sang = 0.086 $\pm$ 0.041 (stat) $\pm$ 0.030 (syst), or, at 90% CL, 0.015 $<$ \sang $\ <$ 0.16.Comment: 7 pages, 4 figures, (new version after PRL referee's comments

Estimation of the spontaneous nutation rate in Heliconius melpomene

This is the final published version. It first appeared at mbe.oxfordjournals.org/content/early/2014/11/03/molbev.msu302.abstract.We estimated the spontaneous mutation rate in Heliconius melpomene by genome sequencing of\ud a pair of parents and 30 of their offspring, based on the ratio of number of de novo heterozygotes\ud to the number of callable site-individuals. We detected nine new mutations, each one affecting a\ud single site in a single offspring. This yields an estimated mutation rate of 2.9 x 10-9 (95%\ud confidence interval, 1.3 x 10-9 - 5.5 x 10-9), which is similar to recent estimates in Drosophila\ud melanogaster, the only other insect species in which the mutation rate has been directly estimated.\ud We infer that recent effective population size of H. melpomene is about 2 million, a substantially\ud lower value than its census size, suggesting a role for natural selection reducing diversity. We\ud estimate that H. melpomene diverged from its M?llerian co-mimic H. erato about 6 MYA, a\ud somewhat later date than estimates based on a local molecular clock.CJ was funded by BBSRC [H01439X/1], JWD was funded by the Herchel Smith Fund and PDK and\ud RWN were funded by the BBSRC