Detection system for neutron β decay correlations in the UCNB and Nab experiments

We describe a detection system designed for precise measurements of angular correlations in neutron β decay. The system is based on thick, large area, highly segmented silicon detectors developed in collaboration with Micron Semiconductor, Ltd. The prototype system meets specifications for β electron detection with energy thresholds below 10 keV, energy resolution of ∼3 keV FWHM, and rise time of ∼50 ns with 19 of the 127 detector pixels instrumented. Using ultracold neutrons at the Los Alamos Neutron Science Center, we have demonstrated the coincident detection of β particles and recoil protons from neutron β decay. The fully instrumented detection system will be implemented in the UCNB and Nab experiments to determine the neutron β decay parameters B, a, and b

MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

<p>Abstract</p> <p>Background</p> <p>MTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs.</p> <p>Results</p> <p>Simulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's <it>Ψ_W</it>). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred.</p> <p>Conclusions</p> <p>To retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at <url>http://msbayes.sourceforge.net/</url> under an open source license (GNU Public License).</p

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

Background Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) soft vicariance , where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs). Results Given the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling. Conclusion Although soft vicariance and colonization are likely to produce similar genetic patterns when a single taxon-pair is used, our hierarchical Bayesian model can potentially detect if either history is a dominant process across co-distributed taxon-pairs. As comparative phylogeographic datasets grow to include \u3e 100 co-distributed taxon-pairs, the HABC approach will be well suited to dissect temporal patterns in community assembly and evolution, thereby providing a bridge linking comparative phylogeography with community ecology

Total cross sections for ultracold neutrons scattered from gases

We have followed up on our previous measurements of upscattering of ultracold neutrons (UCNs) from a series of gases by making measurements of total cross sections on the following gases hydrogen, ethane, methane, isobutene, n-butane, ethylene, water vapor, propane, neopentane, isopropyl alcohol, and ^3He. The values of these cross sections are important for estimating the loss rate of trapped neutrons due to residual gas and are relevant to neutron lifetime measurements using UCNs. The effects of the UCN velocity and path-length distributions were accounted for in the analysis using a Monte Carlo transport code. Results are compared to our previous measurements and with the known absorption cross section for ^3He scaled to our UCN energy. We find that the total cross sections for the hydrocarbon gases are reasonably described by a function linear in the number of hydrogen atoms in the molecule

Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis. Evolution

Abstract. Recurrent glacial advances have shaped community histories across the planet. While biogeographic responses to glaciations likely varied with latitude, the consequences for temperate marine communities histories are less clear. By coalescent analyses of multiloci DNA sequence data (mitochondrial DNA control region, ␣-enolase intron, and ␣-tropomyosin intron) collected from a low-dispersing sister pair of rocky intertidal fishes commonly found from southeastern Alaska to California (Xiphister atropurpureus and X. mucosus), we uncover two very different responses to historical glaciations. A variety of methods that include a simulation analysis, coestimates of migration and divergence times, and estimates of minimum ages of populations sampled up and down the North American Pacific coast all strongly revealed a history of range persistence in X. atropurpureus and extreme range contraction and expansion from a southern refugium in X. mucosus. Furthermore, these conclusions are not sensitive to the independent estimates of the DNA substitution rates we obtain. While gene flow and dispersal are low in both species, the widely different histories are rather likely to have arisen from ecological differences such as diet breadth, generation time, and habitat specificity. The periodic glacial epochs of the Quaternary were prolonged and occupied nearly 80% of the last 2 million years The community composition of temperate intertidal areas such as the northeastern Pacific is likely to be the result of both historical processes such as these cyclical glaciations as well as contemporary oceanographic processes and changes To this end, phylogeographic studies of this region have focused on testing two general hypotheses of Pleistocene range stability that are suggested from geological and ecological data: (1) the southern refugium hypothesis; and (2) the range persistence hypothesis. While incomplete coastal glaciation would suggest persistence (Pielou 1991), wintertime SST were much lower during these glacial period

Behavioural response to song and genetic divergence in two subspecies of white-crowned sparrows (Zonotrichia leucophrys)

© 2016 John Wiley & Sons Ltd Divergence in sexual signals may drive reproductive isolation between lineages, but behavioural barriers can weaken in contact zones. Here, we investigate the role of song as a behavioural and genetic barrier in a contact zone between two subspecies of white-crowned sparrows (Zonotrichia leucophrys). We employed a reduced genomic data set to assess population structure and infer the history underlying divergence, gene flow and hybridization. We also measured divergence in song and tested behavioural responses to song using playback experiments within and outside the contact zone. We found that the subspecies form distinct genetic clusters, and demographic inference supported a model of secondary contact. Song phenotype, particularly length of the first note (a whistle), was a significant predictor of genetic subspecies identity and genetic distance along the hybrid zone, suggesting a close link between song and genetic divergence in this system. Individuals from both parental and admixed localities responded significantly more strongly to their own song than to the other subspecies song, supporting song as a behavioural barrier. Putative parental and admixed individuals were not significantly different in their strength of discrimination between own and other songs; however, individuals from admixed localities tended to discriminate less strongly, and this difference in discrimination strength was explained by song dissimilarity as well as genetic distance. Therefore, we find that song acts as a reproductive isolating mechanism that is potentially weakening in a contact zone between the subspecies. Our findings also support the hypothesis that intraspecific song variation can reduce gene flow between populations

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation

<p>Abstract</p> <p>Background</p> <p>Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate the gene tree and population/species tree thereby ignoring stochastic coalescent variance in their conclusions of temporal incongruence. In contrast to other available phylogeographic software packages, msBayes is the only one that analyses data from multiple species/population pairs under a hierarchical model.</p> <p>Results</p> <p>msBayes employs approximate Bayesian computation (ABC) under a hierarchical coalescent model to test for simultaneous divergence (TSD) in multiple co-distributed population-pairs. Simultaneous isolation is tested by estimating three hyper-parameters that characterize the degree of variability in divergence times across co-distributed population pairs while allowing for variation in various within population-pair demographic parameters (sub-parameters) that can affect the coalescent. msBayes is a software package consisting of several C and R programs that are run with a Perl "front-end".</p> <p>Conclusion</p> <p>The method reasonably distinguishes simultaneous isolation from temporal incongruence in the divergence of co-distributed population pairs, even with sparse sampling of individuals. Because the estimate step is decoupled from the simulation step, one can rapidly evaluate different ABC acceptance/rejection conditions and the choice of summary statistics. Given the complex and idiosyncratic nature of testing multi-species biogeographic hypotheses, we envision msBayes as a powerful and flexible tool for tackling a wide array of difficult research questions that use population genetic data from multiple co-distributed species. The msBayes pipeline is available for download at <url>http://msbayes.sourceforge.net/</url> under an open source license (GNU Public License). The msBayes pipeline is comprised of several C and R programs that are run with a Perl "front-end" and runs on Linux, Mac OS-X, and most POSIX systems. Although the current implementation is for a single locus per species-pair, future implementations will allow analysis of multi-loci data per species pair.</p

Performance of the Los Alamos National Laboratory spallation-driven solid-deuterium ultra-cold neutron source

In this paper, we describe the performance of the Los Alamos spallation-driven solid-deuterium ultra-cold neutron (UCN) source. Measurements of the cold neutron flux, the very low energy neutron production rate, and the UCN rates and density at the exit from the biological shield are presented and compared to Monte Carlo predictions. The cold neutron rates compare well with predictions from the Monte Carlo code MCNPX and the UCN rates agree with our custom UCN Monte Carlo code. The source is shown to perform as modeled. The maximum delivered UCN density at the exit from the biological shield is 52(9) UCN/cc with a solid deuterium volume of ∼1500 cm^3