Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

BUCKLED LAYER STRUCTURE FOR ATOMIC ADSORPTION ON W(100) - THE (ROOT-2X-ROOT-2)R45-DEGREES NITROGEN STRUCTURE FROM ATLEED

Adsorption of 0.5 monolayer of N adatoms on W{100} results in a sharp (root 2 X root 2)R45 degrees LEED pattern. The only previous quantitative LEED study of this system gave a simple overlayer model with a Pendry R-factor of 0.55. An exhaustive search has been made of possible structures, including a novel vacancy reconstruction, displacive reconstructions and underlayer adsorption. From this work a new overlayer structure is derived with an R(p) value of 0.22, displaying a considerable buckling of 0.27 +/- 0.05 Angstrom within the second W layer and consequently involving large changes in the interlayer spacings of the surface. The N adatom is pseudo-five-fold coordinated to the W surface, bonding to a second-layer W atom with a nearest-neighbour bond length of 2.13 Angstrom and with the four next-nearest-neighbour W atoms in the surface plane at 2.27 Angstrom. The structure does not resolve the work function anomaly observed on this surface.

AN ADSORBATE-STABILIZED VACANCY STRUCTURE FOR CU ON W(100) - A SURFACE ALLOY

Deposition of 0.5 ML of Cu on W(100) leads to the formation of a sharp c(2 x 2) structure when the surface is annealed at 800 K. A LEED intensity analysis reveals that the Cu atoms are adsorbed displacively into W sites, forming an ordered 2D surface alloy. Due to the lattice mismatch between copper and tungsten, a substantial buckling of the first layer of the alloy is also observed. The clean, bulk terminated W(100) surface is only just stable relative to the c(2 x 2) vacancy covered W(100) surface. This relative stability of the vacancy structure explains the driving force behind the formation of this alloy.

Energy levels, radiative rates, and lifetimes for transitions in W LVIII

Energy levels and radiative rates are reported for transitions in Cl-like W LVIII. Configuration interaction (CI) has been included among 44 configurations (generating 4978 levels) over a wide energy range up to 363 Ryd, and the general-purpose relativistic atomic structure package (grasp) adopted for the calculations. Since no other results of comparable complexity are available, calculations have also been performed with the flexible atomic code (fac), which help in assessing the accuracy of our results. Energies are listed for the lowest 400 levels (with energies up to ~98 Ryd), which mainly belong to the 3s²3p⁵, 3s3p⁶, 3s²3p⁴3d, 3s²3p³3d², 3s3p⁴3d², 3s²3p²3d³, and 3p⁶3d configurations, and radiative rates are provided for four types of transitions, i.e.E1, E2, M1, and M2. Our energy levels are assessed to be accurate to better than 0.5%, whereas radiative rates (and lifetimes) should be accurate to better than 20% for a majority of the strong transitions.

Energy levels, radiative rates, and lifetimes for transitions in W XL

Energy levels and radiative rates are reported for transitions in Br-like tungsten, W XL, calculated with the general-purpose relativistic atomic structure package (grasp). Configuration interaction (CI) has been included among 46 configurations (generating 4215 levels) over a wide energy range up to 213 Ryd. However, for conciseness results are only listed for the lowest 360 levels (with energies up to ~43 Ryd), which mainly belong to the 4s²4p⁵,4s²4p⁴4d,4s²4p⁴4f,4s4p⁶,4p⁶4d,4s4p⁵4d,4s²4p³4d², and 4s²4p³4d4f configurations, and provided for four types of transitions, E1, E2, M1, and M2. Comparisons are made with existing (but limited) results. However, to fully assess the accuracy of our data, analogous calculations have been performed with the flexible atomic code, including an even larger CI than in grasp. Our energy levels are estimated to be accurate to better than 0.02 Ryd, whereas results for radiative rates (and lifetimes) should be accurate to better than 20% for a majority of the strong transitions.

Radiative rates for E1, E2, M1, and M2 transitions among the 3s23p5, 3s3p6, and 3s23p43d configurations of Cl-like W LVIII

We report calculations of energy levels, radiative decay rates, and lifetimes for transitions among the 3s²3p⁵, 3s3p⁶, and 3s²3p⁴3d configurations of Cl-like W LVIII. The general-purpose relativistic atomic structure package (GRASP) has been adopted for our calculations. Comparisons are made with the most recent results of Mohan et al. (Can. J. Phys. 92, 177 (2014). doi:10.1139/cjp-2013-0348) and discrepancies in lifetimes are noted, up to four orders of magnitude in some instances. Our energy levels are estimated to be accurate to better than 0.5%, whereas results for radiative rates and lifetimes should be accurate to better than 20%.

Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5–20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here we compare the fitness of communally-reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically-based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.

Gamma-ray emission in near critical density plasmas at laser intensities of 1021 W/cm2

We study synchrotron radiation emission from laser interaction with near critical density (NCD) plasmas at intensities of 1021 W∕cm2 using three-dimensional particle-in-cell simulations. It is found that the electron dynamics depend on the laser shaping process in NCD plasmas, and thus the angular distribution of the emitted photons changes as the laser pulse evolves in space and time. The final properties of the resulting synchrotron radiation, such as its overall energy, the critical photon energy, and the radiation angular distribution, are strongly affected by the laser polarization and plasma density. By using a 420 TW∕50 fs laser pulse at the optimal plasma density (∼1nc ), about 108 photons/0.1% bandwidth are produced at multi-MeV photon energies, providing a route to ultraintense, femtosecond gamma ray pulses.