What can be learned by scanning the genome for molecular convergence in wild populations?

This is the final version. Available on open access from Wiley via the DOI in this recordConvergent evolution, where independent lineages evolve similar phenotypes in response to similar challenges, can provide valuable insight into how selection operates and the limitations it encounters. However, it has only recently become possible to explore how convergent evolution is reflected at the genomic level. The overlapping outlier approach (OOA), where genome scans of multiple independent lineages are used to find outliers that overlap and therefore identify convergently evolving loci, is becoming popular. Here, we present a quantitative analysis of 34 studies that used this approach across many sampling designs, taxa, and sampling intensities. We found that OOA studies with increased biological sampling power within replicates have increased likelihood of finding overlapping, “convergent” signals of adaptation between them. When identifying convergent loci as overlapping outliers, it is tempting to assume that any false‐positive outliers derived from individual scans will fail to overlap across replicates, but this cannot be guaranteed. We highlight how population demographics and genomic context can contribute toward both true convergence and false positives in OOA studies. We finish with an exploration of emerging methods that couple genome scans with phenotype and environmental measures, leveraging added information from genome data to more directly test hypotheses of the likelihood of convergent evolution.European Research Counci

Contingent Convergence: The Ability To Detect Convergent Genomic Evolution Is Dependent on Population Size and Migration

This is the author accepted manuscript. The final version is available from the Genetics Society of America via the DOI in this recordData availability: A full set of scripts including all bash, Eidos and R scripts necessary to repeat this analysis can be downloaded from Github (https://github.com/JimWhiting91/Contingent_Convergence_Pipeline). Supplementary figures (S1-49) have been uploaded through the GSA figshare portal. Supplementary figures include results for different mutation/recombination rates, PhenoNull and neutral data across sampling generations along with additional figures.Outlier scans, in which the genome is scanned for signatures of selection, have become a prominent tool in studies of local adaptation, and more recently studies of genetic convergence in natural populations. However, such methods have the potential to be confounded by features of demographic history, such as population size and migration, which are considerably varied across natural populations. In this study, we use forward-simulations to investigate and illustrate how several measures of genetic differentiation commonly used in outlier scans (FST, DXY and Δπ) are influenced by demographic variation across multiple sampling generations. In a factorial design with 16 treatments, we manipulate the presence/absence of founding bottlenecks (N of founding individuals), prolonged bottlenecks (proportional size of diverging population) and migration rate between two populations with ancestral and diverged phenotypic optima. Our results illustrate known constraints of individual measures associated with reduced population size and a lack of migration; but notably we demonstrate how relationships between measures are similarly dependent on these features of demography. We find that false-positive signals of convergent evolution (the same simulated outliers detected in independent treatments) are attainable as a product of similar population size and migration treatments (particularly for DXY), and that outliers across different measures (for e.g. FST and DXY) can occur with little influence of selection. Taken together, we show how underappreciated, yet quantifiable measures of demographic history can influence commonly employed methods for detecting selection.European Research Council (ERC

Atomic and Molecular Absorption in Redshifted Radio Sources

We report on a survey for associated HI 21-cm and OH 18-cm absorption with the Giant Metrewave Radio Telescope at redshifts z = 0.2-0.4. Although the low redshift selection ensures that our targets are below the critical ultra-violet luminosity, which is hypothesised to ionise all of the neutral gas in the host galaxy, we do not obtain any detections in the six sources searched. Analysing these in context of the previous surveys, in addition to the anti-correlation with the ultra-violet luminosity (ionising photon rate), we find a correlation between the strength of the absorption and the blue -- near-infrared colour, as well as the radio-band turnover frequency. We believe that these are due to the photo-ionisation of the neutral gas, an obscured sight-line being more conducive to the presence of cold gas and the compact radio emission being better intercepted by the absorbing gas, maximising the flux coverage, respectively. Regarding the photo-ionisation, the compilation of the previous surveys increases the significance of the critical ionising photon rate, above which all of the gas in the host galaxy is hypothesised to be ionised, to >5 sigma. This reaffirms that this is an ubiquitous effect, which has profound implications for the detection of neutral gas in these objects with the Square Kilometre Array.Comment: Accepted by MNRA

Estimating Waterfowl Densities in a Flooded Forest: a Comparison of Methods

During winter, aerial surveys are used to estimate densities of ducks that occupy open-water habitats. However, such surveys are ineffective for sampling forest-dwelling species, especially Aix sponsa (Wood Ducks), Anas platyrhynchos (Mallards), and Lophodytes cucullatus (Hooded Mergansers). We evaluated fixed-radius plot (FRP) and Reynolds and Goodrum variable-radius plot (VRP) methods for estimating waterfowl densities in a flooded hardwood bottomland. We constructed 15 elevated blinds on the Angelina River flood plain in eastern Texas and established a 1-ha FRP around each blind; color-coded markers were placed at fixed intervals from each blind. Observers surveyed waterfowl from blinds for 21 mornings during January–March, 1990. For FRPs, species, sex, and time a bird entered and exited the plot were recorded. For VRPs, similar data and estimated observer-to-bird distance were recorded. Data were arranged in a randomized block design and tested using 1-way analyses of variances. Wood Ducks, Mallards, and Hooded Mergansers comprised 68, 18, and 10% of the birds recorded, respectively. Wood Duck density estimates (per ha) for FRP, Reynolds VRP, and Goodrum VRP methods were 0.65, 0.49, and 1.00 (P \u3c 0.001), respectively; for Mallards, estimates were 0.27, 0.20, and 0.33 (P \u3c 0.001), respectively; and estimates were 0.09, 0.13, and 0.15 (P = 0.003) for Hooded Mergansers, respectively. Based on ease of implementation, complexity of data analyses, and precision of density estimates, the FRP and Goodrum VRP methods are recommended for sampling waterfowl in flooded forests

Activity Patterns and Habitat Use of Northern Bobwhite Females in 2 Grazing Systems

During spring and summer of 1985 and 1986, we investigated activity patterns and habitat use of female northern bobwhite (Colinus virginianus) on 2 sites in south Texas. One site had been subjected to a short duration grazing (SDG) system and the other to a continuous grazing (CG) system. Nineteen females were radio-tagged in 1985 and 28 in 1986. Rainfall was above average in 1985 and below average in 1986; as a result, herbaceous ground cover was more dense in 1985 than in 1986. Due to extensive fencing, 58% of the SDG cell was within 25 m of a mowed roadside, fencerow, or pipeline right-of-way; the same was true for 30% of the CG pasture. There were no differences (P \u3e 0.05) in distances moved between successive locations or in the breeding season home range sizes of females in the 2 systems. In 1985, females preferred zones within 25 m of mowed areas and avoided those ~50 m from such areas. In the SDG cell during 1986 only, females preferred recently grazed paddocks. The results suggest that the most important difference between the 2 grazing systems was the increased proportion of mowed areas in the SDG cell during the abnormally wet year. In the Texas Coastal Bend, landowners unable to adjust stocking rates during wet years should consider mowing to improve bobwhite habitat

Activity Patterns and Habitat Use of Northern Bobwhite Females in 2 Grazing Systems

During spring and summer of 1985 and 1986, we investigated activity patterns and habitat use of female northern bobwhite (Colinus virginianus) on 2 sites in south Texas. One site had been subjected to a short duration grazing (SDG) system and the other to a continuous grazing (CG) system. Nineteen females were radio-tagged in 1985 and 28 in 1986. Rainfall was above average in 1985 and below average in 1986; as a result, herbaceous ground cover was more dense in 1985 than in 1986. Due to extensive fencing, 58% of the SDG cell was within 25 m of a mowed roadside, fencerow, or pipeline right-of-way; the same was true for 30% of the CG pasture. There were no differences (P \u3e 0.05) in distances moved between successive locations or in the breeding season home range sizes of females in the 2 systems. In 1985, females preferred zones within 25 m of mowed areas and avoided those ~50 m from such areas. In the SDG cell during 1986 only, females preferred recently grazed paddocks. The results suggest that the most important difference between the 2 grazing systems was the increased proportion of mowed areas in the SDG cell during the abnormally wet year. In the Texas Coastal Bend, landowners unable to adjust stocking rates during wet years should consider mowing to improve bobwhite habitat

Winter Food Habits and Preferences of Northern Bobwhites in East Texas

During late winter, 1994 and 1995, we investigated food habits and preferences of northern bobwhites (Colinus virginianus; hereafter, bobwhites) collected on forested lands in east Texas. Crops for bobwhites were collected from areas under 3 management regimes, namely intensively managed for bobwhites (QMA) (i.e., tree basal area reduced, annually burned, numerous multi-stage food plots, etc.), extensively managed for timber and wildlife (NBS) (i.e., burned every 3-5 years, scattered 2-stage food plots with corn feeders), and unmanaged for wildlife (i.e., burned every 5-7 years). With years pooled, partridge pea (Cassia fasciculata), Hercules club (Zanthoxylum clava-herculis), and pine (Pinus spp.) seeds, and clover leaflets (Trifolium spp.) comprised 93% by weight of foods of 79 bobwhites foods on QMA. On NBS, 81% of 40 bobwhite diets was butterfly pea (Centrosema virginianum), browntop millet, pine, wild bean (Strophostyles spp.), and corn seeds and clover leaflets; millet and corn were from food plots and feeders, respectively. For unmanaged areas, 79% of 19 bobwhite diets was butterfly pea, rush (Juncus spp.), pine, partridge pea, and American beautyberry (Callicarpa americana) seeds, and clover leaflets. Top-ranked food items on QMA were pine, hairy vetch, and Hercules club seeds in 1994 and butterfly pea, partridge pea, and wax myrtle (Myrica cerifera) seeds in 1995 (P \u3c 0.05). On NBS, hawthorn (Crataegus spp.) and beautyberry seeds were top-ranked in 1994 as were kobe lespedeza, wild bean, and butterfly pea seeds in 1995. On unmanaged areas, butterfly pea and partridge pea seeds and clover leaflets were highest ranked in 1995. On forested lands, activities (e.g., disking, burning, establishing food plots) which provide seed-bearing plants, especially legumes, and clover greenery benefit bobwhites

Quasilocal Energy for a Kerr black hole

The quasilocal energy associated with a constant stationary time slice of the Kerr spacetime is presented. The calculations are based on a recent proposal \cite{by} in which quasilocal energy is derived from the Hamiltonian of spatially bounded gravitational systems. Three different classes of boundary surfaces for the Kerr slice are considered (constant radius surfaces, round spheres, and the ergosurface). Their embeddings in both the Kerr slice and flat three-dimensional space (required as a normalization of the energy) are analyzed. The energy contained within each surface is explicitly calculated in the slow rotation regime and its properties discussed in detail. The energy is a positive, monotonically decreasing function of the boundary surface radius. It approaches the Arnowitt-Deser-Misner (ADM) mass at spatial infinity and reduces to (twice) the irreducible mass at the horizon of the Kerr black hole. The expressions possess the correct static limit and include negative contributions due to gravitational binding. The energy at the ergosurface is compared with the energies at other surfaces. Finally, the difficulties involved in an estimation of the energy in the fast rotation regime are discussed.Comment: 22 pages, Revtex, Alberta-Thy-18-94. (the approximations in Section IV have been improved. To appear in Phys. Rev. D