Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations.

PublishedJournal ArticleHumans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.Environment AgencyWest Country Rivers TrustUniversity of Exete

Lost in parameter space: A road map for Stacks

PublishedThis is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.1.Restriction site-Associated DNA sequencing (RAD-seq) has become a widely adopted method for genotyping populations of model and non-model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. 2.Using three empirical RAD-seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. 3.Visualisation of the metrics plotted for the three RAD-seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating alignment positions is more effective than aligning raw reads directly to a reference genome. 4.Our methods will help the community in honing the analytical skills necessary to accurately assemble a RAD-seq dataset.This work was co-funded by the Environment Agency, Westcountry Rivers Trust and the University of Exeter. Overseas collaboration for the project was made possible by funding from The Genetics Society, Santander and the University of Exeter. Thank you to many RAD-seq workshop participants for invaluable insight and new ideas. We thank Dr Nicolas Rochette for his insights into parameter analysis. Thanks also to Dr Andy King for assistance with the brown trout data molecular work and analysis, and Guy Freeman and Martin Young for the species illustrations. Prof Peter Kille and Dr Luis Cunha, Cardiff School of Biosciences, Cardiff University, kindly provided the reference genome of L. rubellus

A new process for the production of aircraft-engine fuels

Report describes experiments conducted on a new method of producing high-grade aviation gasoline at a test laboratory established at Charleston, W. Va. For the National Advisory Committee for Aeronautics

Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis

This is the final version. Available on open access from Nature Research via the DOI in this recordData Availability: The authors state that all data necessary for confirming the conclusions presented in the article are represented fully within the article.The publisher correction to this article is available in ORE at http://hdl.handle.net/10871/40821Metal pollution has made a significant impact on the earth’s ecosystems and tolerance to metals in a wide variety of species has evolved. Metallothioneins, a group of cysteine-rich metal-ion binding proteins, are known to be a key physiological mechanism in regulating protection against metal toxicity. Many rivers across the southwest of England are detrimentally affected by metal pollution, but brown trout (Salmo trutta L.) populations are known to reside within them. In this body of work, two isoforms of metallothionein (MetA and MetB) isolated from trout occupying a polluted and a control river are examined. Using synthetic genetic array (SGA) analyses in the model yeast, Saccharomyces cerevisiae, functional genomics is used to explore the role of metallothionein isoforms in driving metal tolerance. By harnessing this experimental system, S. cerevisiae is used to (i) determine the genetic interaction maps of MetA and MetB isoforms; (ii) identify differences between the genetic interactions in both isoforms and (iii) demonstrate that pre-exposure to metals in metal-tolerant trout influences these interactions. By using a functional genomics approach leveraged from the model yeast Saccharomyces cerevisiae, we demonstrate how such approaches could be used in understanding the ecology and evolution of a non-model species

Trade-offs in the use of direct and indirect indicators of ecosystem degradation for risk assessment

Ecosystem risk assessments estimate the likelihood of major transformations (ecosystem collapse) over a specified time frame. They require an understanding of the biotic and abiotic processes that drive declines. Relative Severity and Extent of Decline quantify essential dimensions of ecosystem degradation as part of the International Union for the Conservation of Nature (IUCN) Red List of Ecosystems risk assessment protocol. These flexible and powerful concepts are operationalised through ecosystem-specific indicators of functional decline. Here, we examine trade-offs in risk assessment between direct, yet data-demanding indicators and indirect indicators that are more widely applicable with global data sets. Using a case study of multiple tropical glacier ecosystems, we compared estimates of risk based on a direct indicator of functional decline (ice mass) with those based on an indirect indicator (bioclimatic suitability). The direct estimate of Relative Severity was based on the projected changes in ice mass using a glacier ice mass balance and dynamics model, while the indirect estimate was calculated from the expected changes in suitability based on a correlative habitat suitability model parameterised with current occurrence records. For reference, we calculated probability of ecosystem collapse from simulations of the ice mass balance and dynamics model. We found that the indirect indicator systematically underestimated risks of ecosystem collapse compared to the direct indicator and returned a different rank order of risks across glaciers due to prominent discrepancies in some units. Small and isolated glaciers located outside the tropical Andes are uniformly exposed to high levels of degradation and have high probabilities of collapse before 2080, whereas tropical Andean glaciers exhibit different rates of degradation, but are expected to undergo very severe degradation before 2100. For these larger units a detailed analysis of spatial differences in future projections could inform regional and local strategies for future monitoring, management and conservation action that can benefit people and nature. Evaluating Relative Severity and Extent of Decline over time and with different ecosystem-specific indicators allowed us to describe trends across a group of functionally similar ecosystem types and compare their performance in assessment units of different size and risk of collapse. The methods could be applied to other ice or snow-dependent ecosystems, while the case study should be instructive for development of risk indicators in many other ecosystem types

Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordRecent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.This research was funded by the Game & Wildlife Conservation Trust and the Atlantic Salmon Trust, with additional support from the Salmon and Trout Association, the Westcountry Rivers Trust and the University of Exeter

Shifting cultivation and hunting across the savanna-forest mosaic in the Gran Sabana, Venezuela: Facing changes

Background. Human encroachment and overexploitation of natural resources in the Neotropics is constantly increasing. Indigenous communities all across the Amazon, are trapped between a population rise and a hot debate about the sustainability of hunting rates. The Garden Hunting hypothesis states that shifting cultivation schemes (conucos) used by Amazon indigenous communities may generate favorable conditions, increasing abundance of small and medium wildlife species close to the `gardens' providing game for indigenous hunters. Methods. Here, we combined camera trap surveys and spatially explicit interview dataset on Pemón indigenous hunting scope and occurrence in a mosaic of savanna and forest in the Gran Sabana, Venezuela to evaluate to what extent the wildlife resource use corresponds to Garden Hunting hypothesis. We applied the Royle_Nichols model and binomial regression in order to: (1) assess whether abundance of small and medium wildlife species is higher close to conucos and (2) evaluate whether hunters select hunting localities based on accessibility to wildlife resources (closeness to conuco) more than wildlife abundance. Results. We find mixed evidence supporting the Garden Hunting hypothesis predictions. Abundance of small and medium species was high close to conucos but the pattern was not statistically significant for most of them. Pemón seem to hunt in locations dominated by forest, where species abundance was predicted to be higher, than in close vicinity to conucos. Hunting scope was focused on the most abundant species located close to the conuco (Cuniculus paca), but also in less abundant and unavailable species (Crax alector, Tapirus terrestris and Odocoileus virginianus). Conclusions. Our research provided the first attempt of a systematic sampling survey in the Gran Sabana, generating a quantitative dataset that not only describes the current pattern of wildlife abundance, but sets the base-line to monitor temporal and spatial change in this region of highland Amazon. We discuss the applicability of the estimates generated as a baseline as well as, environmental challenges imposed by economic, social and cultural changes such as mining encroachment for wildlife management. Subjects Anthropology, Biodiversity, Conservation Biology, Ecology, Natural Resource Management

Leveraging limited data from wildlife monitoring in a conflict affected region in Venezuela

Efficient monitoring of biodiversity-rich areas in conflict-affected areas with poor rule of law requires a combination of different analytical approaches to account for data biases and incompleteness. In the upland Amazon region of Venezuela, in Canaima National Park, we initiated biodiversity monitoring in 2015, but it was interrupted by the establishment of a large-scale mining development plan in 2016, compromising the temporal and geographical extent of monitoring and the security of researchers. We used a resource selection function model framework that considers imperfect detectability and supplemented detections from camera trap surveys with opportunistic off-camera records (including animal tracks and direct sighting) to (1) gain insight into the value of additional occurrence records to accurately predict wildlife resource use in the perturbated area (deforestation, fire, swidden agriculture, and human settlements vicinity), (2) when faced with security and budget constraints. Our approach maximized the use of available data and accounted for biases and data gaps. Adding data from poorly sampled areas had mixed results on estimates of resource use for restricted species, but improved predictions for widespread species. If budget or resources are limited, we recommend focusing on one location with both on-camera and off-camera records over two with cameras. Combining camera trap records with other field observations (28 mammals and 16 birds) allowed us to understand responses of 17 species to deforestation, 15 to fire, and 13 to swidden agriculture. Our study encourages the use of combinations of methods to support conservation in high-biodiversity sites, where access is restricted, researchers are vulnerable, and unequal sampling efforts exist

Development of a Molecular Identification Key for the Freshwater Mussels of East Texas

This poster was presented at the National Collegiate Honors Council Conference in New Orleans, Louisiana.https://scholarworks.uttyler.edu/student_posters/1009/thumbnail.jp

Monotonic properties of the shift and penetration factors

We study derivatives of the shift and penetration factors of collision theory with respect to energy, angular momentum, and charge. Definitive results for the signs of these derivatives are found for the repulsive Coulomb case. In particular, we find that the derivative of the shift factor with respect to energy is positive for the repulsive Coulomb case, a long anticipated but heretofore unproven result. These results are closely connected to the properties of the sum of squares of the regular and irregular Coulomb functions; we also present investigations of this quantity.Comment: 13 pages, 1 figur