Identification of Robust Microsatellite Markers for Wild Pig Fecal DNA

Collection of fecal samples for use in a genetic capture-mark-recapture framework has become popular as a noninvasive method of monitoring wildlife populations. A major caveat to this process, however, is that fecal samples often yield low quality DNA that is prone to genotyping errors, potentially leading to biases in population parameter estimation. Therefore, considerable care is required to identify robust genetic markers, especially in hot or humid conditions that may accelerate DNA degradation. We identified microsatellite loci in wild pig (Sus scrofa) fecal samples that were robust and informative within warm, humid ecosystems. To examine how degradation affected genotyping success, we sampled pig feces across 5 days and calculated how the number of quantitative polymerase chain reaction (qPCR) cycles required to reach the fluorescent threshold (Ct) changed over time. We identified 17 microsatellite loci that had high polymorphism and amplification success and low genotyping error rates (0–0.050 per locus). In the degradation experiment, Ct increased over the 5 days, but in the absence of rain, the majority of samples produced accurate genotypes after 5 days (2,211/2,550 genotypes). Based on the high amplification success and low error rates, even after 5 days of exposure to warm, humid conditions, these loci are useful for estimating population parameters in pig fecal samples

A comparison of cost and quality of three methods for estimating density for wild pig (\u3ci\u3eSus scrofa\u3c/i\u3e)

A critical element in effective wildlife management is monitoring the status of wildlife populations; however, resources to monitor wildlife populations are typically limited. We compared cost effectiveness of three common population estimation methods (i.e. non-invasive DNA sampling, camera sampling, and sampling from trapping) by applying them to wild pigs (Sus scrofa) across three habitats in South Carolina, U.S.A where they are invasive. We used mark-recapture analyses for fecal DNA sampling data, spatially-explicit capture-recapture analyses for camera sampling data, and a removal analysis for removal sampling from trap data. Density estimates were similar across methods. Camera sampling was the least expensive, but had large variances. Fecal DNA sampling was the most expensive, although this technique generally performed well. We examined how reductions in effort by method related to increases in relative bias or imprecision. For removal sampling, the largest cost savings while maintaining unbiased density estimates was from reducing the number of traps. For fecal DNA sampling, a reduction in effort only minimally reduced costs due to the need for increased lab replicates while maintaining high quality estimates. For camera sampling, effort could only be marginally reduced before inducing bias. We provide a decision tree for researchers to help make monitoring decisions

Feral swine harming insular sea turtle reproduction: The origin, impacts, behavior and elimination of an invasive species

Feral swine are among the world\u27s most destructive invasive species wherever they are found, with translocations figuring prominently in their range expansions. In contrast, sea turtles are beloved species that are listed as threatened or endangered throughout the world and are the focus of intense conservation efforts. Nest predation by feral swine severely harms sea turtle reproduction in many locations around the world. Here we quantify and economically assess feral swine nest predation at North Island, South Carolina, an important loggerhead sea turtle nesting beach. Feral swine depredation of North Island sea turtle nests was first detected in 2005, with annual nest monitoring initiated in 2010 documenting nearly total losses to feral swine in 2010 and 2011. The cumulative valuation of annual losses for North Island from 2010 to 2016 ranged as high as $1,166,500. To improve nesting success, an integrated approach for eliminating feral swine was implemented in 2010 and greatly intensified in 2013 by adding federal experts. Removal efforts were challenging due to the island\u27s remoteness and impenetrable habitats, weather, hazards in accessing the island, and wariness of the animals, especially as their population diminished. Removal of the final 11 swine required efforts from 2014 to 2016. Nest predation was highly variable and provided another example of the significance of conditioning by feral swine to sea turtle nests on the consequent severity of nest predation. Even the final individual inflicted heavy losses before his removal. Genetic analyses of feral swine removed from North Island and the adjacent mainland revealed that the island\u27s population did not originate from the nearby mainland, meaning they were (illegally) introduced to the island

Feral swine harming insular sea turtle reproduction: The origin, impacts, behavior and elimination of an invasive species

Feral swine are among the world\u27s most destructive invasive species wherever they are found, with translocations figuring prominently in their range expansions. In contrast, sea turtles are beloved species that are listed as threatened or endangered throughout the world and are the focus of intense conservation efforts. Nest predation by feral swine severely harms sea turtle reproduction in many locations around the world. Here we quantify and economically assess feral swine nest predation at North Island, South Carolina, an important loggerhead sea turtle nesting beach. Feral swine depredation of North Island sea turtle nests was first detected in 2005, with annual nest monitoring initiated in 2010 documenting nearly total losses to feral swine in 2010 and 2011. The cumulative valuation of annual losses for North Island from 2010 to 2016 ranged as high as $1,166,500. To improve nesting success, an integrated approach for eliminating feral swine was implemented in 2010 and greatly intensified in 2013 by adding federal experts. Removal efforts were challenging due to the island\u27s remoteness and impenetrable habitats, weather, hazards in accessing the island, and wariness of the animals, especially as their population diminished. Removal of the final 11 swine required efforts from 2014 to 2016. Nest predation was highly variable and provided another example of the significance of conditioning by feral swine to sea turtle nests on the consequent severity of nest predation. Even the final individual inflicted heavy losses before his removal. Genetic analyses of feral swine removed from North Island and the adjacent mainland revealed that the island\u27s population did not originate from the nearby mainland, meaning they were (illegally) introduced to the island

Identification of Robust Microsatellite Markers for Wild Pig Fecal DNA

Collection of fecal samples for use in a genetic capture-mark-recapture framework has become popular as a noninvasive method of monitoring wildlife populations. A major caveat to this process, however, is that fecal samples often yield low quality DNA that is prone to genotyping errors, potentially leading to biases in population parameter estimation. Therefore, considerable care is required to identify robust genetic markers, especially in hot or humid conditions that may accelerate DNA degradation. We identified microsatellite loci in wild pig (Sus scrofa) fecal samples that were robust and informative within warm, humid ecosystems. To examine how degradation affected genotyping success, we sampled pig feces across 5 days and calculated how the number of quantitative polymerase chain reaction (qPCR) cycles required to reach the fluorescent threshold (Ct) changed over time. We identified 17 microsatellite loci that had high polymorphism and amplification success and low genotyping error rates (0–0.050 per locus). In the degradation experiment, Ct increased over the 5 days, but in the absence of rain, the majority of samples produced accurate genotypes after 5 days (2,211/2,550 genotypes). Based on the high amplification success and low error rates, even after 5 days of exposure to warm, humid conditions, these loci are useful for estimating population parameters in pig fecal samples

Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments

The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, similar to 70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHe(corr)-0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available

Impact of the food industry on the environment in Poland

Celem badań było przedstawienie zakresu oddziaływania przemysłu spożywczego na środowisko w Polsce. Przeprowadzono analizę danych statystycznych za lata 2000-2012, dotyczących głównych form presji, tj.: wykorzystania wody, emisji ścieków, emisji zanieczyszczeń powietrza oraz ilości wytwarzanych odpadów. Wyniki badań pokazały, że najbardziej uciążliwymi dla środowiska branżami przemysłu spożywczego w 2012 roku były: w zakresie ilości wykorzystywanej wody – przemysł mleczarski i produkujący napoje, w zakresie emisji ścieków – przemysł mleczarski, w odniesieniu do ilości emitowanych zanieczyszczeń powietrza – przemysł cukrowniczy, natomiast pod względem ilości generowanych odpadów – przemysł cukrowniczy i produkujący napoje.The aim of this paper is to present the scale of the impact of the food industry on the environment in Poland. For these purpose a comparative analysis of statistical data for the years 2000-2012 was carried out, including especially: water use, wastewater emissions, air emissions, and waste generation. Results showed that the most burdensome for the environment of food industry sectors in 2012 were: in the quantity of water used – dairy and beverage industries, in waste water emissions – the dairy industry, in relation to the amount of emissions of air pollutants – the sugar industry, and in terms of waste generated – the sugar and beverage industries

Zróżnicowanie regionalne w pozyskiwaniu środków unijnych wspierających konkurencyjność sektora rolno-żywnościowego w Polsce w latach 2002–2013

This paper presents the EU support for the competitiveness of the Polish agri- -food sector in the years 2002–2013. Authors singled out 15 measures of SAPARD, SPOROL, RDP programmes, which directly and indirectly affected the achievement of the objective of this analysis. Authors evaluated budget support across the country and in particular provinces (voivodships). Agri-food entities and general business environment in rural Poland has been subsidised to the tune of PLN 30,452 million. Most of the funds were assigned to farmers (80%), whereas the processing industry and infrastructure improvements acquired similar amounts of around 10% of the budget allocated for this purpose.W artykule przedstawiono unijne wsparcie konkurencyjności gospodarki rolno-żywnościowej Polski w latach 2002–2013. Wyodrębniono 15 działań z programów SAPARD, SPO-ROL, PROW, które w sposób bezpośredni i pośredni miały wpływ na realizację celu niniejszej analizy. Oceniono budżet wsparcia w skali kraju i w układzie województw. Analiza wykazała, że na poprawę warunków prowadzenia działalności gospodarczej na obszarach wiejskich Polski oraz na rozwój podmiotów sektora rolno-żywnościowego wydano kwotą 30 452 milionów PLN. Najwięcej środków trafiło do rolników (80%), natomiast na przemysł przetwórczy oraz poprawę infrastruktury pozyskano zbliżone kwoty wynoszące ok. 10% budżetu wykorzystanego na ten cel

Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats () at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure