How Does Spatial Study Design Influence Density Estimates from Spatial Capture-Recapture Models?

When estimating population density from data collected on non-invasive detector arrays, recently developed spatial capture-recapture (SCR) models present an advance over non-spatial models by accounting for individual movement. While these models should be more robust to changes in trapping designs, they have not been well tested. Here we investigate how the spatial arrangement and size of the trapping array influence parameter estimates for SCR models. We analysed black bear data collected with 123 hair snares with an SCR model accounting for differences in detection and movement between sexes and across the trapping occasions. To see how the size of the trap array and trap dispersion influence parameter estimates, we repeated analysis for data from subsets of traps: 50% chosen at random, 50% in the centre of the array and 20% in the South of the array. Additionally, we simulated and analysed data under a suite of trap designs and home range sizes. In the black bear study, we found that results were similar across trap arrays, except when only 20% of the array was used. Black bear density was approximately 10 individuals per 100 km2. Our simulation study showed that SCR models performed well as long as the extent of the trap array was similar to or larger than the extent of individual movement during the study period, and movement was at least half the distance between traps. SCR models performed well across a range of spatial trap setups and animal movements. Contrary to non-spatial capture-recapture models, they do not require the trapping grid to cover an area several times the average home range of the studied species. This renders SCR models more appropriate for the study of wide-ranging mammals and more flexible to design studies targeting multiple species

Selective Enrichment and Sequencing of Whole Mitochondrial Genomes in the Presence of Nuclear Encoded Mitochondrial Pseudogenes (Numts)

Numts are an integral component of many eukaryote genomes offering a snapshot of the evolutionary process that led from the incorporation of an α-proteobacterium into a larger eukaryotic cell some 1.8 billion years ago. Although numt sequence can be harnessed as molecular marker, these sequences often remain unidentified and are mistaken for genuine mtDNA leading to erroneous interpretation of mtDNA data sets. It is therefore indispensable that during the process of amplifying and sequencing mitochondrial genes, preventive measures are taken to ensure the exclusion of numts to guarantee the recovery of genuine mtDNA. This applies to mtDNA analyses in general but especially to studies where mtDNAs are sequenced de novo as the launch pad for subsequent mtDNA-based research. By using a combination of dilution series and nested rolling circle amplification (RCA), we present a novel strategy to selectively amplify mtDNA and exclude the amplification of numt sequence. We have successfully applied this strategy to de novo sequence the mtDNA of the Black Field Cricket Teleogryllus commodus, a species known to contain numts. Aligning our assembled sequence to the reference genome of Teleogryllus emma (GenBank EU557269.1) led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error

Evaluation of groundwater quality and its suitability for drinking and agricultural use in Thanjavur city, Tamil Nadu, India

As groundwater is a vital source of water for domestic and agricultural activities in Thanjavur city due to lack of surface water resources, groundwater quality and its suitability for drinking and agricultural usage were evaluated. In this study, 102 groundwater samples were collected from dug wells and bore wells during March 2008 and analyzed for pH, electrical conductivity, temperature, major ions, and nitrate. Results suggest that, in 90% of groundwater samples, sodium and chloride are predominant cation and anion, respectively, and NaCl and CaMgCl are major water types in the study area. The groundwater quality in the study site is impaired by surface contamination sources, mineral dissolution, ion exchange, and evaporation. Nitrate, chloride, and sulfate concentrations strongly express the impact of surface contamination sources such as agricultural and domestic activities, on groundwater quality, and 13% of samples have elevated nitrate content (>45 mg/l as NO3). PHREEQC code and Gibbs plots were employed to evaluate the contribution of mineral dissolution and suggest that mineral dissolution, especially carbonate minerals, regulates water chemistry.Groundwater suitability for drinking usage was evaluated by the World Health Organization and Indian standards and suggests that 34% of samples are not suitable for drinking. Integrated groundwater suitability map for drinking purposes was created using drinking water standards based on a concept that if the groundwater sample exceeds any one of the standards, it is not suitable for drinking. This map illustrates that wells in zones 1, 2, 3, and 4 are not fit for drinking purpose. Likewise, irrigational suitability of groundwater in the study region was evaluated, and results suggest that 20% samples are not fit for irrigation. Groundwater suitability map for irrigation was also produced based on salinity and sodium hazards and denotes that wells mostly situated in zones 2 and 3 are not suitable for irrigation. Both integrated suitability maps for drinking and irrigation usage provide overall scenario about the groundwater quality in the study area. Finally, the study concluded that groundwater quality is impaired by man-made activities, and proper management plan is necessary to protect valuable groundwater resources inThanjavur city

Spatio-temporal variation in predation by urban domestic cats (Felis catus) and the acceptability of possible management actions in the UK

Urban domestic cat (Felis catus) populations can attain exceedingly high densities and are not limited by natural prey availability. This has generated concerns that they may negatively affect prey populations, leading to calls for management. We enlisted cat-owners to record prey returned home to estimate patterns of predation by free-roaming pets in different localities within the town of Reading, UK and questionnaire surveys were used to quantify attitudes to different possible management strategies. Prey return rates were highly variable: only 20% of cats returned ≥4 dead prey annually. Consequently, approximately 65% of owners received no prey in a given season, but this declined to 22% after eight seasons. The estimated mean predation rate was 18.3 prey cat−1 year−1 but this varied markedly both spatially and temporally: per capita predation rates declined with increasing cat density. Comparisons with estimates of the density of six common bird prey species indicated that cats killed numbers equivalent to adult density on c. 39% of occasions. Population modeling studies suggest that such predation rates could significantly reduce the size of local bird populations for common urban species. Conversely, most urban residents did not consider cat predation to be a significant problem. Collar-mounted anti-predation devices were the only management action acceptable to the majority of urban residents (65%), but were less acceptable to cat-owners because of perceived risks to their pets; only 24% of cats were fitted with such devices. Overall, cat predation did appear to be of sufficient magnitude to affect some prey populations, although further investigation of some key aspects of cat predation is warranted. Management of the predation behavior of urban cat populations in the UK is likely to be challenging and achieving this would require considerable engagement with cat owners

Jaguar Densities across Human-Dominated Landscapes in Colombia: The Contribution of Unprotected Areas to Long Term Conservation

Large carnivores such as jaguars (Panthera onca) are species of conservation concern because they are suffering population declines and are keystone species in their ecosystems. Their large area requirements imply that unprotected and ever-increasing agricultural regions can be important habitats as they allow connectivity and dispersal among core protected areas. Yet information on jaguar densities across unprotected landscapes it is still scarce and crucially needed to assist management and range-wide conservation strategies. Our study provides the first jaguar density estimates of Colombia in agricultural regions which included cattle ranching, the main land use in the country, and oil palm cultivation, an increasing land use across the Neotropics. We used camera trapping across two agricultural landscapes located in the Magdalena River valley and in the Colombian llanos (47–53 stations respectively; >2000 trap nights at both sites) and classic and spatially explicit capture-recapture models with the sex of individuals as a covariate. Density estimates were 2.52±0.46–3.15±1.08 adults/100 km2 in the Magdalena valley, whereas 1.12±0.13–2.19±0.99 adults/100 km2 in the Colombian llanos, depending on analysis used. We suggest that jaguars are able to live across unprotected human-use areas and co-exist with agricultural landscapes including oil-palm plantations if natural areas and riparian habitats persist in the landscape and hunting of both jaguar and prey is limited. In the face of an expanding agriculture across the tropics we recommend land-use planning, adequate incentives, regulations, and good agricultural practices for range-wide jaguar connectivity and survival