Integrating occupancy modeling and interview data for corridor identification: A case study for jaguars in Nicaragua

Corridors are critical elements in the long-term conservation of wide-ranging species like the jaguar (Panthera onca). Jaguar corridors across the range of the species were initially identified using a GIS-based least-cost corridor model. However, due to inherent errors in remotely sensed data and model uncertainties, these corridors warrant field verification before conservation efforts can begin. We developed a novel corridor assessment protocol based on interview data and site occupancy modeling. We divided our pilot study area, in southeastern Nicaragua, into 71, 6 × 6 km sampling units and conducted 160 structured interviews with local residents. Interviews were designed to collect data on jaguar and seven prey species so that detection/non-detection matrices could be constructed for each sampling unit. Jaguars were reportedly detected in 57% of the sampling units and had a detection probability of 28%. With the exception of white-lipped peccary, prey species were reportedly detected in 82–100% of the sampling units. Though the use of interview data may violate some assumptions of the occupancy modeling approach for determining ‘proportion of area occupied’, we countered these shortcomings through study design and interpreting the occupancy parameter, psi, as ‘probability of habitat used’. Probability of habitat use was modeled for each target species using single state or multistate models. A combination of the estimated probabilities of habitat use for jaguar and prey was selected to identify the final jaguar corridor. This protocol provides an efficient field methodology for identifying corridors for easily-identifiable species, across large study areas comprised of unprotected, private lands.     

Estimating the density of a jaguar population in the Brazilian Pantanal using camera-traps and capture-recapture sampling in combination with GPS radio-telemetry

The jaguar (Panthera onca) is the largest feline in the Americas and third largest world-wide, smaller in size only to the tiger (P. tigris) and lion (P. leo). Yet, in comparison, relatively few studies on jaguar population densities have been conducted and baseline data for management purposes are needed. Camera trapping and capture-recapture sampling methods were used to estimate the size of a jaguar population in the Pantanal’s open wet grassland habitat, an important area for the long-term survival of the species. This study is the first jaguar population estimate conducted in co-operation with a GPS-telemetry study providing an important opportunity for comparing different methods of density estimation. An accessible area within a 460 km² privately-owned ranch was sampled with equal effort during the dry seasons of 2003 and 2004. Thirty-one and twenty-five individual jaguars were identified in 2003 and 2004, respectively. Estimates of jaguar abundance were generated by program CAPTURE. Density estimates were produced according to different methods used to calculate the effectively sampled areas which ranged from 274 to 568 km². For 2003, the currently-used mean maximum distance moved (MMDM) method produced a density of 10.3 jaguars/100 km², while GPS-telemetry-based calculations produced a mean density of 6.6 jaguars/100 km². For 2004, the MMDM method produced an estimate of 11.7 jaguars/100 km² while GPS-telemetry calculations produced a density of 6.7 jaguars/100 km². Our results suggest that the widely-used MMDM method used to calculate effectively sampled areas is significantly under-reflecting maximum distances moved by jaguars and their range-use and, thereby, considerably inflating cat density estimates. This overestimation could place a population in a difficult situation by lengthening the time taken to initiate protection measures because of underestimating the risk to that population.     

Genetic Diversity for Morphological and Quality Traits in Quinoa(<Emphasis Type="Italic">Chenopodium quinoa</Emphasis> Willd.) Germplasm

Twenty nine germplasm lines of Chenopodium quinoa and two of Chenopodium berlandieri subsp. nuttalliae were evaluated for 12 morphological and 7 quality traits for two test seasons. The 19 traits were analyzed for cluster and principal component analysis. The first four PCs contributed 78.70 % of the variability among the germplasm lines. The first PC accounted for 39.5% of the variation and had inflorescence/plant, plant height and stem diameter as the traits with largest coefficients, all with positive sign. The characters with greatest positive weight on PC₂ were days to maturity (0.309), inflorescence length (0.260) and branches/plant. All the germplasm lines were grouped into six clusters based on average linkage method. Cluster III had high values for seed yield and most of the quality traits but showed a small seed size. The dendrogram separated the two lines of C. berlandieri subsp. nuttalliae from the quinoa lines.     

Hierarchical Bayesian models for soil CO2 flux using soil texture: a case study in central Hokkaido,Japan

Hierarchical Bayesian (HB) methods are useful tools for modeling multifaceted, nonlinear phenomena such as those encountered in ecology, and have been increasingly applied in environmental sciences, e.g., to estimate soil gas flux from different soil textures or sites. We have developed a model of soil carbon dioxide (CO₂) flux based on soil temperature (T, 5 cm depth) and water-filled pore space (WFPS, 5 cm depth) using HB theory. The HB model was calibrated using a dataset of CO₂ flux measured from bare soils belonging to four texture classes in 14 upland field sites in a watershed in central Hokkaido, Japan, in the nonsnow-cover season from 2003 to 2011. The numerical software HYDRUS-1D was used to simulate daily WFPS, and the estimated values were significantly correlated with the measured WFPS (R² = 0.68, P < 0.001). Compared to a nonhierarchical Bayesian model (Bayesian pooled model), the CO₂ predictions with the HB model more accurately represented texture-specific observations. The simulation–observation fit of the CO₂ flux model was R² = 0.64 (P < 0.001). More than 90% of the observed daily data were within the 95% confidence interval. The HB model exhibited high uncertainty for high CO₂ flux values. The HB model calibration revealed differing sensitivity of CO₂ flux to T and WFPS in different soil texture classes. CO₂ flux increased with an increase in T, and it increased to a lesser degree with a finer texture, possibly because the clay and silt facilitated soil aggregation, thus reducing temperature fluctuations. WFPS values between 0.48 and 0.64 resulted in optimal conditions for CO₂ flux. The minimum WFPS value increased with an increase in clay content (P < 0.05). Although only a small number of soil types were studied in only one season in this study, the HB model may provide a method for predicting how the effects of soil temperature and moisture on CO₂ flux change with texture, and soil texture could be regarded as an upscaling factor in future research on regional extrapolation.     

PCR Marker-based Analysis of Wild and Cultivated Yams (<Emphasis Type="Italic">Dioscorea</Emphasis> spp.) in Nigeria: Genetic Relationships and Implications for <Emphasis Type="Italic">ex situ</Emphasis> Conservation

Reliable characterization of the variation among wild and cultivated yams in Nigeria is essential for improved management and efficient utilization of yam genetic resources. RAPD and double stringency PCR (DS-PCR) analyses were used to investigate genetic relationships and the extent of redundancy among 30 accessions of two cultivated, and 35 accessions of four wild yam species collected from Nigeria. Twenty-five selected random decamer and two microsatellite primers were used individually and in combination to generate DNA profiles for each accession of the six Dioscorea species. The number of amplified fragments varied from 7 to 18 fragments per primer/primer combination. Different levels of intraspecific genetic diversity were found, with Dioscorea rotundata Poir. being the most variable. Based on identical profiles for the RAPD and DS-PCR primers, 12 duplication groups consisting of a total number of 37 accessions were observed in the present study. An UPGMA analysis grouped the majority of plants according to the species. Cultivated yams belonging to the D. cayenensis–rotundata species complex, which were classified into seven morphotypes/varietal groups, could be clearly separated into two major groups corresponding to D. rotundata Poir. and D. cayenensis Lam. D. cayenensis cultivars exhibited a low level of intraspecific variation and were genetically close to the wild species Dioscorea burkilliana J. Miège. D. rotundata cultivars classified into six varietal groups showed a high degree of DNA polymorphism and were separated into two major groups that appeared most closely related to Dioscorea praehensilis Benth. and Dioscorea liebrechtsiana de Wild. We propose, based on these results, that cultivars classified into D. cayenensis should be considered as a taxon separate from D. rotundata. The implications of intraspecific variability for the ex situ conservation of wild and cultivated yam germplasm in Nigeria are discussed.     

Propagule Quantity and Quality in Traditional Makushi Farming of Cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis>): A Case Study for Understanding Domestication and Evolution of Vegetatively Propagated Crops

Modeling how crop plants evolve under domestication requires estimating among-plant variation in important parameters of the reproductive system, including fecundity – the number of propagules produced – and propagule quality. Measuring these traits poses particular problems in vegetatively propagated crop plants. Unlike seeds, vegetative propagules are not intrinsic biological entities but are prepared by farmers. Propagule number and quality are thus determined by the interaction between plant traits and how farmers prepare propagules. We conducted observations, interviews and experiments to study this interaction in cassava grown by Makushi Amerindians, examining how both sources of variation, in plant traits and in farmers’ practices, combine to determine the number and quality of propagules produced. Increased stake mass, determined mostly by stem diameter, leads to increased yield and also to increased asexual ‘fecundity’ of the resulting plant. Farmers’ practices reflect knowledge of this relationship. Diameter is the key criterion in the selection of stems for stakes. Larger diameters are preferred; when thinner stems are used, stakes are cut longer, partially compensating for reduced mass. These results suggest that conscious and unconscious selection to increase ‘fecundity’ and propagule quality in cassava would act to favor plants with thicker stems. Mean stem diameter is greater, and variation in stem diameter is lower, in little-branched plants. Selection for increased asexual ‘fecundity’ can thus have led to reduction in the degree of branching, one of the most striking differences between domesticated cassava and its wild ancestors. Measuring variation in asexual fecundity is a key step in analyzing evolution of the mixed clonal/sexual reproductive systems that characterize many vegetatively propagated crop plants.     

Microsatellite diversity and effective population size in a germplasm bank of <Emphasis Type="Italic">Hymenaea courbaril</Emphasis> var. <Emphasis Type="Italic">stilbocarpa</Emphasis> (Leguminosae), an endangered tropical tree: recommendations for conservation

Deforestation in southeast Brazil has led to the extinction of Hymenaea courbaril var. stilbocarpa and ex situ conservation has been established. In this study, the levels of genetic diversity and the effective population size of H. courbaril in a germplasm bank were investigated using six nuclear microsatellite loci. A total of 79 and 91 alleles were found in 65 seed-trees and their 176 offspring, respectively. Offspring have a higher average number of alleles per locus (A = 15.2) than seed-trees (A = 13.2), but lower observed heterozygosity (offspring: H _o = 0.566; seed-trees: H _o = 0.607). The estimate of outcrossing rate shows that the study population is perfectly outcrossed (t _m  = 0.978, P > 0.05). Significant deviations from random mating were detected through mating among relatives and correlated matings. The average variance in effective population size for each family was 2.63, with a total effective population size retained in the bank of 170.1. These results confirm that the preserved population of H. courbaril retains substantial genetic variability. Moacyr Antonio Mestriner and Ana Lilia Alzate-Marin—CEEFLORUSP Members.