Combining data from 43 standardized surveys to estimate densities of female American black bears by spatially explicit capture–recapture

Spatially explicit capture–recapture (SECR) models are gaining popularity for estimating densities of mammalian carnivores. They use spatially explicit encounter histories of individual animals to estimate a detection probability function described by two parameters: magnitude (g ₀), and spatial scale (σ). Carnivores exhibit heterogeneous detection probabilities and home range sizes, and exist at low densities, so g ₀ and σ likely vary, but field surveys often yield inadequate data to detect and model the variation. We sampled American black bears (Ursus americanus) on 43 study areas in ON, Canada, 2006–2009. We detected 713 animals 1810 times; however, study area-specific samples were sometimes small (6–34 individuals detected 13–93 times). We compared AIC _c values from SECR models fit to the complete data set to evaluate support for various forms of variation in g ₀ and σ, and to identify a parsimonious model for aggregating data among study areas to estimate detection parameters more precisely. Models that aggregated data within broad habitat classes and years were supported over those with study area-specific g ₀ and σ (ΔAIC _c  ≥ 30), and precision was enhanced. Several other forms of variation in g ₀ and σ, including individual heterogeneity, were also supported and affected density estimates. If study design cannot eliminate detection heterogeneity, it should ensure that samples are sufficient to detect and model it. Where this is not feasible, combing sparse data across multiple surveys could allow for improved inference.     

Effective size of density‐dependent two‐sex populations: the effect of mating systems

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N_e in short‐lived, density‐dependent animal populations with different mating systems. We study the impact of a fluctuating, density‐dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N_e/N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male‐biased, density‐dependent sex ratio reduces the rate of genetic drift compared to an equal, density‐independent sex ratio, but a stochastic change towards male bias reduces the N_e/N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.     

Estimating population size by spatially explicit capture–recapture

The number of animals in a population is conventionally estimated by capture–recapture without modelling the spatial relationships between animals and detectors. Problems arise with non‐spatial estimators when individuals differ in their exposure to traps or the target population is poorly defined. Spatially explicit capture–recapture (SECR) methods devised recently to estimate population density largely avoid these problems. Some applications require estimates of population size rather than density, and population size in a defined area may be obtained as a derived parameter from SECR models. While this use of SECR has potential benefits over conventional capture–recapture, including reduced bias, it is unfamiliar to field biologists and no study has examined the precision and robustness of the estimates. We used simulation to compare the performance of SECR and conventional estimators of population size with respect to bias and confidence interval coverage for several spatial scenarios. Three possible estimators for the sampling variance of realised population size all performed well. The precision of SECR estimates was nearly the same as that of the null‐model conventional population estimator. SECR estimates of population size were nearly unbiased (relative bias 0–10%) in all scenarios, including surveys in randomly generated patchy landscapes. Confidence interval coverage was near the nominal level. We used SECR to estimate the population of a species of skink Oligosoma infrapunctatum from pitfall trapping. The estimated number in the area bounded by the outermost traps differed little between a homogeneous density model and models with a quadratic trend in density or a habitat effect on density, despite evidence that the latter models fitted better. Extrapolation of trend models to a larger plot may be misleading. To avoid extrapolation, a large region of interest should be sampled throughout, either with one continuous trapping grid or with clusters of traps dispersed widely according to a probability‐based and spatially representative sampling design.     

Guidelines for standardizing the application of discriminant analysis of principal components to genotype data

Despite the popularity of discriminant analysis of principal components (DAPC) for studying population structure, there has been little discussion of best practice for this method. In this work, I provide guidelines for standardizing the application of DAPC to genotype data sets. An often overlooked fact is that DAPC generates a model describing genetic differences among a set of populations defined by a researcher. Appropriate parameterization of this model is critical for obtaining biologically meaningful results. I show that the number of leading PC axes used as predictors of among-population differences, p_axes, should not exceed the k−1 biologically informative PC axes that are expected for k effective populations in a genotype data set. This k−1 criterion for p_axes specification is more appropriate compared to the widely used proportional variance criterion, which often results in a choice of p_axes ≫ k−1. DAPC parameterized with no more than the leading k−1 PC axes: (i) is more parsimonious; (ii) captures maximal among-population variation on biologically relevant predictors; (iii) is less sensitive to unintended interpretations of population structure; and (iv) is more generally applicable to independent sample sets. Assessing model fit should be routine practice and aids interpretation of population structure. It is imperative that researchers articulate their study goals, that is, testing a priori expectations vs. studying de novo inferred populations, because this has implications on how their DAPC results should be interpreted. The discussion and practical recommendations in this work provide the molecular ecology community with a roadmap for using DAPC in population genetic investigations.     

Spatiotemporal mating pattern variation in a wind‐pollinated Mediterranean shrub

Spatiotemporal variation in mating patterns is poorly known in wind‐pollinated plant species. Here, we analysed mating patterns of the wind‐pollinated dioecious shrub Pistacia lentiscus by genotyping 904 seeds from 30 mother plants with eight microsatellite markers in a high‐density population in two consecutive flowering seasons. We found significant differences in some mating system estimates between years, particularly in the levels of correlated paternity. Overall, within‐mothers correlated paternity was higher in 2007 than in 2006 (r_pWM = 0.085 and 0.030), which translated into an effective number of fathers (N_ep) of 11.8 and 33.6 respectively. Using a smoothing interpolation technique, we show that the effective pollen cloud was spatially structured in patches of high‐ and low‐genetic diversity, which do not remain constant from year to year. In 2006, the among‐mothers correlated paternity (r_pAM) showed no trend with distance, suggesting no restriction of pollen dispersal. However, in 2007, r_pAM was greater than zero at short distances, revealing the existence of small‐scale patterns of pollen dispersal. The fact that the studied seasons were climatically homogeneous during the flowering time suggested that the observed differences might be ascribed to between‐year phenological variation of individuals in the studied population or other (unknown) factors. Numerical simulations, based on the real data set, indicated that the clumping of males and decreasing plant density, which is related to different types of pollen limitation, greatly increase correlated mating in this wind‐pollinated species, which is of relevance under the frame of the continuous anthropogenic habitat disturbance suffered by Mediterranean ecosystems.     

Optimal age of maturity in fluctuating environments under r‐ and K‐selection

Optimality models for evolution of life histories have shown that increased environmental stochasticity promotes early age of maturity. Here we argue that if r‐selection for early maturation implies a tradeoff making those phenotypes more sensitive to a change in population size than phenotypes maturing at older ages, K‐selection can favor delayed onset of maturation. We analyze a general stochastic Leslie‐matrix model with a simplified density regulation affecting all survivals equally through a function of the population vector, often called the ‘critical age class’. We show that the outcome of such an age‐dependent r‐ and K‐selection is that the expected value of the ‘critical age class’ is maximized by evolution, a strategy strongly influenced by the magnitude of the environmental stochasticity. We also demonstrate that evolution caused by such density‐dependent selection influences the population dynamics, showing a possible reciprocal effect between ecology and evolution in age‐structured populations. This modeling approach reveals that changes in population size affecting the fitness of phenotypes with different age of maturity may be an important selective agent for variation in onset of reproduction in fluctuating environments. This provides a testable hypothesis for how patterns in the population dynamics should affect life history variation.     

Genetic diversity,population structure and sex‐biased dispersal in three co‐evolving species

Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analysed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost’s D_est ), we detected strong population structuring in all species and less male‐biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post‐glacial colonization routes – northern populations are as variable as more southern populations. We conclude that conditions for Thompson’s geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.     

Consequences of multiple mating‐system shifts for population and range‐wide genetic structure in a coastal dune plant

Evolutionary transitions from outcrossing to selfing can strongly affect the genetic diversity and structure of species at multiple spatial scales. We investigated the genetic consequences of mating‐system shifts in the North American, Pacific coast dune endemic plant Camissoniopsis cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and six chloroplast (cp) microsatellite (SSR) loci for 38 populations across the species range. As predicted from the expected reduction in effective population size (N_e) caused by selfing, small‐flowered, predominantly selfing (SF) populations had much lower nSSR diversity (but not cpSSR) than large‐flowered, predominantly outcrossing (LF) populations. The reduction in nSSR diversity was greater than expected from the effects of selfing on N_e alone, but could not be accounted for by indirect effects of selfing on population density. Although selfing should reduce gene flow, SF populations were not more genetically differentiated than LF populations. We detected five clusters of nSSR genotypes and three groups of cpSSR haplotypes across the species range consisting of parapatric groups of populations that usually (but not always) differed in mating system, suggesting that selfing may often initiate ecogeographic isolation. However, lineage‐wide genetic variation was not lower for selfing clusters, failing to support the hypothesis that selection for reproductive assurance spurred the evolution of selfing in this species. Within three populations where LF and SF plants coexist, we detected genetic differentiation among diverged floral phenotypes suggesting that reproductive isolation (probably postzygotic) may help maintain the striking mating‐system differentiation observed across the range of this species.     

Climate‐driven vital rates do not always mean climate‐driven population

Current climatic changes have increased the need to forecast population responses to climate variability. A common approach to address this question is through models that project current population state using the functional relationship between demographic rates and climatic variables. We argue that this approach can lead to erroneous conclusions when interpopulation dispersal is not considered. We found that immigration can release the population from climate‐driven trajectories even when local vital rates are climate dependent. We illustrated this using individual‐based data on a trans‐equatorial migratory seabird, the Scopoli's shearwater Calonectris diomedea, in which the variation of vital rates has been associated with large‐scale climatic indices. We compared the population annual growth rate λ_i, estimated using local climate‐driven parameters with ρ_i, a population growth rate directly estimated from individual information and that accounts for immigration. While λ_i varied as a function of climatic variables, reflecting the climate‐dependent parameters, ρ_i did not, indicating that dispersal decouples the relationship between population growth and climate variables from that between climatic variables and vital rates. Our results suggest caution when assessing demographic effects of climatic variability especially in open populations for very mobile organisms such as fish, marine mammals, bats, or birds. When a population model cannot be validated or it is not detailed enough, ignoring immigration might lead to misleading climate‐driven projections.     

Enantiomeric Recognition of Racemic 4‐Aryl‐1,4‐dihydropyridine Derivatives via Chiralpak AD‐H Stationary Phases

The chromatographic chiral resolution of two new series of racemic 4‐substituted‐1,4‐dihydropyridine derivatives was studied on a commercial Chiralpak AD‐H column. Analytes without 5,5‐dimethyl substituents ( 1–15 ) are more efficiently resolved than analytes with 5,5‐dimethyl groups ( 16–30 ). The AD‐H column discriminated between enantiomers through both hydrogen bonding attractions and π–π interactions. This interpretation is in accord with plots of the logarithm of separation factors, log(α), versus σ (Hammett–Swain substituent parameter) and σ⁺ (Brown substituent constant) plots. By elucidating the effects of the remote substituents on these chiral separations, it was shown that the influence of π–π interaction forces increase when steric bulk effects act to decrease the hydrogen bonding attractive forces on the AD‐H column. Chirality 24:854–859, 2012. © 2012 Wiley Periodicals, Inc.     

Land tenure shapes black bear density and abundance on a multi‐use landscape

Global biodiversity is decreasing rapidly. Parks and protected lands, while designed to conserve wildlife, often cannot provide the habitat protection needed for wide‐ranging animals such as the American black bear (Ursus americanus). Conversely, private lands are often working landscapes (e.g., farming) that have high human footprints relative to protected lands. In southwestern Alberta, road densities are highest on private lands and black bears can be hunted year‐round. On protected lands, road densities are lowest, and hunting is prohibited. On public lands under the jurisdiction of the provincial government (Crown lands), seasonal hunting is permitted. Population estimates are needed to calculate sustainable harvest levels and to monitor population trends. In our study area, there has never been a robust estimate of black bear density and spatial drivers of black bear density are poorly understood. We used non‐invasive genetic sampling and indices of habitat productivity and human disturbance to estimate density and abundance for male and female black bears in 2013 and 2014 using two methods: spatially explicit capture–recapture (SECR) and resource‐selection functions (RSF). Land tenure best explained spatial variation in black bear density. Black bear densities for females and males were highest on parkland and lowest on Crown lands. Sex ratios were female‐biased on private lands, likely a result of lower harvests and movement of females out of areas with high male density. Synthesis and application: Both SECR and RSF methods clearly indicate spatial structuring of black bear density, with a strong influence based on how lands are managed. Land tenure influences the distribution of available foods and risk from humans. We emphasize the need for improved harvest reporting, particularly for non‐licensed hunting on private land, to estimate the extent of black bear harvest mortality.     

Least Favorable Parameter Configurations for a Step‐down Subset Selection Procedure

Given a k‐dimensional vector X , k≥2, the range‐type statistic with J⊆I≡{1, …, k}, plays an important role in stepwise subset selection as well as in testing whether a<?tlb> prespecified subset of k populations exclusively consists of good ones. Although in previous papers least favorable parameter configurations (LFC's) for this statistic, which are worth knowing for the calculations of critical values, have been already shown to be from a small finite subset of the parameter space, further reduction has been conjectured. Under the assumption of a log‐concave and symmetric Lebesgue density with shift parameter, it is proved that in many cases the LFC can be uniquely given or, at least, found among only a few candidates. The resulting step‐down selection procedure will be illustrated for data from a balanced incomplete block design.     

Evaluating the potential biases in carnivore capture–recapture studies associated with the use of lure and varying density estimation techniques using photographic-sampling data of the Malagasy civet

Estimating density of elusive carnivores with capture–recapture analyses is increasingly common. However, providing unbiased and precise estimates is still a challenge due to uncertainties arising from the use of (1) bait or lure to attract animals to the detection device and (2) ad hoc boundary-strip methods to compensate for edge effects in area estimation. We used photographic-sampling data of the Malagasy civet Fossa fossana collected with and without lure to assess the effects of lure and to compare the use of four density estimators which varied in methods of area estimation. The use of lure did not affect permanent immigration or emigration, abundance and density estimation, maximum movement distances, or temporal activity patterns of Malagasy civets, but did provide more precise population estimates by increasing the number of recaptures. The spatially-explicit capture–recapture (SECR) model density estimates ±SE were the least precise as they incorporate spatial variation, but consistent with each other (Maximum likelihood-SECR = 1.38 ± 0.18, Bayesian-SECR = 1.24 ± 0.17 civets/km²), whereas estimates relying on boundary-strip methods to estimate effective trapping area did not incorporate spatial variation, varied greatly and were generally larger than SECR model estimates. Estimating carnivore density with ad hoc boundary-strip methods can lead to overestimation and/or increased uncertainty as they do not incorporate spatial variation. This may lead to inaction or poor management decisions which may jeopardize at-risk populations. In contrast, SECR models free researchers from making subjective decisions associated with boundary-strip methods and they estimate density directly, providing more comparable and valuable population estimates.     

Using time‐of‐detection to evaluate detectability assumptions in temporally replicated aural count indices: an example with Ring‐necked Pheasants

ABSTRACT The validity of treating counts as indices to abundance is based on the assumption that the expected detection probability, E(p), is constant over time or comparison groups or, more realistically, that variation in p is small relative to variation in population size that investigators seek to detect. Unfortunately, reliable estimates of E(p) and var(p) are lacking for most index methods. As a case study, we applied the time‐of‐detection method to temporally replicated (within season) aural counts of crowing male Ring‐necked Pheasants (Phasianus colchicus) at 18 sites in southern Minnesota in 2007 to evaluate the detectability assumptions. More specifically, we used the time‐of‐detection method to estimate E(p) and var(p), and then used these estimates in a Monte Carlo simulation to evaluate bias‐variance tradeoffs associated with adjusting count indices for imperfect detection. The estimated mean detection probability in our case study was 0.533 (SE = 0.030) and estimated spatial variation in E(p) was 0.081 (95% CI: 0.057–0.126). On average, both adjusted (for) and unadjusted counts of crowing males qualitatively described the simulated relationship between pheasant abundance and grassland abundance, but the bias‐variance tradeoff was smaller for adjusted counts (MSE = 0.003 vs. 0.045, respectively). Our case study supports the general recommendation to use, whenever feasible, formal population‐estimation procedures (e.g., mark‐recapture, distance sampling, double sampling) to account for imperfect detection. However, we caution that interpreting estimates of absolute abundance can be complicated, even if formal estimation methods are used. For example, the time‐of‐detection method was useful for evaluating detectability assumptions in our case study and the method could be used to adjust aural count indices for imperfect detection. Conversely, using the time‐of‐detection method to estimate absolute abundances in our case study was problematic because the biological populations and sampling coverage could not be clearly delineated. These estimation and inference challenges may also be important in other avian surveys that involve mobile species (whose home ranges may overlap several sampling sites), temporally replicated counts, and inexact sampling coverage.     

The effects of selection,drift and genetic variation on life‐history trait divergence among insular populations of natterjack toad,Bufo calamita

Although loss of genetic variation is frequently assumed to be associated with loss of adaptive potential, only few studies have examined adaptation in populations with little genetic variation. On the Swedish west coast, the northern fringe populations of the natterjack toad Bufo calamita inhabit an atypical habitat consisting of offshore rock islands. There are strong among‐population differences in the amount of neutral genetic variation, making this system suitable for studies on mechanisms of trait divergence along a gradient of within‐population genetic variation. In this study, we examined the mechanisms of population divergence using Q_ST–F_ST comparisons and correlations between quantitative and neutral genetic variation. Our results suggest drift or weak stabilizing selection across the six populations included in this study, as indicated by low Q_ST–F_ST values, lack of significant population × temperature interactions and lack of significant differences among the islands in breeding pond size. The six populations included in this study differed in both neutral and quantitative genetic variation. Also, the correlations between neutral and quantitative genetic variation tended to be positive, however, the relatively small number of populations prevents any strong conclusions based on these correlations. Contrary to the majority of Q_ST–F_ST comparisons, our results suggest drift or weak stabilizing selection across the examined populations. Furthermore, the low heritability of fitness‐related traits may limit evolutionary responses in some of the populations.     

SEXUAL SELECTION CAN INCREASE THE EFFECT OF RANDOM GENETIC DRIFT—A QUANTITATIVE GENETIC MODEL OF POLYMORPHISM IN OOPHAGA PUMILIO,THE STRAWBERRY POISON‐DART FROG

The variation in color pattern between populations of the poison‐dart frog Oophaga pumilio across the Bocas del Toro archipelago in Panama is suggested to be due to sexual selection, as two other nonsexually selecting Dendrobatid species found in the same habitat and range do not exhibit this variation. We theoretically test this assertion using a quantitative genetic sexual selection model incorporating aposematic coloration and random drift. We find that sexual selection could cause the observed variation via a novel process we call “coupled drift.” Within our model, for certain parameter values, sexual selection forces frog color to closely follow the evolution of female preference. Any between‐population variation in preference due to genetic drift is passed on to color. If female preference in O. pumilio is strongly affected by drift, whereas color in the nonsexually selecting Dendrobatid species is not, coupled drift will cause increased between‐population phenotypic variation. However, with different parameter values, coupled drift will result in between‐population variation in color being suppressed compared to its neutral value, or in little or no effect. We suggest that coupled drift is a novel theoretical process that could have a role linking sexual selection with speciation both in O. pumilio, and perhaps more generally.     

Pre‐Hispanic Mesoamerican demography approximates the present‐day ancestry of Mestizos throughout the territory of Mexico

Over the last 500 years, admixture among Amerindians, Europeans, and Africans, principally, has come to shape the present‐day gene pool of Mexicans, particularly Mestizos, who represent about 93% of the total Mexican population. In this work, we analyze the genetic data of 13 combined DNA index system‐short tandem repeats (CODIS‐STRs) in 1,984 unrelated Mestizos representing 10 population samples from different regions of Mexico, namely North, West, Central, and Southeast. The analysis of molecular variance (AMOVA) test demonstrated low but significant differentiation among Mestizos from different regions (F_ST = 0.34%; P = 0.0000). Although the spatial analysis of molecular variance (SAMOVA) predicted clustering Mestizo populations into four well‐delimited groups, the main differentiation was observed between Northwest when compared with Central and Southeast regions. In addition, we included analysis of individuals of Amerindian (Purepechas), European (Huelva, Spain), and African (Fang) origin. Thus, STRUCTURE analysis was performed identifying three well‐differentiated ancestral populations (k = 3). STRUCTURE results and admixture estimations by means of LEADMIX software in Mestizo populations demonstrated genetic heterogeneity or asymmetric admixture throughout Mexico, displaying an increasing North‐to‐South gradient of Amerindian ancestry, and vice versa regarding the European component. Interestingly, this distribution of Amerindian ancestry roughly reflects pre‐Hispanic Native‐population density, particularly toward the Mesoamerican area. The forensic, epidemiological, and evolutionary implications of these findings are discussed herein. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.