Population assessment without individual identification using camera-traps: A comparison of four methods

The use of camera traps to estimate population size when animals are not individually recognizable is gaining traction in the ecological literature, because of its applicability in population conservation and management.We estimated population size of synthetic animals with four camera trap sampling-based statistical models that do not rely on individual recognition. Using a realistic model of animal movement to generate synthetic data, we compared the random encounter model, the random encounter and staying time model, the association model and the time-to-event-model and we investigated the impact of violation of assumptions on the population size estimates.While under ideal conditions these models provide reliable population estimates, when synthetic animal movements were characterised by differences in speed (due to diverse behaviours such as locomotion, grazing and resting) none of the model provided both unbiased and precise density estimates. The random encounter model and the time-to-event-model provided precise results but tended to overestimate population size, while the random encounter and staying time model was less precise and tended to underestimate population size. Lastly, the association model was unable to provide precise results. We found that each tested model was very sensitive to the method used to estimate the range of the field-of-view of camera traps. Density estimates from both random encounter model and time-to-event-model were also very sensitive to biases in the estimate of animals’ speed. We provide guidelines on how to use these statistical models to get population size estimates that could be useful to wildlife managers and practitioners.     

Planning and Assessment of Activity Budget Studies Employing Instantaneous Sampling

To obtain accurate estimates of activity budget parameters, samples must be unbiased and precise. Many researchers have considered how biased data may affect their ability to draw conclusions and examined ways to decrease bias in sampling efforts, but few have addressed the implications of not considering estimate precision. We propose a method to assess whether the number of instantaneous samples collected is sufficient to obtain precise activity budget parameter estimates. We draw on sampling theory to determine the number of observations per animal required to reach a desired bound on the error of estimation based on a stratified random sample, with individual animals acting as strata. We also discuss the optimal balance between the number of individuals sampled and the number of observations sampled per individual for a variety of sampling conditions. We present an empirical dataset on pronghorn (Antilocapra americana) as an example of the utility of the method. The required numbers of observation to reach precise estimates for pronghorn varied between common and rare behaviors, but precise estimates were achieved with <255 observations per individual for common behaviors. The two most apparent factors affecting the required number of observations for precise estimates were the number of individuals sampled and the complexity of the activity budget. This technique takes into account variation associated with individual activity budgets and population variation in activity budget parameter estimates, and helps to ensure that estimates are precise. The method can also be used for planning future sampling efforts.     

Correcting for measurement error in individual ancestry estimates in structured association tests

We present theoretical explanations and show through simulation that the individual admixture proportion estimates obtained by using ancestry informative markers should be seen as an error-contaminated measurement of the underlying individual ancestry proportion. These estimates can be used in structured association tests as a control variable to limit type I error inflation or reduce loss of power due to population stratification observed in studies of admixed populations. However, the inclusion of such error-containing variables as covariates in regression models can bias parameter estimates and reduce ability to control for the confounding effect of admixture in genetic association tests. Measurement error correction methods offer a way to overcome this problem but require an a priori estimate of the measurement error variance. We show how an upper bound of this variance can be obtained, present four measurement error correction methods that are applicable to this problem, and conduct a simulation study to compare their utility in the case where the admixed population results from the intermating between two ancestral populations. Our results show that the quadratic measurement error correction (QMEC) method performs better than the other methods and maintains the type I error to its nominal level.     

Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population

The effects of intermating on recombination and the development of linkage maps were assessed in maize. Progeny derived from a common population (B73 × Mo17) before and after five generations of intermating were genotyped at the same set of 190 RFLP loci. Intermating resulted in nearly a four-fold increase in the genetic map distance and increased the potential for improved genetic resolution in 91% of the intervals evaluated. This mapping population and related information should connect research involving dense genetic maps, physical mapping, gene isolation, comparative genomics, analysis of quantitative trait loci and investigations of heterosis.     

Correlation studies on yield and fibre traits in upland cotton (Gossypium hirsutum L.)

Summary Two diverse parents of upland cotton namely J.34 and I.C. 1926 were crossed. A comparison between biparental intermated progenies and F₃ families indicated alteration of correlation coefficient between yield and halo length. The significant negative correlation in F₃ population between these two attributes changed to a positive but non significant one in biparental intermated progenies. A change in correlation coefficients was expected due to breakage of linkage upon intermating. An increase in the correlation coefficients could also be expected when linkages are predominantly in the repulsion phase. It is suggested that intermating in early generations coupled with selection of desirable segregants may prove a useful method for improving yield and quality simultaneously. The diallel selective mating system may also supplement intermating to improve yield and quality in cotton.Part of Ph.D. Thesis submitted to the Haryana Agricultural University. Hissar-125004, India     

Linkage disequilibrium in two European F<Subscript>2</Subscript> flint maize populations under modified recurrent full-sib selection

According to quantitative genetic theory, linkage disequilibrium (LD) can hamper the short- and long-term selection response in recurrent selection (RS) programs. We analyzed LD in two European flint maize populations, KW1265 x D146 (A x B) and D145 x KW1292 (C x D), under modified recurrent full-sib selection. Our objectives were to investigate (1) the decay of initial parental LD present in F(2) populations by three generations of intermating, (2) the generation of new LD in four (A x B) and seven (C x D) selection cycles, and (3) the relationship between LD changes and estimates of the additive genetic variance. We analyzed the F(2) and the intermated populations as well as all selection cycles with 104 (A x B) and 101 (C x D) simple sequence repeat (SSR) markers with a uniform coverage of the entire maize genome. The LD coefficient D and the composite LD measure Delta were estimated and significance tests for LD were performed. LD was reduced by intermating as expected from theory. A directional generation of negative LD between favorable alleles could not be observed during the selection cycles. However, considerable undirectional changes in D were observed, which we attributed to genetic sampling due to the finite population size used for recombination. Consequently, a long-term reduction of the additive genetic variance due to negative LD was not observed. Our experimental results support the hypothesis that in practical RS programs with maize, LD generated by selection is not a limiting factor for obtaining a high selection response.     

Comparison of single seed descent,selective intermating and mass selection for seed size in greengram (Vigna radiata (L.) Wilczek)

Summary Three selection methods (single seed descent (SSD), mass selection and selective intermating) were applied simultaneously to a highly heterogeneous and broadly based population of greengram. Progeny developing after two cycles of selection were evaluated for yield and seven other economic characters. The relative efficacy of each selection method was judged on the basis of the number of high yielding progeny, mean yield of top 10% progeny, and mean of the highest yielding progeny. Selection after two cycles of selective intermating was found to be the best method for generating productive progeny although mass selection favouring smaller seeds was an equally efficient method. Both of these were found superior to SSD selection.     

Comparative efficacy of pedigree selection and selective intermating in greengram (Vigna radiata (L.) Wilczek)

Summary Selective intermating and pedigree selection methods were applied simultaneously to highly heterogeneous and heterozygous base populations of greengram in order to compare their relative efficacy in terms of evolving the number of productive lines as well as their production potential. Selection after two cycles of selective intermating was found to be a better method than traditional pedigree selection. The demerits of pedigree selection and merits of selective intermating are discussed. It is suggested that selective intermating replace the widely adopted but less effective pedigree selection for generating promising new material in such autogamous crops as greengram.Part of Ph.D. Thesis submitted by the senior author to the Haryana Agricultural University, Hisar, India     

Genetic improvement of anther culture response in maize: relationships with molecular, Mendelian and agronomic traits

 Two cycles of androgenetic in vitro doubled haploid (DH) plant production and intermating were implemented in an experimental synthetic population of maize. In vitro traits, including androgenetic embryo production, the regeneration potential and the frequency of spontaneous chromosome doubling, were studied. The success of the regenerated plants to self pollinate was also observed. Impressive genetic progress is reported for all the steps of the androgenetic process including seed set. Differential genetic progress is recorded according to the trait measured. Using a set of Mendelian and molecular markers that mapped to the different maize chromosomes, we were able to characterize the variation in the genetic variability in the population. Progress in the in vitro response was not found to be associated with any noticeable decline in global genetic variability. In addition, the QTL chromosomic regions tested, which were involved in androgenetic response, were not found to be subjected to a strong variation during the breeding experiment. Some phenotypical and morphological traits were also evaluated, and these showed that there was no depreciation effect in the agronomic value of the population. DH plant production and intermating the regenerated plants may be considered for the introduction and use of androgenesis in material which responds poorly. Received: 3 October 1997 / Accepted: 25 November 1997     

An Evaluation of Sex-Age-Kill (SAK) Model Performance

ABSTRACT The sex-age-kill (SAK) model is widely used to estimate abundance of harvested large mammals, including white-tailed deer (Odocoileus virginianus). Despite a long history of use, few formal evaluations of SAK performance exist. We investigated how violations of the stable age distribution and stationary population assumption, changes to male or female harvest, stochastic effects (i.e., random fluctuations in recruitment and survival), and sampling efforts influenced SAK estimation. When the simulated population had a stable age distribution and λ > 1, the SAK model underestimated abundance. Conversely, when λ < 1, the SAK overestimated abundance. When changes to male harvest were introduced, SAK estimates were opposite the true population trend. In contrast, SAK estimates were robust to changes in female harvest rates. Stochastic effects caused SAK estimates to fluctuate about their equilibrium abundance, but the effect dampened as the size of the surveyed population increased. When we considered both stochastic effects and sampling error at a deer management unit scale the resultant abundance estimates were within ±121.9% of the true population level 95% of the time. These combined results demonstrate extreme sensitivity to model violations and scale of analysis. Without changes to model formulation, the SAK model will be biased when λ ≠ 1. Furthermore, any factor that alters the male harvest rate, such as changes to regulations or changes in hunter attitudes, will bias population estimates. Sex-age-kill estimates may be precise at large spatial scales, such as the state level, but less so at the individual management unit level. Alternative models, such as statistical age-at-harvest models, which require similar data types, might allow for more robust, broad-scale demographic assessments.     

Evaluating sampling designs by computer simulation: a case study with the Missouri bladderpod

To effectively manage rare populations, accurate monitoring data are critical. Yet many monitoring programs are initiated without careful consideration of whether chosen sampling designs will provide accurate estimates of population parameters. Obtaining accurate estimates is especially difficult when natural variability is high, or limited budgets determine that only a small fraction of the population can be sampled. The Missouri bladderpod, Lesquerella filiformis Rollins, is a federally threatened winter annual that has an aggregated distribution pattern and exhibits dramatic interannual population fluctuations. Using the simulation program SAMPLE, we evaluated five candidate sampling designs appropriate for rare populations, based on 4 years of field data: (1) simple random sampling, (2) adaptive simple random sampling, (3) grid-based systematic sampling, (4) adaptive grid-based systematic sampling, and (5) GIS-based adaptive sampling. We compared the designs based on the precision of density estimates for fixed sample size, cost, and distance traveled. Sampling fraction and cost were the most important factors determining precision of density estimates, and relative design performance changed across the range of sampling fractions. Adaptive designs did not provide uniformly more precise estimates than conventional designs, in part because the spatial distribution of L. filiformis was relatively widespread within the study site. Adaptive designs tended to perform better as sampling fraction increased and when sampling costs, particularly distance traveled, were taken into account. The rate that units occupied by L. filiformis were encountered was higher for adaptive than for conventional designs. Overall, grid-based systematic designs were more efficient and practically implemented than the others. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors

Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human population experienced a severe size reduction in its early evolutionary history. In this study, the Bayesian method of ancestral inference of Rannala and Yang (2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656) was extended to accommodate variable mutation rates among loci and random species-specific sequencing errors. The model was applied to analyze a genome-wide data set of approximately 15,000 neutral loci (7.4 Mb) aligned for human, chimpanzee, gorilla, orangutan, and macaque. We obtained robust and precise estimates for effective population sizes along the hominoid lineage extending back approximately 30 Myr to the cercopithecoid divergence. The results showed that ancestral populations were 5-10 times larger than modern humans along the entire hominoid lineage. The estimates were robust to the priors used and to model assumptions about recombination. The unusually low X chromosome divergence between human and chimpanzee could not be explained by variation in the male mutation bias or by current models of hybridization and introgression. Instead, our parameter estimates were consistent with a simple instantaneous process for human-chimpanzee speciation but showed a major reduction in X chromosome effective population size peculiar to the human-chimpanzee common ancestor, possibly due to selective sweeps on the X prior to separation of the 2 species.     

Estimating Abundance of an Unmarked,Low-Density Species using Cameras

Estimating abundance of wildlife populations can be challenging and costly, especially for species that are difficult to detect and that live at low densities, such as cougars (Puma concolor). Remote, motion-sensitive cameras are a relatively efficient monitoring tool, but most abundance estimation techniques using remote cameras rely on some or all of the population being uniquely identifiable. Recently developed methods estimate abundance from encounter rates with remote cameras and do not require identifiable individuals. We used 2 methods, the time-to-event and space-to-event models, to estimate the density of 2 cougar populations in Idaho, USA, over 3 winters from 2016–2019. We concurrently estimated cougar density using the random encounter model (REM), an existing camera-based method for unmarked populations, and genetic spatial capture recapture (SCR), an established method for monitoring cougar populations. In surveys for which we successfully estimated density using the SCR model, the time-to-event estimates were more precise and showed comparable variation between survey years. The space-to-event estimates were less precise than the SCR estimates and were more variable between survey years. Compared to REM, time-to-event was more precise and consistent, and space-to-event was less precise and consistent. Low sample sizes made the space-to-event and SCR models inconsistent from survey to survey, and non-random camera placement may have biased both of the camera-based estimators high. We show that camera-based estimators can perform comparably to existing methods for estimating abundance in unmarked species that live at low densities. With the time- and space-to-event models, managers could use remote cameras to monitor populations of multiple species at broader spatial and temporal scales than existing methods allow. © 2020 The Wildlife Society.     

Estimating genetic drift and effective population size from temporal shifts in dominant gene marker frequencies

Measurement of temporal change in allele frequencies represents an indirect method for estimating the genetically effective size of populations. When allele frequencies are estimated for gene markers that display dominant gene expression, such as, e.g. random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers, the estimates can be seriously biased. We quantify bias for previous allele frequency estimators and present a new expression that is generally less biased and provides a more precise assessment of temporal allele frequency change. We further develop an estimator for effective population size that is appropriate when dealing with dominant gene markers. Comparison with estimates based on codominantly expressed genes, such as allozymes or microsatellites, indicates that about twice as many loci or sampled individuals are required when using dominant markers to achieve the same precision.     

Precision and accuracy of divergence time estimates from STR and SNPSTR variation

Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically < 500 bp) to one or more single-nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should, therefore, be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3% to 7% bias for SNPSTR versus 11% to 20% bias for STR) and more precise than STR-based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.     

Genetic relatedness in the antCamponotus herculeanus. A comparison of estimates from allozyme and DNA microsatellite markers

Summary Genetic structure ofCamponotus herculeanus populations was studied using both traditional allozyme markers and recently discovered DNA microsatellites. Relatedness among worker nest mates was high in one study population (0.70), but lower in another (0.48). The estimates lower than 0.75, together with the multilocus genotype patterns, indicate either multiple mating by queens, or multiple queens reproducing in the colonies. These two could not be distinguished with the current data, although multiple matings seem a more probable explanation for the relatedness estimates bearing social biology of the species in mind. Inbreeding coefficients suggested random mating in both populations. Both allozyme and DNA microsatellite markers gave the same result concerning genetic parameters estimated, but the higher variability of the microsatellites resulted in more precise estimates of both parameters.     

A statistical analysis of subsampling and an evaluation of the Folsom plankton splitter

Subsampling techniques are important for the determination of precise plankton density estimates. A binomial model of random subsampling, and its Poisson extension, were developed for the purpose of evaluating the performance of compartment-type plankton subsamplers. Two approaches were used to assess the performance of the Folsom plankton splitter on an extensive series of nearshore Lake Michigan crustacean zooplankton samples collected between 1974 and 1979. First, Folsom subsamples were observed to be significantly (p < 0.05) more variable than expected from the random model of subsampling. Second, a random effects ANOVA model was used to compare fractions of the total variance in density estimates that were attributable to subsampling and sampling phases of a specially designed study. Departures from randomness in subsampling were sufficiently small that an analysis of optimal allocation of effort between subsampling and sampling phases, based on the ANOVA model, indicated that only one to three subsamples needed to be examined per sample.     

AN OCEAN-BASIN-WIDE MARK-RECAPTURE STUDY OF THE NORTH ATLANTIC HUMPBACK WHALE (MEGAPTERA NOVAEANGLIAE)

Although much is known about the humpback whale, Megaptera novaeangliae, regional studies have been unable to answer several questions that are central to the conservation and management of this endangered species. To resolve uncertainties about population size, as well as the spatial and genetic structure of the humpback whale population in the North Atlantic, we conducted a two-year ocean-basin-wide photographic and biopsy study in 1992-1993. Photographic and skin-biopsy sampling was conducted of animals in feeding and breeding areas throughout most of the range of this species in the North Atlantic, from the West Indies breeding grounds through all known feeding areas as far north as arctic Norway. A standardized sampling protocol was designed to maximize sample sizes while attempting to ensure equal probability of sampling, so that estimates of abundance would be as accurate and as precise as possible. During 666 d at sea aboard 28 vessels, 4,207 tail fluke photographs and 2,326 skin biopsies were collected. Molecular analyses of all biopsies included determination of sex, genotype using six microsatellite loci, and mitochondrial control region sequence. The photographs and microsatellite loci were used to identify 2,998 and 2,015 individual whales, respectively. Previously published results from this study have addressed spatial distribution, migration, and genetic relationships. Here, we present new estimates of total abundance in this ocean using photographic data, as well as overall and sex-specific estimates using biopsy data. We identify several potential sampling biases using only breeding-area samples and report a consistent mark-recapture estimate of oceanwide abundance derived from photographic identification, using both breeding and feeding-area data, of 10,600 (95% confidence interval 9,300-12,100). We also report a comparable, but less precise, biopsy-based estimate of 10,400 (95% confidence interval of 8,000-13,600). These estimates are significantly larger and more precise than estimates made for the 1980s, potentially reflecting population growth. In contrast, significantly lower and less consistent estimates were obtained using between-feeding-area or between-breeding-area sampling. Reasons for the lower estimates using the results of sampling in the same areas in subsequent years are discussed. Overall, the results of this ocean-basin-wide study demonstrate that an oceanwide approach to population assessment of baleen whales is practicable and results in a more comprehensive understanding of population abundance and biology than can be gained from smaller-scale efforts.     

Linkage disequilibrium in two European F<Subscript>2</Subscript> flint maize populations under modified recurrent full-sib selection

According to quantitative genetic theory, linkage disequilibrium (LD) can hamper the short- and long-term selection response in recurrent selection (RS) programs. We analyzed LD in two European flint maize populations, KW1265 × D146 (A × B) and D145 × KW1292 (C × D), under modified recurrent full-sib selection. Our objectives were to investigate (1) the decay of initial parental LD present in F₂ populations by three generations of intermating, (2) the generation of new LD in four (A × B) and seven (C × D) selection cycles, and (3) the relationship between LD changes and estimates of the additive genetic variance. We analyzed the F₂ and the intermated populations as well as all selection cycles with 104 (A × B) and 101 (C × D) simple sequence repeat (SSR) markers with a uniform coverage of the entire maize genome. The LD coefficient D and the composite LD measure Δ were estimated and significance tests for LD were performed. LD was reduced by intermating as expected from theory. A directional generation of negative LD between favorable alleles could not be observed during the selection cycles. However, considerable undirectional changes in D were observed, which we attributed to genetic sampling due to the finite population size used for recombination. Consequently, a long-term reduction of the additive genetic variance due to negative LD was not observed. Our experimental results support the hypothesis that in practical RS programs with maize, LD generated by selection is not a limiting factor for obtaining a high selection response.     

Performance of sampling strategies in the presence of known spatial patterns

In crop protection and ecology accurate and precise estimates of insect populations are required for many purposes. The spatial pattern of the organism sampled, in relation to the sampling scheme adopted, affects the difference between the actual and estimated population density, the bias, and the variability of that estimate, the precision. Field monitoring schemes usually adopt time‐efficient sampling regimes involving contiguous units rather than the most efficient for estimation, the completely random sample. This paper uses spatially‐explicit ecological field data on aphids and beetles to compare common sampling regimes. The random sample was the most accurate method and often the most precise; of the contiguous schemes the line transect was superior to more compact arrangements such as a square block. Bias depended on the relationship between the size and shape of the group of units comprising the sample and the dominant cluster size underlying the spatial pattern. Existing knowledge of spatial pattern to inform the choice of sampling scheme may provide considerable improvements in accuracy. It is recommended to use line transects longer than the grain of the spatial pattern, where grain is defined as the average dimension of clusters over both patches and gaps, and with length at least twice the dominant cluster size.