Estimating the encounter rate variance in distance sampling

Summary .  The dominant source of variance in line transect sampling is usually the encounter rate variance. Systematic survey designs are often used to reduce the true variability among different realizations of the design, but estimating the variance is difficult and estimators typically approximate the variance by treating the design as a simple random sample of lines. We explore the properties of different encounter rate variance estimators under random and systematic designs. We show that a design-based variance estimator improves upon the model-based estimator of Buckland et al. (2001, Introduction to Distance Sampling. Oxford: Oxford University Press, p. 79) when transects are positioned at random. However, if populations exhibit strong spatial trends, both estimators can have substantial positive bias under systematic designs. We show that poststratification is effective in reducing this bias.     

Comparison of distance sampling estimates to a known population size of Ant-eating Chats Myrmecocichla formicivora

Line-transect sampling was used to obtain abundance estimates of an Ant-eating Chat Myrmecocichla formicivora population to compare these with the true size of the population. The population size was determined by a long-term banding study, and abundance estimates were obtained by surveying line transects. The sampling effort was quadrupled to determine potential improvements in accuracy and precision. Abundance estimates of the single surveys differed up to 19.8% from the true number of birds and showed relatively high coefficients of variation. Estimates of the cumulative analyses only differed up to 5.8% while coefficients of variation improved considerably, and provided thus reliable population estimates compared with the true number of chats.     

Comparison of point transect distance and traditional acoustic point-count sampling of hoolock gibbons in Htamanthi Wildlife Sanctuary,Myanmar

Effective conservation demands more accurate and reliable methods of survey and monitoring of populations. Surveys of gibbon populations have relied mostly on mapping of groups in “listening areas” using acoustical point-count data. Traditional methods of estimating density in have usually used counts of gibbon groups within fixed-radius areas or areas bounded by terrain barriers to sound transmission, and have not accounted for possible decline in detectability with distance. In this study we sampled the eastern hoolock gibbon (Hoolock leucogenys) population in Htamanthi Wildlife Sanctuary (WS), Myanmar, using two methods: the traditional point-count method with fixed-radius listening areas, and a newer method using point-transect Distance analysis from a sample point established in the center of each listening point array. The basic data were obtained by triangulating on singing groups from four LPs for 4 days, in 10 randomly selected sample areas within the sanctuary. The point transect method gave an average density of 3.13 groups km⁻², higher than the estimates of group density within fixed-radius areas without correction for detectability. A new method of analysis of singing probability per day (p[1]) gave an estimate of 0.547. Htamanthi WS is an important conservation area containing an estimated 7000 (95% confidence interval: 5000–10,000) hoolock groups. Surveys at Htamanthi WS and locations in the Hukaung Valley suggest that the extensive evergreen forests in northern Myanmar have the capacity to support 2–4 (average about 3) groups of hoolock gibbons per km², but most forests in its range have yet to be surveyed.     

截线抽样法用于鄱阳湖江豚种群数量研究初报

运用截线抽样法调查了在春季 4月间鄱阳湖区长江江豚（Neophocaena phocaenoides asiaeorientalis）的种群密度和数量,得出该地区长江江豚种群密度估计值为 0．1940头／km²,估计数量为 388头。探讨了截线抽样法用于浅水型淡水湖泊调查的可行性和有效性以及要注意的问题。     

Estimating population size of endangered brush-tailed rock-wallaby (Petrogale penicillata) colonies using faecal DNA

The brush-tailed rock-wallaby (Petrogale penicillata) is an endangered species in southeastern Australia and many of the remaining populations are declining. The steep rocky habitat and shy nature of the species make it difficult to obtain data on population parameters such as abundance and recruitment. Faecal pellet counts from scat plots are commonly used to monitor population trends but these are imprecise and difficult to relate to absolute population size. We conducted a noninvasive genetic sampling 'mark-recapture' study over a 2-year period to identify individuals from faecal DNA samples and estimate the population size of four brush-tailed rock-wallaby colonies located in Wollemi National Park, New South Wales. Scat plots in rock-wallaby colonies were used as sample collection points for this study. Two separate population estimates were carried out for three of the colonies to determine if we could detect recruitment and changes in population size. We determined that there was one large colony of an estimated 67 individuals (95% confidence interval: 55-91) and three smaller colonies. Monitoring of the smaller colonies also detected possible population size increases in all three. Our results indicate that faecal DNA analysis may be a promising method for estimating and monitoring population trends in this species particularly when used with a traditional field survey method.     

Hematology and serum chemistry in the white-crowned mangabey (Cercocebus torquatus lunulatus) and in the mandrill (Mandrillus sphinx)

Abstract: Reference values of some hematologic and plasma chemical parameters were established in two species of clinically normal Cercopithecidae. The following variables were studied in seven mandrills (Mandrillus sphinx) and nine white-crowned mangabeys (Cercocebus torquatus lunulatus): hematocrit, hemoglobin concentration, erythrocyte and leucocyte counts, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, glucose, urea, uric acid, cholesterol, creatinine, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, creatinine phosphokinase, lactic dehydrogenase, gamma glutamyl transpeptidase, total serum proteins, albumin, globulins, albumin-globulin ratio, sodium, potassium, calcium, magnesium, total phosphorus, chloride, and serum osmolality. Few differences were observed when compared with human hematological data and with other species of Cercopithecidae Primates.     

First record of Alicia mirabilis (Anthozoa: Actiniaria) from the Aegean Sea and density assessment with distance sampling in a site of high abundance

The occurrence of the actiniarian Alicia mirabilis in the Aegean Sea is documented for the first time from five sites in the Saronikos Gulf. The density of A. mirabilis was assessed in one site (Lychnari bay) with line transects (underwater distance sampling with SCUBA). Its density ranged between 0 and 4.3 individuals are^-1 (1 are=100 m²) with a mean of 1.1±0.5 individuals are^-1. The species was found in a variety of substrates (sandy bottoms, weeds, seagrass beds, rocks, litter) and its distribution was aggregated. Distance sampling was an efficient way to estimate the density of A. mirabillis and is proposed as a good choice for density estimations of actiniarians and other benthic fauna.     

Estimating effective population size from linkage disequilibrium: severe bias in small samples

Effective population size (N _e) is a central concept in evolutionary biology and conservation genetics. It predicts rates of loss of neutral genetic variation, fixation of deleterious and favourable alleles, and the increase of inbreeding experienced by a population. A method exists for the estimation of N _e from the observed linkage disequilibrium between unlinked loci in a population sample. While an increasing number of studies have applied this method in natural and managed populations, its reliability has not yet been evaluated. We developed a computer program to calculate this estimator of N _e using the most widely used linkage disequilibrium algorithm and used simulations to show that this estimator is strongly biased when the sample size is small (<‰100) and below the true N _e. This is probably due to the linkage disequilibrium generated by the sampling process itself and the inadequate correction for this phenomenon in the method. Results suggest that N _e estimates derived using this method should be regarded with caution in many cases. To improve the method’s reliability and usefulness we propose a way to determine whether a given sample size exceeds the population N _e and can therefore be used for the computation of an unbiased estimate.     

Seasonal variation in grey crowned crane (Balearica regulorum) abundance in the Ngorongoro Crater,Tanzania

There are few quantitative estimates of numbers of Africa's endangered grey crowned cranes (Balearica regulorum), yet conservation of this species will depend on such estimates. We used line-transect distance sampling on multiple 2-km segments of an existing road network to estimate the abundance of grey crowned cranes in a portion of the Ngorongoro Crater, Tanzania, during the wet (April) and dry (August) seasons of 2016. We analysed data from 106 transects on which we observed 174 groups of 1–61 cranes (median and mode = 2). Abundance and density estimates on the areas surveyed were best modelled without group size as a covariate and indicated that mean crane densities were significantly lower in the wet season (2.4/km²) than in the dry season (20.2 cranes/km²). Even based on survey areas of different size, minimum estimated numbers of cranes in the Crater (wet season: 108–133; dry season: 362–401) likely reflect the concentration of cranes in the nonbreeding (dry) season in the perennial wetlands of the Crater and reinforce the notion of the Crater being a key seasonal habitat for crane populations in northern Tanzania, as previously suggested in the literature.     

A field test of the distance sampling method using Golden‐cheeked Warblers

ABSTRACT Criteria for delisting Golden‐cheeked Warblers (Dendroica chrysoparia) include protection of sufficient breeding habitat to ensure the continued existence of 1000 to 3000 singing males in each of eight recovery regions for ≥10 consecutive years. Hence, accurate abundance estimation is an integral component in the recovery of this species. I conducted a field test to determine if the distance sampling method provided unbiased abundance estimates for Golden‐cheeked Warblers and develop recommendations to improve the accuracy of estimates by minimizing the effects of violating this method's assumptions. To determine if observers could satisfy the assumptions that birds are detected at the point with certainty and at their initial locations, I compared point‐transect sampling estimates from 2‐, 3‐, 4‐, and 5‐min time intervals to actual abundance determined by intensive territory monitoring. Point‐transect abundance estimates were 15%, 29%, 43%, and 59% greater than actual abundance (N= 156) for the 2‐, 3‐, 4‐, and 5‐min intervals, respectively. Point‐transect sampling produced unbiased estimates of Golden‐cheeked Warbler abundance when counts were limited to 2 min (N= 154–207). Abundance estimates derived from point‐transect sampling were likely greater than actual abundance because observers did not satisfy the assumption that birds were detected at their initial locations due to the frequent movements and large territory sizes of male Golden‐cheeked Warblers. To minimize the effect of movement on abundance estimates, I recommend limiting counts of singing males to 2‐min per point. Counts for other species in similar habitats with similar behavior and movement patterns also should be limited to 2 min when unbiased estimates are important and conducting field tests of the point‐transect distance sampling method is not possible.     

Some comments on anderson and pospahala's correction of bias in line transect sampling

ANDERSON and POSPAHALA (1970) investigated the estimation of wildlife population size using the belt or line transect sampling method and devised a correction for bias, thus leading to an estimator with interesting characteristics. This work was given a uniform mathematical framework in BURNHAM and ANDERSON (1976). In this paper we show that the ANDERSON-POSPAHALA estimator is optimal in the sense of being the (unique) best linear unbiased estimator within the class of estimators which are linear combinations of cell frequencies, provided certain assumptions are met.     

Estimating animal population density using passive acoustics

Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture‐recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast‐developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics‐based density estimation, illustrated with examples from real‐world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic‐based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture‐recapture. The methods are also applicable to other aquatic and terrestrial sound‐producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here.     

Validation of radioimmunoassays for LH and FSH in the sooty mangabey (Cercocebus atys): Characterization of LH and the response to GnRH

Heterologous radioimmunoassays (RIA) for macaque LH and FSH were validated for the measurement of these hormones in the sooty mangabey and mangabey pituitary LH was characterized relative to rhesus monkey LH. Dilutions of a pituitary mangabey extract and a partially purified preparation of mangabey LH ran parallel to a rhesus monkey standard (LER 1909-2) in the ovine-ovine (o-o) LH assay but showed some deviation from parallelism in the rhesus monkey FSH assay. The LH potency of the mangabey extract and standard were six and 190 times more potent, respectively, than LER 1909-2 in the LH RIA. Mangabey LH was estimated to have a molecular weight of 40,000–42,000 daltons vs 35,000–38,000 daltons for rhesus LH on Sephadex G-100 chromatography. Plasma levels of radioimmunoreactive LH, FSH, and testosterone were assayed before and after a bolus administration of 25, 50, or 100 μg synthetic go-nadotropin releasing hormone (GnRH) to adult male mangabeys. A significant increase in serum levels of LH was seen within 30 min with levels more than fourfold higher than the basal level of LH after administration of 100 μg GnRH. However, no consistent increases in plasma FSH values were detected. The integrated mean LH response above preinjection levels following 25, 50, or 100 μg GnRH was dose related. Serum levels of testosterone were also elevated after administration of GnRH, but peak concentrations of testosterone lagged behind peak levels of LH by approximately 30 min. These studies indicate that the heterologous RIAs may be used for measuring gonadotropins in the mangabey and that the male mangabey is apparently more sensitive to GnRH than the rhesus monkey.     

Combining species distribution modeling and distance sampling to assess wildlife population size: A case study with the northern yellow-cheeked gibbon (Nomascus annamensis)

Population size and distribution data for wildlife species play an important role in conservation and management, especially for endangered species. However, scientists seriously lack data on the population status of many species. The northern yellow-cheeked gibbon (Nomascus annamensis) is found in southern Lao PDR, central Vietnam, and northeastern Cambodia. The population of the species has significantly declined due to hunting, habitat loss, and the wildlife trade. To examine the population size and distribution of N. annamensis, we conducted a field survey in Song Thanh Nature Reserve, Quang Nam Province, central Vietnam from February to April 2019 using the audio point count method. We combined Distance Sampling and Ecological Niche Modeling to estimate the population of the gibbons. Results showed that the total suitable area for the gibbons was about 302.32 km², with the two most important variables of the habitat model being the distance-to-villages and forest type. We detected 36 gibbon groups through field surveys and estimated 443 (95% CI, 278–707) gibbon groups in Song Thanh Nature Reserve. Our results indicate that the gibbon population in Song Thanh Nature Reserve is the largest known population of N. annamensis in Vietnam. In addition, our study was the first to combine species distribution modeling with distance sampling to estimate gibbon density and population size. This approach might be useful in surveying and monitoring gibbon populations because it takes imperfect detection probability into account in estimating gibbon population density while estimating the area of potential habitat using environmental variables.     

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Effective population size (N_e) is a key parameter of population genetics. However, N_e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on N_e estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F_IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of N_eestimates decreased with the number of SNPs. Mean N_e estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased N_e estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.