Balancing bias and precision in capture-recapture estimates of abundance

Capture‐recapture estimates of abundance using photographic identification data are sensitive to the quality of photographs used and distinctiveness of individuals in the population. Here analyses are presented for examining the effects of photographic quality and individual animal distinctiveness scores and for objectively selecting a subset of data to use for capture‐recapture analyses using humpback whale (Megaptera novaeangliae) data from a 2‐year study in the North Atlantic. Photographs were evaluated for their level of quality and whales for their level of individual distinctiveness. Photographic quality scores had a 0.21 probability of changing by a single‐quality level, and there were no changes by two or more levels. Individual distinctiveness scores were not independent of photographic quality scores. Estimates of abundance decreased as poor‐quality photographs were removed. An appropriate balance between precision and bias in abundance estimates was achieved by removing the lowest‐quality photographs and those of incompletely photographed flukes given our assumptions about the true population abundance. A simulation of the selection process implied that, if the estimates are negatively biased by heterogeneity, the increase in bias produced by decreasing the sample size is not more than 2%. Capture frequencies were independent of individual distinctiveness scores.     

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.     

Recommendations for photo‐identification methods used in capture‐recapture models with cetaceans

Capture‐recapture methods are frequently employed to estimate abundance of cetaceans using photographic techniques and a variety of statistical models. However, there are many unresolved issues regarding the selection and manipulation of images that can potentially impose bias on resulting estimates. To examine the potential impact of these issues we circulated a test data set of dorsal fin images from bottlenose dolphins to several independent research groups. Photo‐identification methods were generally similar, but the selection, scoring, and matching of images varied greatly amongst groups. Based on these results we make the following recommendations. Researchers should: (1) determine the degree of marking, or level of distinctiveness, and use images of sufficient quality to recognize animals of that level of distinctiveness; (2) ensure that markings are sufficiently distinct to eliminate the potential for “twins” to occur; (3) stratify data sets by distinctiveness and generate a series of abundance estimates to investigate the influence of including animals of varying degrees of markings; and (4) strive to examine and incorporate variability among analysts into capture‐recapture estimation. In this paper we summarize these potential sources of bias and provide recommendations for best practices for using natural markings in a capture‐recapture framework.     

USE OF PHOTOGRAPHIC IDENTIFICATION IN CAPTURE-RECAPTURE STUDIES OF MEDITERRANEAN MONK SEALS

The use of photo-identification and its reliability in capture-recapture studies of Mediterranean monk seals were assessed using slides collected in the colony at Cap Blanc, western Sahara, from 1993 to 1996. Five tests indicated that researchers involved in photo-identification were proficient in matching slides of identified seals, consistent in classifying the side of the seal shown in slides and in assigning the morphological stage of the seal, and that changes of markings over a period of three years were insufficient to affect matching success. The certainty of identifying a seal was not dependent on the number of slides used but on distinctiveness of the markings and the quality of the slides taken. Capture-recapture abundance estimates were biased upwards when including poor quality slides. The exclusive use of excellent- and good quality slides provided the best estimates. The proportion of distinctive seals varied between morphological stages and was significantly lower in juveniles. When including the identification histories of juveniles, the heterogeneity of capture probabilities was higher. Therefore, abundance estimates were less biased when all juveniles were considered as non-distinctive seals. Reliable abundance estimates required a balance between duration of capture occasions and time interval between these.     

SELECTION AND SCREENING OF A DESCRIPTIVE PANEL FOR EWES MILK CHEESE SENSORY PROFILING

The aim of this work was to select a competent sensory panel considering its ability to describe ewes milk cheese sensory properties. The panelists evaluated the sensory characteristics of several ewes milk cheeses in terms of odor, flavor and texture. The performance of judges was assessed taking into account the following aspects: (1) individual discriminatory ability and reproducibility for each sensory attribute; (2) group discriminatory ability and reproducibility and agreement between judges for each attribute; (3) panel homogeneity; (4) panel consonance; and (5) overall panel discriminatory ability. The panel performance was checked with a set of statistical procedures. The results obtained by the selected group were better than the initial panel from the point of view of discriminant power, reproducibility and agreement. The suggested method can be easily applied in routine control of assessors performance and to discover deviant behavior or differences in individual perception of the samples.     

A COMPARISON OF METHODS FOR EVALUATING THE PERFORMANCE OF A TRAINED SENSORY PANEL1

Cluster analysis, consonance analysis, principal component analysis (PCA) and the GRAPES program (Schlich 1994) were compared for the evaluation of panel performance. Ten judges evaluated 25 Merlot wines for 24 color, aroma and flavor attributes. Cluster analysis grouped similar judges. PCA identified judges according to their attribute use. Consonance analysis determined a numerical index for attribute agreement and the GRAPES program compared judges in their use of the scale, reliability, discrimination and disagreement. Three of the four techniques provided a graphical representation of similarities and differences between judges. Methodologies were best used in conjunction with one another. Ultimately the application of these tools will serve to improve the quality of sensory evaluations.     

Genetic fingerprinting proves cross‐correlated automatic photo‐identification of individuals as highly efficient in large capture–mark–recapture studies

Capture–mark–recapture (CMR) approaches are the backbone of many studies in population ecology to gain insight on the life cycle, migration, habitat use, and demography of target species. The reliable and repeatable recognition of an individual throughout its lifetime is the basic requirement of a CMR study. Although invasive techniques are available to mark individuals permanently, noninvasive methods for individual recognition mainly rest on photographic identification of external body markings, which are unique at the individual level. The re‐identification of an individual based on comparing shape patterns of photographs by eye is commonly used. Automated processes for photographic re‐identification have been recently established, but their performance in large datasets (i.e., > 1000 individuals) has rarely been tested thoroughly. Here, we evaluated the performance of the program AMPHIDENT, an automatic algorithm to identify individuals on the basis of ventral spot patterns in the great crested newt (Triturus cristatus) versus the genotypic fingerprint of individuals based on highly polymorphic microsatellite loci using GENECAP. Between 2008 and 2010, we captured, sampled and photographed adult newts and calculated for 1648 samples/photographs recapture rates for both approaches. Recapture rates differed slightly with 8.34% for GENECAP and 9.83% for AMPHIDENT. With an estimated rate of 2% false rejections (FRR) and 0.00% false acceptances (FAR), AMPHIDENT proved to be a highly reliable algorithm for CMR studies of large datasets. We conclude that the application of automatic recognition software of individual photographs can be a rather powerful and reliable tool in noninvasive CMR studies for a large number of individuals. Because the cross‐correlation of standardized shape patterns is generally applicable to any pattern that provides enough information, this algorithm is capable of becoming a single application with broad use in CMR studies for many species.     

Genotyping validates the efficacy of photographic identification in a capture‐mark‐recapture study based on the head scale patterns of the prairie lizard (Sceloporus consobrinus)

Population studies often incorporate capture‐mark‐recapture (CMR) techniques to gather information on long‐term biological and demographic characteristics. A fundamental requirement for CMR studies is that an individual must be uniquely and permanently marked to ensure reliable reidentification throughout its lifespan. Photographic identification involving automated photographic identification software has become a popular and efficient noninvasive method for identifying individuals based on natural markings. However, few studies have (a) robustly assessed the performance of automated programs by using a double‐marking system or (b) determined their efficacy for long‐term studies by incorporating multi‐year data. Here, we evaluated the performance of the program Interactive Individual Identification System (I³S) by cross‐validating photographic identifications based on the head scale pattern of the prairie lizard (Sceloporus consobrinus) with individual microsatellite genotyping (N = 863). Further, we assessed the efficacy of the program to identify individuals over time by comparing error rates between within‐year and between‐year recaptures. Recaptured lizards were correctly identified by I³S in 94.1% of cases. We estimated a false rejection rate (FRR) of 5.9% and a false acceptance rate (FAR) of 0%. By using I³S, we correctly identified 97.8% of within‐year recaptures (FRR = 2.2%; FAR = 0%) and 91.1% of between‐year recaptures (FRR = 8.9%; FAR = 0%). Misidentifications were primarily due to poor photograph quality (N = 4). However, two misidentifications were caused by indistinct scale configuration due to scale damage (N = 1) and ontogenetic changes in head scalation between capture events (N = 1). We conclude that automated photographic identification based on head scale patterns is a reliable and accurate method for identifying individuals over time. Because many lizard or reptilian species possess variable head squamation, this method has potential for successful application in many species.     

The selfie trap: A novel camera trap design for accurate small mammal identification

Camera traps are a popular tool for monitoring wildlife though they can fail to capture enough morphological detail for accurate small mammal species identification. Camera trapping small mammals is often limited by the inability of camera models to: (i) record at close distances; and (ii) provide standardised photos. This study aims to provide a camera trapping method that captures standardised images of the faces of small mammals for accurate species identification, with further potential for individual identification. A novel camera trap design coined the ‘selfie trap’ was developed. The selfie trap is a camera contained within an enclosed PVC pipe with a modified lens that produces standardised close images of small mammal species encountered in this study, including: Brown Antechinus (Antechinus stuartii), Bush Rat (Rattus fuscipes) and Sugar Glider (Petaurus breviceps). Individual identification was tested on the common arboreal Sugar Glider. Five individual Sugar Gliders were identified based on unique head stripe pelage. The selfie trap is an accurate camera trapping method for capturing detailed and standardised images of small mammal species. The design described may be useful for wildlife management as a reliable method for surveying small mammal species. However, intraspecies individual identification using the selfie trap requires further testing.     

SURVIVAL RATES OF PHOTOGRAPHICALLY IDENTIFIED HECTOR'S DOLPHINS FROM 1984 TO 1988

Re-sightings of photographically identified individuals were used to estimate survival rates for a free-living population of Hector's dolphins Cephalorhynchus hectori , a species endemic to New Zealand waters. Most individuals were identified from injuries to the dorsal fin. Consequently, the photographic catalog contained very few young individuals. Our analysis included no newborn calves or yearlings, and provided estimates of survival rates only after the first year of life. We used two complementary methods for calculating survival rates: a modified Jolly-Seber model, and a simpler method which corrects in a more explicit way for individual dolphins being alive but not sighted. Selection of the most reliable subset of the data had a greater effect on computed survival rates than did the difference between the two methods. We conclude that careful inspection of resighting data before analysis, and, if necessary, selection of a subset, is very important in studies of this kind. Survival rate estimates came from a population which was subject to relatively heavy mortality from gillnet entanglement. Standard errors of the survival rate estimates have been used to assess the conditional probability of population decline given three fertility scenarios. The high probability that the Banks Peninsula Hector's dolphin population was decreasing during the study period (0.78 to 0.99) suggests that gillnet entanglement constituted a serious risk to this population.     

ABUNDANCE OF BOTTLENOSE DOLPHINS IN THE BAYS, SOUNDS, AND ESTUARIES OF NORTH CAROLINA

We conducted a mark-recapture survey of bottlenose dolphins Tursiops truncatus in the bays, sounds, and estuaries of North Carolina during July 2000, using photographic identification techniques. During this survey we took 7,682 photographs of dolphins and, of these, 3,457 images were of sufficient quality for analysis. We identified 306 dolphins from distinctive nicks and notches on their dorsal fins. Eighry-six dolphins were photographed on more than one occasion during the course of the survey; one dolphin was photographed on four separate days. We then applied the results of our photographic analyses to several mark-recapture models and examined potential violations of the assumptions of these models, including an unexpected correlation between photo quality and mark distinctiveness. Our analysis suggests that our results are robusr to possible violations of these assumptions. The resulting estimates were then scaled to account for the proportion (0.46) of unmarked dolphins in the population. Our best estimate of the number of dolphins present in the inshore waters of North Carolina during July 2000 is 1,033 with a 95% Confidence Interval of 860–1,266 (CV = 0.099). Most dolphins were found in the northern part of the study area, which includes the second largest estuarine system in the United States.     

The reliability of pigment pattern‐based identification of wild bottlenose dolphins

Long‐term studies often rely on natural markings for individual identification across time. The primary method for identification in small cetaceans relies on dorsal fin shape, scars, and other natural markings. However, dorsal fin markings can vary substantially over time and the dorsal fin can become unrecognizable after an encounter with a boat or shark. Although dorsal fins have the advantage in that they always break the water surface when the cetacean breathes, other physical features, such as body scars and pigmentation patterns can supplement. The goal of this study was to explore the use of dorso‐lateral pigment patterns to identify wild bottlenose dolphins. We employed photographic pigment matching tests to determine if pigmentation patterns showed (1) longitudinal consistency and (2) bilateral symmetry using a 30 yr photographic database of bottlenose dolphins (Tursiops aduncus). We compared experienced dolphin researchers and inexperienced undergraduate student subjects in their ability to accurately match images. Both experienced and inexperienced subjects correctly matched dolphin individuals at a rate significantly above chance, even though they only had 10 s to make the match. These results demonstrate that pigment patterns can be used to reliably identify individual wild bottlenose dolphins, and likely other small cetacean species at other sites.     

Layman versus Professional Musician: Who Makes the Better Judge?

The increasing number of casting shows and talent contests in the media over the past years suggests a public interest in rating the quality of vocal performances. In many of these formats, laymen alongside music experts act as judges. Whereas experts'' judgments are considered objective and reliable when it comes to evaluating singing voice, little is known about laymen’s ability to evaluate peers. On the one hand, layman listeners–who by definition did not have any formal training or regular musical practice–are known to have internalized the musical rules on which singing accuracy is based. On the other hand, layman listeners’ judgment of their own vocal skills is highly inaccurate. Also, when compared with that of music experts, their level of competence in pitch perception has proven limited. The present study investigates laypersons'' ability to objectively evaluate melodies performed by untrained singers. For this purpose, laymen listeners were asked to judge sung melodies. The results were compared with those of music experts who had performed the same task in a previous study. Interestingly, the findings show a high objectivity and reliability in layman listeners. Whereas both the laymen''s and experts'' definition of pitch accuracy overlap, differences regarding the musical criteria employed in the rating task were evident. The findings suggest that the effect of expertise is circumscribed and limited and supports the view that laypersons make trustworthy judges when evaluating the pitch accuracy of untrained singers.     

gemini: software for testing the effects of genotyping errors and multitubes approach for individual identification

Improvements in the determination of individual genotypes from samples with low DNA quantity and quality are of prime importance in molecular ecology and conservation for reliable genetic individual identification (molecular tagging using microsatllites loci). Thus, errors (e.g. allelic dropout and false allele) appearing during samples genotyping must be monitored and eliminated as far as possible. The multitubes approach is a very effective but a costly and time‐consuming solution. In this paper, we present a simulation software that allows evaluation of the effect of genotyping errors on genetic identification of individuals and the effectiveness of a multitubes approach to correct these errors.     

A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer

To develop a reliable tool for the identification and classification of the different Ensifer species, without the need for sequencing, a prototype DNA microarray that targets the rpsA housekeeping gene was designed and tested. Internal segments of the rpsA gene from 34 reference strains, representing the different Ensifer species, were sequenced and the sequences were used to select 44 diagnostic oligonucleotides that served as probes for the identification microarray. Both, genomic DNA and specific rpsA PCR-products were tested as a target in hybridisation experiments. Experimental conditions were optimised and the diagnostic oligonucleotides were validated. Hybridisation results with the rpsA PCR-products showed reliable identification of the reference strains to species and genomovar level. Our data indicate that a microarray targeting housekeeping genes is a promising, accurate and relatively simple genotyping technique that would also be applicable for the identification and characterization of other bacterial groups of interest.     

NOTES ON THE BREEDING OF THE BOKMAKIRI

Counting Saddle-billed Storks in a study area the size of the Kruger National Park, at 2.2 million ha, is difficult because the birds are long-lived, sparse in the landscape and have large home ranges. Aerial surveys conducted to date provide an estimate with no measure of data dispersion, thence precision. The aim of this study was to estimate the population size within associated confidence limits using a modified mark–recapture field method. The vehicle survey, conducted shortly after rainfall in the area, did not produce results with known precision under these conditions. A repeat of this census in spring, after the peak breeding season and when surface water is confined to the larger rivers and dams, should yield different results. A photographic census technique yielded sufficient information to construct a population registration database. Individual identification profiles indicate that there are at least 40 adult Saddle-billed Storks in the southern part of the Kruger National Park. This is considered the minimum number of known-to-be-alive individuals in this area. In this paper, the Cormack–Jolly–Seber mark– recapture model was used to return an estimate of the population size for each capture occasion.     

Comparison of two commercial methods with PCR restriction fragment length polymorphism of the tuf gene in the identification of coagulase-negative staphylococci

AIMS: Two commercial methods for the identification of coagulase-negative staphylococci (CNS) were compared with the restriction fragment length polymorphism (RFLP) of the amplified tuf gene, which served as the reference method. METHODS AND RESULTS: One hundred and forty-five CNS were evaluated using the API 32 Staph ID and the Crystal GP/ID BBL systems. The PCR-RFLP of the tuf gene served as the reference method. The APIStaph and the GP/ID BBL had an overall rate of agreement with the molecular method of 58.6% and 46.2% respectively, with the inability of the GP/ID BBL to characterize 11.7% of the isolates. The APIStaph showed higher sensitivity and better agreement than the GP/ID BBL with the PCR-RFLP, except for Staphylococcus hominis and Staphylococcus capitis. CONCLUSIONS: Neither of the commercial systems was as reliable as the PCR-RFLP method for identifying isolates of CNS. Overall the APIStaph had better agreement with the PCR-RFLP than the GP/ID system. SIGNIFICANCE AND IMPACT OF THE STUDY: The results indicate that the PCR-RFLP method is more reliable than the two commercial systems tested, suggesting that it is more reliable for routinely identifying CNS.     

随机引物PCR技术在个体认定及亲权鉴定中的应用

随机引物ＰＣＲ技术（ＡＰ－ＰＣＲ）检测人ＤＮＡ指纹图用于法医学个体认定及亲权鉴定是一个非常有效和经济的方法。应用该技术对１００例无关个体ＡＰ－ＰＣＲ的ＤＮＡ指纹进行分析和１０个肯定亲生关系的家庭进行亲权鉴定,结果该技术的个体识别力非常高,亲权鉴定时的非父排除率也很高,且操作简便、快速,是一个值得推广的方法。     

An automated program to find animals and crop photographs for individual recognition

Detailed data on individual animals are critical to ecological and evolutionary studies, but attaching identifying marks can alter individual fates and behavior leading to biases in parameter estimates and ethical issues. Individual-recognition software has been developed to assist in identifying many species from non-invasive photographic data. These programs utilize algorithms to find unique individual characteristics and compare images to a catalogue of known individuals. Currently, all applications for individual identification require manual processing to crop images so only the area of interest remains, or the area of interest must be manually delineated in each image. Thus, one of the main bottlenecks in processing data from photographic capture-recapture surveys is in cropping to an area of interest so that matching algorithms can identify the individual. Here, we describe the development and testing of an automated cropping program. The methods and techniques we describe are broadly applicable to any system where raw photos must be cropped down to a specific area of interest before pattern recognition software can be used for individual identification. We developed and tested the program for use with identification photos of wild giraffes.