Nicks and notches of the dorsal ridge: Promising mark types for the photo-identification of narwhals

The narwhal is a hunted species for which we have many knowledge gaps. Photo-identification, which uses photographs of natural markings to identify individuals, is widely used in cetacean studies and can address a broad range of biological questions. However, it has not been developed for narwhals. The marks used for other cetaceans are inappropriate for this species either because narwhals lack the body part on which these marks are found or because the marks are known to change with time. We investigated the marks apparent in photographs of narwhals. Nicks and notches on the dorsal ridge are the mark types most promising for photo-identification. They are found on 91%–98% of the individuals, thus allowing the identification of a large part of the population. They can be used to differentiate between individuals, in part because they are variable in their location, numbers, shape, and size. Although our results suggest that nicks and notches are relatively stable over time, rates of change should be formally measured to assess the probability of photographic matches over multiple years. However, we are confident that these marks can be used in studies spanning at least a field season.     

Recommendations for estimating mark rate of cetaceans in photo-ID research: A critique of field sampling protocols and variance estimation

Mark rate, or the proportion of the population with unique, identifiable marks, must be determined in order to estimate population size from photographic identification data. In this study we address field sampling protocols and estimation methods for robust estimation of mark rate and its uncertainty in cetacean populations. We present two alternatives for estimating the variance of mark rate: (1) a variance estimator for clusters of unequal sizes (SRCS) and (2) a hierarchical Bayesian model (SRCS-Bayes), and compare them to the simple random sampling (SRS) variance estimator. We tested these variance estimators using a simulation to see how they perform at varying mark rates, number of groups sampled, photos per group, and mean group sizes. The hierarchical Bayesian model outperformed the frequentist variance estimators, with the true mark rate of the population held in its 95% HDI 91.9% of the time (compared with coverage of 79% for the SRS method and 76.3% for the SRCS-Cochran method). The simulation results suggest that, ideally, mark rate and its precision should be quantified using hierarchical Bayesian modeling, and researchers should attempt to sample as many unique groups as possible to improve accuracy and precision.     

AN ASSESSMENT OF CHANGES WITH TIME IN THE MARKING PATTERNS USED FOR PHOTOIDENTIFICATION OF INDIVIDUAL SPERM WHALES, PHYSETER MACROCEPHALUS

We observed changes with time in the patterns of characteristic fluke markings used to identify sperm whales. Changes were categorized as minor, moderate, or major based on their severity. These change types were found to occur at rates of 0.9%, 11.8%, and 1.3% per individual per year, respectively. Gain and loss rates for each of seven different mark types were also calculated. The highest estimated rate was the gain of small nicks at 0.08 per individual per year. Most individuals identified by us possess at least a few characteristic marks and, therefore, changes of the type observed in this study are unlikely to severely affect their recognizability. For all but one mark type, gain rates were higher than loss rates, indicating that individuals may be accumulating marks with age. Over long periods this could eventually make individuals unrecognizable, with the result that population sizes calculated from these data may be overestimated. As long as photoidentification studies are conducted sufficiently often, and these changes are as gradual as they appear to be, this problem should be minimal.     

PHOTOGRAPHIC IDENTIFICATION OF NORTHERN BOTTLENOSE WHALES (HYPEROODON AMPULLATUS): SOURCES OF HETEROGENEITY FROM NATURAL MARKS

The use of natural marks in capture-recapture studies can lead to unequal capture probabilities. This paper examined a catalog of northern bottlenose whale ( Hyperoodon ampullatus ) photographs from the Gully, Nova Scotia, to identify potential sources of heterogeneity. This information can be used to select appropriate individuals and photographs to include in analyses. Individual northern bottlenose whales were sufficiently marked to uniquely identify individuals (= 14.5 marks/individual; range 1-67), but not all mark types persisted over time. Reliable marks were defined as mark types that were not lost over the nine-yeat study period (notches, back indentation, and mottled patches). Individuals were considered reliably marked if they possessed at least one back indentation or mottled patch (located within one dorsal fin width, at the base of the dorsal fin) or a notch on the dorsal fin. Sixty-six percent (SE = 5%) of the population were reliably marked. Longterm analyses (months to years) should use only reliably marked individuals, and the results scaled to account for the rest of the population. Our results also showed that photographic quality affected an observer's ability to identify individuals. For this catalog, quantitative analysis indicated only photographs of Q ≥ 4 (on a 6-point scale with 6 representing the highest quality) should be included in mark-recapture analyses sensitive to heterogeneity.     

标记重捕法在中华白海豚种群动态研究的应用及建议

早期的中华白海豚考察主要依赖样线调查法了解其资源分布,而近期研究更多采纳标记重捕法获取种群动态信息。在辨识个体的基础上,后者能够获取多种种群参数开展种群生存力分析。本文回顾在我国海域开展的中华白海豚种群动态研究进展及各地区种群标记重捕数据的累积情况;通过数据模拟评估努力值如何影响种群大小统计的误差和偏差;综合阐述野外考察方案设计、标志筛选和数据处理对数据分析的潜在影响;强调模型拟合优度检验和模型选择的重要性;最后,针对比较不同时期或不同方法获取的种群信息时的常见误解提出我们的意见。本文旨在帮助完善我国中华白海豚的后期资源监测工作。     

DIRECT ESTIMATION OF WITHIN-GROUP HETEROGENEITY IN PHOTO-IDENTIFICATION OF SPERM WHALES

Heterogeneity in photo-identification rates among individuals is a potentially serious problem in many studies of cetacean biology, especially the analysis of populations. However, this heterogeneity is usually difficult to identify or measure. Two instances in which closed groups of female and immature sperm whales ( Physeter macrocepbalus ) were tracked and identified using fluke photographs over periods of days off the Galápagos Islands allowed direct examination of heterogeneity in identification rates. A group of nine animals followed in 1999 provided almost no evidence for heterogeneity (permutation test for heterogeneity, P = 0.48), with an estimated coefficient of variation in identification rates of 0.03 (95% CI from 1,000 bootstrap replications: 0.00–0.10). In contrast, the identification rates of a group of 22 animals followed in 1995 seemed to show potentially important differences ( P = 0.058, CV = 0.20, 95% CI = 0.07–0.28). These differences were not related to the internal social structure of the group or to differences in numbers of markings on the flukes, but smaller whales had lower identification rates. Thus, young sperm whales may be underrepresented in photo-identification studies, but adults within groups seem to have similar identification rates. Situations in which animals are photo-identified from closed populations of known size are particularly useful for examining heterogeneity. They should be vigorously exploited by those who use photo-identification to examine population or behavioral biology.     

Visual Implant Elastomer Mark Retention Through Metamorphosis in Amphibian Larvae

Abstract: Questions in population ecology require the study of marked animals, and marks are assumed to be permanent and not overlooked by observers. I evaluated retention through metamorphosis of visual implant elastomer marks in larval salamanders and frogs and assessed error in observer identification of these marks. I found 1) individual marks were not retained in larval wood frogs (Rana sylvatica), whereas only small marks were likely to be retained in larval salamanders (Eurycea bislineata), and 2) observers did not always correctly identify marked animals. Evaluating the assumptions of marking protocols is important in the design phase of a study so that correct inference can be made about the population processes of interest. This guidance should be generally useful to the design of mark-recapture studies, with particular application to studies of larval amphibians.     

POPULATION ANALYSIS OF NORTHERN BOTTLENOSE WHALES IN THE GULLY, NOVA SCOTIA

Northern bottlenose whales ( Hyperoodon ampullatus ) are consistently found through the year in the Gully, a prominent submarine canyon on the edge of the Scotian Shelf. Individuals were photographically identified during field studies between 1988 and 1995. About 70% of the population is identifiable, and 29% have markings which persist reliably over periods of years. A mark-recapture analysis of photographic individual identifications collected between 1988 and 1995 indicates that the population using the Gully numbers about 230 animals (approximate 95% confidence interval 160-360). The rate of mortality plus emigration plus mark change (in animals with reliable long-term marks) is about 12% per year, although this estimate has wide and uncertain confidence limits. Members of the Gully population, which includes calves and mature males, are shorter than animals caught off Labrador. The small size of the Gully population and its persistent use of a very small, bathy-metrically unique ocean area make it vulnerable to human disturbance.     

CAPTURE-RECAPTURE ESTIMATES OF HECTOR'S DOLPHIN ABUNDANCE AT BANKS PENINSULA, NEW ZEALAND

Capture-recapture techniques have been extensively used to estimate survival rates of Hector's dolphins at Banks Peninsula, but not abundance. We analyzed nine seasons of photo-identification data using a model-fitting approach in the computer program MARK, and then used MARK's estimates of capture probabilities to calculate the abundance of distinctive individuals. We extrapolated these estimates to include unmarked individuals using five seasons of data on the proportion of identifiable individuals in this population, obtained from "random photography." This capture-recapture approach suggests a 1996 population of about 1,100 (CV = 0.21). This is very similar to the 1997 line-transect estimate of about 900 (CV = 0.28), especially considering that the two techniques do not necessarily measure the same thing. An important advantage of the capture-recapture approach stems from the inherent versatility of photo-ID data. If the sampling design is appropriate, an unbiased abundance estimate can be achieved as a spin-off from work directed at other questions. However, in our view, line-transect estimates are easier to interpret because the sampling design is explicit.     

REPLICATED ORIGIN OF FEMALE‐BIASED ADULT SEX RATIO IN INTRODUCED POPULATIONS OF THE TRINIDADIAN GUPPY (POECILIA RETICULATA)

There are many theoretical and empirical studies explaining variation in offspring sex ratio but relatively few that explain variation in adult sex ratio. Adult sex ratios are important because biased sex ratios can be a driver of sexual selection and will reduce effective population size, affecting population persistence and shapes how populations respond to natural selection. Previous work on guppies (Poecilia reticulata) gives mixed results, usually showing a female‐biased adult sex ratio. However, a detailed analysis showed that this bias varied dramatically throughout a year and with no consistent sex bias. We used a mark‐recapture approach to examine the origin and consistency of female‐biased sex ratio in four replicated introductions. We show that female‐biased sex ratio arises predictably and is a consequence of higher male mortality and longer female life spans with little effect of offspring sex ratio. Inconsistencies with previous studies are likely due to sampling methods and sampling design, which should be less of an issue with mark‐recapture techniques. Together with other long‐term mark‐recapture studies, our study suggests that bias in offspring sex ratio rarely contributes to adult sex ratio in vertebrates. Rather, sex differences in adult survival rates and longevity determine vertebrate adult sex ratio.     

Accounting for transients when estimating abundance of bottlenose dolphins in Choctawhatchee Bay,Florida

We investigated the potential for using mark–recapture models to estimate abundance of bottlenose dolphin populations in open systems (e.g., bays, estuaries). A major challenge in these systems is that immigration and emigration occur during sampling, thus violating one of the most basic assumptions of mark–recapture models. We assumed that dolphins using our study site were composed of both residents (those that used the study area almost exclusively during our study), and transients (those that passed through our study area but did not remain long), and examined several mark–recapture estimators for their ability to accurately and precisely estimate the abundance of residents and the superpopulation (i.e., residents + transients). Using simulated data, we found that a novel approach accounting for transients resulted in estimators with less bias, smaller absolute relative error, and confidence interval coverage closer to nominal than other approaches, but this novel approach required intensive sampling and that the “correct” transient pattern be specified. In contrast, classical mark–recapture estimators for closed populations often overestimated the number of residents and underestimated the superpopulation. Using photo-identification records, a model-averaged estimate of the superpopulation of bottlenose dolphins in and around Choctawhatchee Bay, Florida was 232 (SE = 13) animals. We estimated resident abundance at 179 (SE = 8), which was lower than the number of unique animals we encountered (188). Our results appear promising for developing monitoring programs for bottlenose dolphins and other taxa in open systems. Our estimators should prove useful to wildlife managers who wish to base conservation decisions on estimates of the number of animals that reside primarily in their study or management area. © 2011 The Wildlife Society.     

根田鼠粪便排泄点及其生态学意义初探

The distribution sites of feces marks of root vole were investigated by eyeballing method. The investigations showed that:( 11 There were feces mark or not at the hole of the vole. (2) It distributed mainly at the crotches and the terminals of the channel.(3) Comparison among three kinds of feces mark percentage, the maximum is the percentage at the crotches. The minimum is the percentage at the hole and the middle at the terminals of the channel. The results indicated that the difference of intensity of feces mark distributed in different sites predicated that feces may played an important communication role in territory behavior of root voles.     

Field‐readable alphanumeric flags are valuable markers for shorebirds: use of double‐marking to identify cases of misidentification

Implicit assumptions for most mark‐recapture studies are that individuals do not lose their markers and all observed markers are correctly recorded. If these assumptions are violated, e.g., due to loss or extreme wear of markers, estimates of population size and vital rates will be biased. Double‐marking experiments have been widely used to estimate rates of marker loss and adjust for associated bias, and we extended this approach to estimate rates of recording errors. We double‐marked 309 Piping Plovers (Charadrius melodus) with unique combinations of color bands and alphanumeric flags and used multi‐state mark recapture models to estimate the frequency with which plovers were misidentified. Observers were twice as likely to read and report an invalid color‐band combination (2.4% of the time) as an invalid alphanumeric code (1.0%). Observers failed to read matching band combinations or alphanumeric flag codes 4.5% of the time. Unlike previous band resighting studies, use of two resightable markers allowed us to identify when resighting errors resulted in reports of combinations or codes that were valid, but still incorrect; our results suggest this may be a largely unappreciated problem in mark‐resight studies. Field‐readable alphanumeric flags offer a promising auxiliary marker for identifying and potentially adjusting for false‐positive resighting errors that may otherwise bias demographic estimates.     

Identifying signature whistles from recordings of groups of unrestrained bottlenose dolphins (Tursiops truncatus)

Bottlenose dolphins (Tursiops truncatus) have individually distinctive signature whistles. Each individual dolphin develops its own unique frequency modulation pattern and uses it to broadcast its identity. However, underwater sound localization is challenging, and researchers have had difficulties identifying signature whistles. The traditional method to identify them involved isolating individuals. In this context, the signature whistle is the most commonly produced whistle type of an animal. However, most studies on wild dolphins cannot isolate animals. We present a novel method, SIGnature IDentification (SIGID), that can identify signature whistles in recordings of groups of dolphins recorded via a single hydrophone. We found that signature whistles tend to be delivered in bouts with whistles of the same type occurring within 1–10 s of each other. Nonsignature whistles occur with longer or shorter interwhistle intervals, and this distinction can be used to identify signature whistles in a recording. We tested this method on recordings from wild and captive bottlenose dolphins and show thresholds needed to identify signature whistles reliably. SIGID will facilitate the study of signature whistle use in the wild, signature whistle diversity between different populations, and potentially allow signature whistles to be used in mark‐recapture studies.     

A SIFT-based software system for the photo-identification of the Risso's dolphin

Photo-identification is a commonly used non-invasive technique that has been profitably employed in biological studies throughout the years. It starts from the assumption that a single individual can be recognized in multiple photos captured at different times by exploiting its unique representative and visible physical qualities such as marks, notches or any other definite feature. Hence, photo-identification is performed to infer knowledge about wild species' spatial and temporal distributions as well as population dynamics, thus providing valuable information especially when the species being investigated is ranked as data deficient. Furthermore, the technological improvements of the last decades and the large availability of devices with powerful computing capabilities are driving the research towards a common goal of enriching bio-ecological studies with innovative computer science approaches. In this scenario, computer vision plays a fundamental role, as it can successfully assist researchers in the analysis of large amounts of data. The aim of this paper is, in fact, to effectively provide a computer vision approach for the photo-identification of the Risso's dolphin, exploiting specific visual cues with a feature-based approach relying on SIFT and SURF feature detectors. The experiments have been conducted on image data acquired in the Gulf of Taranto from 2013 to 2017, conducting a comparative analysis of the performance of both SIFT and SURF, as well as a comparison with the state-of-the-art software DARWIN, and they proved the effectiveness of the proposed approach and suggested its application would be suitable to large scale studies. In conclusion, this paper shows an innovative computer vision application for the identification of unknown Risso's dolphin individuals that relies on a feature-based automated approach. The results suggest that the proposed approach can efficiently assist researchers during the photo-identification task of large amounts of data collected in such a challenging domain.     

Synchrony in population counts predicts butterfly movement frequencies

1. Measuring functional connectivity, the ability of species to move between resource patches, is essential for conservation in fragmented landscapes. However, current methods are highly time consuming and expensive. 2. Population synchrony‐ the correlation in time series of counts between two long‐term population monitoring sites, has been suggested as a possible proxy measure of functional connectivity. To date, population synchrony has been shown to correlate with proxies for movement frequency such as the coverage of suitable habitat types in intervening landscapes, and also least cost distances around hostile land cover types. 3. This provides tentative evidence that synchrony is directly driven by movements of the focal species, but an alternative explanation is that these land cover types affect the movement of interacting species (e.g. natural enemies of the focal species) which can also drive synchronous population dynamics. Therefore, what is needed is a test directly relating population synchrony to movement frequencies of a focal species. 4. Here we use data from a 21 year mark‐release‐recapture study and show that population synchrony does indeed predict movements of a focal butterfly species Boloria eunomia (Esper). 5. There is growing evidence that population synchrony can be a useful conservation tool to measure functional connectivity.     

Abundance and residency dynamics of the Indo-Pacific humpback dolphin,Sousa chinensis,in the Dafengjiang River Estuary,China

Robust population size estimates are essential for informing population conservation status. Residency dynamics show population habitat use through time. Population size of Indo-Pacific humpback dolphins (Sousa chinensis) has been extensively investigated in Chinese waters, but their residency dynamics are rarely known. Mark-recapture analysis based on photo-identification records was applied to humpback dolphins in the Dafengjiang River Estuary habitat, one of the key habitats in the northern Beibu Gulf, China. Movement analyses based on lagged identification rate indicated the humpback dolphins spent, on average, 78.5 days inside and 46.9 days outside the survey area. Within the study area, the humpback dolphin abundance was 83 identifiable dolphins. A total of 353–430 humpback dolphins, estimated by POPAN modeling, were involved in this fluid habitat-use dynamic. Robust Design analysis showed strong seasonality in humpback dolphin abundance and emigration probability, implying a movement- and habitat-use pattern likely associated with spatiotemporal distribution of oceanographic characteristics and prey occurrences. Population surveys and conservation measures currently conducted in Chinese waters seldom consider seasonality in movements between habitat patches, which can be addressed by genetic analyses across habitats and cross-matching photo-identification records among neighboring habitats.     

MULTISITE MARK-RECAPTURE FOR CETACEANS: POPULATION ESTIMATES WITH BAYESIAN MODEL AVERAGING

Mark-recapture techniques are widely used to estimate the size of wildlife populations. However, in cetacean photo-identification studies, it is often impractical to sample across the entire range of the population. Consequently, negatively biased population estimates can result when large portions of a population are unavailable for photographic capture. To overcome this problem, we propose that individuals be sampled from a number of discrete sites located throughout the population's range. The recapture of individuals between sites can then be presented in a simple contingency table, where the cells refer to discrete categories formed by combinations of the study sites. We present a Bayesian framework for fitting a suite of log-linear models to these data, with each model representing a different hypothesis about dependence between sites. Modeling dependence facilitates the analysis of opportunistic photo-identification data from study sites located due to convenience rather than by design. Because inference about population size is sensitive to model choice, we use Bayesian Markov chain Monte Carlo approaches to estimate posterior model probabilities, and base inference on a model-averaged estimate of population size. We demonstrate this method in the analysis of photographic mark-recapture data for bottlenose dolphins from three coastal sites around NE Scotland.     

Computer-aided photo-identification of a rare stingray,Megatrygon microps

A protocol for photo-identification of individual Megatrygon microps has been defined. One hundred and four identification photographs were taken between 2005 and 2019. Spot patterns on the dorsal surface were used to identify individuals. Unique scarring on eight M. microps re-observed provided an independent confirmation of pattern stability of up to 761 days. Previous studies lacked statistical testing used to validate this photo-identification approach. I³S photo-matching software was used to successfully match images, identifying 69 individuals. A photo-matching software facilitates an open-source platform for identifying individual M. microps, allowing for better population assessments.     

分子标记技术及其在分离和克隆水稻基因中的应用

分子标记是近些年来发展起来的一种分子生物学技术,利用各种分子标记可以构建水稻高密度的分子遗传图谱,并进行基因定位和克隆。本文概述了几种常用的分子标记及其在研究水稻基因中应用进展。