THE USE OF NATURAL MARKINGS IN STUDIES OF LONG-FINNED PILOT WHALES (GLOBICEPHALA MELAS)

Photo-identification using natural markings has been used for pilot whale ( Globicephala melas ) studies. However, none of these studies investigated the reliability of the marks used. To identify which mark types are reliable and which could improve the method, fifteen mark types, and their distribution within the population, were described. The rates of gain and loss of each mark type were calculated and the variability in visibility was investigated. Although the mark types associated with the current photo-identification method, the notch and the protruding piece, appear to be permanent, they allowed us to identify only 33% of our sample. The prevalence of all but two mark types is independent of the identifiability of a photograph. One of these is already used in the current photo-identification method. This independence indicates that the proportion of the population that is currently identifiable does not differ from the rest of the population in its susceptibility to factors causing marks, such as predation, and thus appears to be representative of the whole population. Using saddle patches in combination with the current photo-identification method would double the percentage of the identifiable individuals. However, due to limitations of matching software, the current method is easier to use.     

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.     

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.     

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.     

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.     

THE POPULATION DYNAMICS OF NORTHERN SEA LIONS, 1975-1985

Abstract: Populations of northern sea lions ( Eumetopias jubatus ) in the vicinity of Marmot Island, Alaska declined during 1975–1985 at about 5% per year (Merrick et al. 1987). The cause of this decline is not known. A life table for the northern sea lion was calculated assuming that life spans follow a Weibull distribution. Samples of northern sea lions taken in the vicinity of Marmot Island, Alaska during 1975–1978 and 1985–1986 indicate that the average age of females older than 3 yr increased about 1.55 yr (SD = 0.35 yr) while the population was declining at about 5% per year. Fecundity rates decreased by 10% over the same period, but the decrease was not statistically significant (Calkins and Goodwin 1988). Possible causes of the population decline and the change in age structure were examined by writing the Leslie matrix population equation in terms of changes in juvenile and adult survival rates and fecundity, and examining the short–term behavior of the trajectories of the average age of adult females, total number of females, and total number of pups with respect to those changes in the vital parameters. From the observed rate of declines of adults and the changes in average age of adult females and fecundity, estimates of the changes in adult and juvenile survival were calculated; estimates of the standard deviations of these changes were estimated via a bootstrap procedure. One purpose of this exercise is to aid in setting priorities for research for determining the cause of the decline. An explanation for the observed declines in numbers of adult sea lions consistent with the observed fecundity rates, a rate of decrease of 5% in the number of adults, and the corresponding increase in average age (of females age 3 yr and older) was a 10%–20% decrease in the survival of juveniles (age 0-3 yr) coupled with an insignificant change in adult survival (0.03%, SD = 1%).     

Incidence of caries and abscesses in archeological Eskimo skeletal samples from point hope and Kodiak Island,Alaska

The incidence of caries and abscesses in 246 archeologically derived skeletal specimens from the Ipiutak and Tigara levels at Point Hope, Alaska, and 79 specimens excavated from Jones Point, Kodiak Island, Alaska were investigated. All three collections span long periods of time. Only pre-white contact specimens were used. Each specimens was sexed and aged in five year groupings, using standard techniques. Caries and abscesses were recorded by type and degree of severity and correlated with age, sex, and site of origin. All samples displayed very low caries rates and few abscesses per tooth and per individual (both observed frequencies, and frequencies corrected for postmortem loss of teeth). DMF scores were tabulated using both observed and corrected frequencies. Very heavy occlusal wear in all three samples could account for the majority of abscesses and pulp exposures, while the low caries rates are attributable to traditional diets totally devoid of refined sugars, starches, and food additives.     

Generalized spatial mark–resight models with incomplete identification: An application to red fox density estimates

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Seahorse fingerprints: a new individual identification technique

Individual identification is particularly important for ethological studies and sampling design. Previous studies have developed various types of marking by tags and chemical marks, but these methods involve significant manipulation of the individuals. Other studies have reported natural marks as an efficient method for individual recognition. Our study aims to elucidate a new method for natural mark identification of seahorses, which we tested with the endangered Brazilian seahorse Hippocampus reidi. We avoid pseudoreplication by recognizing individuals. Seahorses have a hard bony structure on the top of their heads called the coronet, which has a different shape for each individual, corresponding to a fingerprint. We tagged seahorses in the field with collar tags and photographed their coronets. After two days, we identified seahorses by their photographs and verified their identification with the collar tags. We correctly identified all individuals by fingerprint identification. Although this method was only tested with adults, we suggest that it applies to seahorses in general, as all species possess the coronet structure.     

Perspectives on over-marking: is it good to be on top?

What we refer to as over-marking occurs when one individual places its scent mark on top of, touching, or adjacent to the scent mark of another individual, usually a conspecific. Over-marking frequently occurs among mammals that share common paths, trails, and runways. Despite its ubiquity among terrestrial mammals, we know little about how individuals respond to over-marks and the function(s) of over-marking. Studies on voles and golden hamsters indicate that after exploring an over-mark, individuals respond selectively to the mark of the top-scent donor relative to that of the bottom-scent donor. Thus, individuals may be able to focus their attention on a particular scent mark relevant at a particular time and in a particular context, neglecting other scent marks that are present. The function(s) of over-marking are examined within the framework of ten hypotheses. Several hypotheses are plausible. However, the bulk of the literature is consistent with hypotheses stating that over-marking serving a role in olfactory communication between opposite and same-sex conspecifics. Lastly, we postulate the costs and benefits that may be garnered by the top-scent donor of an over-mark.     

Decline in abundance and apparent survival rates of fin whales (Balaenoptera physalus) in the northern Gulf of St. Lawrence

Estimates of abundance and survivorship provide quantifiable measures to monitor populations and to define and understand their conservation status. This study investigated changes in abundance and survival rates of fin whales (Balaenoptera physalus) in the northern Gulf of St. Lawrence in the context of anthropogenic pressures and changing environmental conditions. A long‐term data set, consisting of 35 years of photo‐identification surveys and comprising more than 5,000 identifications of 507 individuals, formed the basis of this mark–recapture study. Based on model selection using corrected Akaike Information Criterion, the most parsimonious Cormack–Jolly–Seber model included a linear temporal trend in noncalf apparent survival rates with a sharp decline in the last 5 years of the study and a median survival rate of 0.946 (95% confidence interval (CI) 0.910–0.967). To account for capture heterogeneity due to divergent patterns of site fidelity, agglomerative hierarchical cluster analysis was employed to categorize individuals based on their annual and survey site fidelity indices. However, the negative trend in survivorship remained and was corroborated by a significant decline in the estimated super‐population size from 335 (95% CI 321–348) individuals in 2004–2010 to 291 (95% CI 270–312) individuals in 2010–2016. Concurrently, a negative trend was estimated in recruitment to the population, supported by a sharp decrease in the number of observed calves. Ship strikes and changes in prey availability are potential drivers of the observed decline in fin whale abundance. The combination of clustering methods with mark–recapture represents a flexible way to investigate the effects of site fidelity on demographic variables and is broadly applicable to other individual‐based studies.     

multimark: an R package for analysis of capture–recapture data consisting of multiple “noninvasive” marks

I describe an open‐source R package, multimark , for estimation of survival and abundance from capture–mark–recapture data consisting of multiple “noninvasive” marks. Noninvasive marks include natural pelt or skin patterns, scars, and genetic markers that enable individual identification in lieu of physical capture. multimark provides a means for combining and jointly analyzing encounter histories from multiple noninvasive sources that otherwise cannot be reliably matched (e.g., left‐ and right‐sided photographs of bilaterally asymmetrical individuals). The package is currently capable of fitting open population Cormack–Jolly–Seber (CJS) and closed population abundance models with up to two mark types using Bayesian Markov chain Monte Carlo (MCMC) methods. multimark can also be used for Bayesian analyses of conventional capture–recapture data consisting of a single‐mark type. Some package features include (1) general model specification using formulas already familiar to most R users, (2) ability to include temporal, behavioral, age, cohort, and individual heterogeneity effects in detection and survival probabilities, (3) improved MCMC algorithm that is computationally faster and more efficient than previously proposed methods, (4) Bayesian multimodel inference using reversible jump MCMC, and (5) data simulation capabilities for power analyses and assessing model performance. I demonstrate use of multimark using left‐ and right‐sided encounter histories for bobcats (Lynx rufus) collected from remote single‐camera stations in southern California. In this example, there is evidence of a behavioral effect (i.e., trap “happy” response) that is otherwise indiscernible using conventional single‐sided analyses. The package will be most useful to ecologists seeking stronger inferences by combining different sources of mark–recapture data that are difficult (or impossible) to reliably reconcile, particularly with the sparse datasets typical of rare or elusive species for which noninvasive sampling techniques are most commonly employed. Addressing deficiencies in currently available software, multimark also provides a user‐friendly interface for performing Bayesian multimodel inference using capture–recapture data consisting of a single conventional mark or multiple noninvasive marks.     

REPRODUCTIVE RATES OF HUMPBACK WHALES OFF CALIFORNIA

From 1986 to 1996 we examined the reproductive rates, calving rates, and reproductive histories of mature females as part of photo-identification studies of humpback whales that feed off California, Oregon, and Washington during summer and fall. Annual reproductive rates were measured by two methods: proportion of all whales that were calves based on sightings (0.6%-5.9% per year, mean = 3.6%, SD = 1.6) and based on individually identified animals (1.1%-8.0% per year, mean = 4.1%, SD = 1.8). The reproductive rate based on sightings varied significantly by year ( G test, P < 0.001), region ( G test, P < 0.001), and by month ( G test, P < 0.05). Seventy-nine sexually mature females were identified with 97 calves out of a total of 844 known individuals over the 11-yr study. Mother-calf separation on the feeding grounds was recorded in several instances. The apparent reproductive rates of this population are considerably lower than rates of 4%–15% reported from other feeding areas for this species. Our estimates are likely biased downward because this population has been increasing at about 5% per year. Calves may have been missed due to early weaning and because of our sampling from small boats late in the season. We also found evidence of geographic segregation of mother-calf pairs within our large study area. Despite these factors, we conclude the reproductive rate of this population appears to be lower than has been reported in other areas.     

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.     

An integrated population model for a long‐lived ungulate: more efficient data use with Bayesian methods

We develop an integrated population model for Svalbard reindeer Rangifer tarandus platyrhynchus, and demonstrate how this type of model can be used to extract more information from the data and separate different sources of variability in population estimates. Our model combines individual mark–recapture data with population counts and harvesting data within a Bayesian model framework, and accounts for observation error, environmental and demographic stochasticity, and age structure. From this model we obtain annual estimates of age‐specific population size, survival and fecundity. The model provides estimates of age structure at a finer scale than that found in the census data, and enables us to estimate survival for the period before calves are first caught and marked, i.e. before they enter the individual mark–recapture data. The modeling framework provides an improved approach to studying age‐structured populations that are imperfectly censused and where the demography of only a sample of individuals is known. We use data from independent censuses of the same population to evaluate population estimates obtained from the model, and show that it is successful at correcting for different types of observation error. Based on our model results, we suggest that allocating resources to the collection of supplementary mark–recapture data could improve the reliability of population projections more than making regular population censuses as exhaustive as possible. Our work demonstrates how integrated Bayesian population modeling can be used to increase the amount of information extracted from collections of data, identifying and disentangling sources of variation in individual performance and population size. This represents an important step towards increasing the predictive ability of population growth models for long‐lived species experiencing changes in environmental conditions and harvesting regimes.     

Female marmoset monkeys (Callithrix jacchus) can be identified from the chemical composition of their scent marks.

The present study analyzed 42 organic solvent extracts of scent mark pools from five dominant female common marmosets by gas chromatography (GC) and combined GC and mass spectrometry. We determined whether there were qualitative or quantitative differences between the chemical composition of scent marks from individual females. Gas chromatography and mass spectral analysis detected the same 162 chemicals in 86% (36/42) of scent mark pools from five dominant females. This near identical chemical composition of scent marks suggested there were few, if any, qualitative differences between the chemical composition of scent marks from individual females. Instead, quantitative differences in scent may provide the key factor distinguishing individual females. Using the relative concentration of highly volatile chemicals detected by GC in scent marks, linear discriminant analysis classified scent mark pools to their correct donor approximately 91% of the time. Such highly reliable statistical matching of scent to donor suggested that each individual female common marmoset has a unique ratio of highly volatile chemicals in their scent marks which may permit individual identification of females from odors in their scent alone.     

Individual forager profits in Apis mellifera unaffected by a range of colony Varroa destructor densities

The parasitic mite Varroa destructor Anderson and Trueman negatively affects honey bee health, flight activity, and foraging behavior, all of which can be expected to affect foraging energetics. We tested this hypothesis in a 3-year field study. In each year, four-frame nucleus colonies with varying loads of varroa were placed under cages with mature rabbiteye blueberry plants, Vaccinium ashei. Individual bee weights consistently decreased as colony varroa populations increased, affirming that the design produced a range of colony mite effects. However, average forager flower handling times and nectar ingestion rates were unaffected by changes in colony varroa levels. Moreover, there were no significant effects of colony varroa levels on individual net foraging energy gain determined per flower, per second handling time, or per second total foraging time. We conclude that individual forager profits in Apis mellifera are unaffected by the range of colony V. destructor densities used in this study. These results are relevant to the question of the extent to which foraging of individuals relates to colony state in social Hymenoptera.     

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.     

Optimising multistage dairy cattle breeding schemes including genomic selection using decorrelated or optimum selection indices

Background

The prediction of the outcomes from multistage breeding schemes is especially important for the introduction of genomic selection in dairy cattle. Decorrelated selection indices can be used for the optimisation of such breeding schemes. However, they decrease the accuracy of estimated breeding values and, therefore, the genetic gain to an unforeseeable extent and have not been applied to breeding schemes with different generation intervals and selection intensities in each selection path.

Methods

A grid search was applied in order to identify optimum breeding plans to maximise the genetic gain per year in a multistage, multipath dairy cattle breeding program. In this program, different values of the accuracy of estimated genomic breeding values and of their costs per individual were applied, whereby the total breeding costs were restricted. Both decorrelated indices and optimum selection indices were used together with fast multidimensional integration algorithms to produce results.

Results

In comparison to optimum indices, the genetic gain with decorrelated indices was up to 40% less and the proportion of individuals undergoing genomic selection was different. Additionally, the interaction between selection paths was counter-intuitive and difficult to interpret. Independent of using decorrelated or optimum selection indices, genomic selection replaced traditional progeny testing when maximising the genetic gain per year, as long as the accuracy of estimated genomic breeding values was ≥ 0.45. Overall breeding costs were mainly generated in the path "dam-sire". Selecting males was still the main source of genetic gain per year.

Conclusion

Decorrelated selection indices should not be used because of misleading results and the availability of accurate and fast algorithms for exact multidimensional integration. Genomic selection is the method of choice when maximising the genetic gain per year but genotyping females may not allow for a reduction in overall breeding costs. Furthermore, the economic justification of genotyping females remains questionable.     

An Industry-Scale Mass Marking Technique for Tracing Farmed Fish Escapees

Farmed fish escape and enter the environment with subsequent effects on wild populations. Reducing escapes requires the ability to trace individuals back to the point of escape, so that escape causes can be identified and technical standards improved. Here, we tested if stable isotope otolith fingerprint marks delivered during routine vaccination could be an accurate, feasible and cost effective marking method, suitable for industrial-scale application. We tested seven stable isotopes, ¹³⁴Ba, ¹³⁵Ba, ¹³⁶Ba, ¹³⁷Ba, ⁸⁶Sr, ⁸⁷Sr and ²⁶Mg, on farmed Atlantic salmon reared in freshwater, in experimental conditions designed to reflect commercial practice. Marking was 100% successful with individual Ba isotopes at concentrations as low as 0.001 µg. g^-1 fish and for Sr isotopes at 1 µg. g^-1 fish. Our results suggest that 63 unique fingerprint marks can be made at low cost using Ba (0.0002 – 0.02 $US per mark) and Sr (0.46 – 0.82 $US per mark) isotopes. Stable isotope fingerprinting during vaccination is feasible for commercial application if applied at a company level within the world’s largest salmon producing nations. Introducing a mass marking scheme would enable tracing of escapees back to point of origin, which could drive greater compliance, better farm design and improved management practices to reduce escapes.