Accounting for female reproductive cycles in a superpopulation capture-recapture framework

Wildlife Population Assessment: Changing Priorities Driven by Technological Advances

Advances in technology are having a large effect on the priorities for innovation in statistical ecology. Collaborations between statisticians and ecologists have always been important in driving methodological development, but increasingly, expertise from computer scientists and engineers is also needed. We discuss changes that are occurring and that may occur in the future in surveys for estimating animal abundance. As technology advances, we expect classical distance sampling and capture-recapture to decrease in importance, as camera (still and video) survey, acoustic survey, spatial capture-recapture and genetic methods continue to develop and find new applications. We explore how these changes are impacting the work of the statistical ecologist.

New Zealand southern right whale (Eubalaena australis; Tohorā nō Aotearoa) behavioural phenology, demographic composition, and habitat use in Port Ross, Auckland Islands over three decades: 1998–2021

Changes in habitat availability and prey abundance are predicted to adversely influence survival and reproduction of wildlife in the Southern Ocean. Some populations of southern right whale (SRW; Eubalaena australis) are showing dramatic changes in habitat use. Surveys were undertaken in the austral winters of 2020 and 2021 at the key nursery and socialising ground for New Zealand SRWs: Port Ross, Auckland Islands, with 548 encounters and 599 skin biopsy samples collected. Data from these two surveys spanned peak periods of use and were used to test the hypothesis there have been shifts in the phenology, demographic composition and behaviour of SRWs using the Auckland Islands over the past three decades. The behavioural phenology and demographic composition of SRW resembles that observed in the 1990s. In contrast, the proportion of groups containing cow-calf pairs increased from 20% in the 1998 survey to 50% in 2020/21. These changes are consistent with a growing population undergoing strong recruitment, not limited by food resources. Continued use of Port Ross by all SRW demographic classes confirms this as key habitat for SRW in New Zealand waters, and we support increased enforcement of existing management measures to reduce whale-vessel interactions in this remote subantarctic archipelago.

Historical reconstruction of the population dynamics of southern right whales in the southwestern Atlantic Ocean

Understanding the recovery of whale populations is critical for developing population-management and conservation strategies. The southern right whale (SRW) Eubalena australis was one of the baleen whale species that has experienced centuries of exploitation. We assess here for the first time the population dynamics of the SRW from the southwestern Atlantic Ocean at the regional level to measure numerically the effect of whaling and estimate the population trend and recovery level after depletion. We reconstructed the catch history of whaling for the period 1670-1973 by an extensive review of different literature sources and developed a Bayesian state-space model to estimate the demographic parameters. The population trajectory indicated that the pre-exploitation abundance was close to 58,000 individuals (median = 58,212; 95% CI = 33,329-100,920). The abundance dropped to its lowest abundance levels in the 1830s when fewer than 2,000 individuals remained. The current median population abundance was estimated at 4,742 whales (95% CI = 3,853-6,013), suggesting that the SRW population remains small relative to its pre-exploitation abundance (median depletion P₂₀₂₁ 8.7%). We estimated that close to 36% of the SRW population visits the waters of the Península Valdés, the main breeding ground, every year. Our results provide insights into the severity of the whaling operation in the southwestern Atlantic along with the population´s response at low densities, thus contributing to understand the observed differences in population trends over the distributional range of the species worldwide.

Ocean warming threatens southern right whale population recovery

Whales contribute to marine ecosystem functioning, and they may play a role in mitigating climate change and supporting the Antarctic krill (Euphausia superba) population, a keystone prey species that sustains the entire Southern Ocean (SO) ecosystem. By analyzing a five-decade (1971–2017) data series of individual southern right whales (SRWs; Eubalaena australis) photo-identified at Península Valdés, Argentina, we found a marked increase in whale mortality rates following El Niño events. By modeling how the population responds to changes in the frequency and intensity of El Niño events, we found that such events are likely to impede SRW population recovery and could even cause population decline. Such outcomes have the potential to disrupt food-web interactions in the SO, weakening that ecosystem’s contribution to the mitigation of climate change at a global scale.

Local Drivers of Change in Southern Ocean Ecosystems: Human Activities and Policy Implications

Local drivers are human activities or processes that occur in specific locations, and cause physical or ecological change at the local or regional scale. Here, we consider marine and land-derived pollution, non-indigenous species, tourism and other human visits, exploitation of marine resources, recovery of marine mammals, and coastal change as a result of ice loss, in terms of their historic and current extent, and their interactions with the Southern Ocean environment. We summarise projected increases or decreases in the influence of local drivers, and projected changes to their geographic range, concluding that the influence of non-indigenous species, fishing, and the recovery of marine mammals are predicted to increase in the future across the Southern Ocean. Local drivers can be managed regionally, and we identify existing governance frameworks as part of the Antarctic Treaty System and other instruments which may be employed to mitigate or limit their impacts on Southern Ocean ecosystems.

Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru.

Satellite derived offshore migratory movements of southern right whales (Eubalaena australis) from Australian and New Zealand wintering grounds

Southern right whales (Eubalaena australis) migrate between Austral-winter calving and socialising grounds to offshore mid- to high latitude Austral-summer feeding grounds. In Australasia, winter calving grounds used by southern right whales extend from Western Australia across southern Australia to the New Zealand sub-Antarctic Islands. During the Austral-summer these whales are thought to migrate away from coastal waters to feed, but the location of these feeding grounds is only inferred from historical whaling data. We present new information on the satellite derived offshore migratory movements of six southern right whales from Australasian wintering grounds. Two whales were tagged at the Auckland Islands, New Zealand, and the remaining four at Australian wintering grounds, one at Pirates Bay, Tasmania, and three at Head of Bight, South Australia. The six whales were tracked for an average of 78.5 days (range: 29 to 150) with average individual distance of 38 km per day (range: 20 to 61 km). The length of individually derived tracks ranged from 645–6,381 km. Three likely foraging grounds were identified: south-west Western Australia, the Subtropical Front, and Antarctic waters, with the Subtropical Front appearing to be a feeding ground for both New Zealand and Australian southern right whales. In contrast, the individual tagged in Tasmania, from a sub-population that is not showing evidence of post-whaling recovery, displayed a distinct movement pattern to much higher latitude waters, potentially reflecting a different foraging strategy. Variable population growth rates between wintering grounds in Australasia could reflect fidelity to different quality feeding grounds. Unlike some species of baleen whale populations that show movement along migratory corridors, the new satellite tracking data presented here indicate variability in the migratory pathways taken by southern right whales from Australia and New Zealand, as well as differences in potential Austral summer foraging grounds.

Temporal variation in the vocal behaviour of southern right whales in the Auckland Islands, New Zealand

Autonomous recorders are frequently used for examining vocal behaviour of animals, and are particularly effective in remote habitats. Southern right whales are known to have an extensive acoustic repertoire. A recorder was moored at the isolated sub-Antarctic Auckland Islands for a year to examine whether the acoustic behaviour of southern right whales differed seasonally and throughout the day at their main calving ground in New Zealand. Recordings were made in each month except June, and vocalizations were audible in all months with recordings except January. A total of 35 487 calls were detected, of which upcalls were the most common (11 623). Call rate peaked in August (288 ± 5.9 [s.e.] calls/hour) and July (194 ± 8.3). Vocal behaviour varied diurnally with highest call rates detected at dusk and night, consistent with the concept that upcalls function primarily as contact calls. Zero-inflated model results confirmed that seasonal variation was the most important factor for explaining differences in vocal behaviour. An automated detector designed to expedite the analysis process for North Atlantic right whales correctly identified 80% of upcalls, although false detections were frequent, particularly when call rates were low. This study is the first to attempt year-round monitoring of southern right whale presence in New Zealand.

Temporal and demographic variation in partial migration of the North Atlantic right whale

Animal movement plays a fundamental role in the ecology of migratory species, and understanding migration patterns is required for effective management. To evaluate intrinsic and environmental factors associated with probabilities of endangered North Atlantic right whales Eubalaena glacialis migrating to a wintering ground off the southeastern United States (SEUS), we applied a multistate temporary emigration capture-recapture model to 22 years of photo-identification data. Migration probabilities for juveniles were generally higher yet more variable than those for adults, and non-calving adult females were the least likely group to migrate. The highest migration probabilities for juveniles and adult males coincided with years of relatively high calving rates, following years of higher prey availability in a fall feeding ground. Right whale migration to the SEUS can be classified as condition-dependent partial migration, which includes skipped breeding partial migration for reproductive females, and is likely influenced by tradeoffs among ecological factors such as reproductive costs and foraging opportunities that vary across individuals and time. The high variability in migration reported in this study provides insight into the ecological drivers of migration but presents challenges to right whale monitoring and conservation strategies.

The recovery of North Atlantic right whales, Eubalaena glacialis, has been constrained by human-caused mortality

North Atlantic right whales (NARW), Eubalaena glacialis, were nearly exterminated by historical whaling. Their abundance slowly increased up until 2010, to a maximum of fewer than 500 whales, and since then they have been in decline. We assessed the extent to which the relatively slow increase demonstrated by NARW was intrinsic, and how much could be due to anthropogenic impacts. In order to do so, we first compared calf counts of three populations of Southern right whales (SRW), E. australis, with that of NARW, over the period 1992-2016. By this index, the annual rate of increase of NARW was approximately one-third of that of SRW. Next we constructed a population projection model for female NARW, using the highest annual survival estimates available from recent mark-resight analysis, and assuming a four-year calving interval. The model results indicated an intrinsic rate of increase of 4% per year, approximately twice that observed, and that adult female mortality is the main factor influencing this rate. Necropsy records demonstrate that anthropogenic mortality is the primary cause of known mortality of NARW. Anthropogenic mortality and morbidity has limited the recovery of NARW, and baseline conditions prior to their recent decline were already jeopardizing NARW recovery.

Coping with intrasexual behavioral differences: Capture-recapture abundance estimation of male cheetah

Population estimates are a fundamental requirement of ecology and conservation. While capture-recapture models are an established method for producing such estimates, their assumption of homogeneous capture probabilities is problematic given that heterogeneity in individual capture probability is inherent to most species. Such variation must be accounted for by abundance models; otherwise, biased estimates are risked.Here, we investigate the performance of four types of heterogeneity models for estimating abundance of male cheetah Acinonyx jubatus, a species with two distinct spatial tactics of territorial and nonterritorial (floater) males. The differences in spatial movements of territory holders and floaters are expected to result in intrasexual heterogeneous capture probabilities. Four heterogeneity models were used to model male abundance at five territories in central Namibia; (a) a spatial tactic model, (b) a finite mixture model, both run in program MARK, (c) a floater-only model, and (d) a heterogeneity Mh model, both run in the program CAPTURE. Camera trap data of cheetah, taken at frequently visited marking trees, were used to derive true abundance. Model results were compared to the true abundance to assess the accuracy of estimates.Only models (a), (b), and (c) were able to consistently produce accurate results. Mixture models do not require prior knowledge regarding spatial tactic of males, which might not always be available. Therefore, we recommend such models as the preferred model type for cheetahs.Results highlight the potential for mixture models in overcoming the challenges of capture probability heterogeneity and in particular their use with species where intrasexual behavioral differences exist.

Next-generation metrics for monitoring genetic erosion within populations of conservation concern

Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.

Genetic and genomic monitoring with minimally invasive sampling methods

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

Understanding how dispersal and gene flow link geographically separated the populations over evolutionary history is challenging, particularly in migratory marine species. In southern right whales (SRWs, Eubalaena australis), patterns of genetic diversity are likely influenced by the glacial climate cycle and recent history of whaling. Here we use a dataset of mitochondrial DNA (mtDNA) sequences (n = 1327) and nuclear markers (17 microsatellite loci, n = 222) from major wintering grounds to investigate circumpolar population structure, historical demography and effective population size. Analyses of nuclear genetic variation identify two population clusters that correspond to the South Atlantic and Indo-Pacific ocean basins that have similar effective breeder estimates. In contrast, all wintering grounds show significant differentiation for mtDNA, but no sex-biased dispersal was detected using the microsatellite genotypes. An approximate Bayesian computation (ABC) approach with microsatellite markers compared the scenarios with gene flow through time, or isolation and secondary contact between ocean basins, while modelling declines in abundance linked to whaling. Secondary-contact scenarios yield the highest posterior probabilities, implying that populations in different ocean basins were largely isolated and came into secondary contact within the last 25,000 years, but the role of whaling in changes in genetic diversity and gene flow over recent generations could not be resolved. We hypothesise that these findings are driven by factors that promote isolation, such as female philopatry, and factors that could promote dispersal, such as oceanographic changes. These findings highlight the application of ABC approaches to infer the connectivity in mobile species with complex population histories and, currently, low levels of differentiation.

State-space mark-recapture estimates reveal a recent decline in abundance of North Atlantic right whales

North Atlantic right whales (Eubalaena glacialis Müller 1776) present an interesting problem for abundance and trend estimation in marine wildlife conservation. They are long lived, individually identifiable, highly mobile, and one of the rarest of cetaceans. Individuals are annually resighted at different rates, primarily due to varying stay durations among several principal habitats within a large geographic range. To date, characterizations of abundance have been produced that use simple accounting procedures with differing assumptions about mortality. To better characterize changing abundance of North Atlantic right whales between 1990 and 2015, we adapted a state–space formulation with Jolly‐Seber assumptions about population entry (birth and immigration) to individual resighting histories and fit it using empirical Bayes methodology. This hierarchical model included accommodation for the effect of the substantial individual capture heterogeneity. Estimates from this approach were only slightly higher than published accounting procedures, except for the most recent years (when recapture rates had declined substantially). North Atlantic right whales' abundance increased at about 2.8% per annum from median point estimates of 270 individuals in 1990 to 483 in 2010, and then declined to 2015, when the final estimate was 458 individuals (95% credible intervals 444–471). The probability that the population's trajectory post‐2010 was a decline was estimated at 99.99%. Of special concern was the finding that reduced survival rates of adult females relative to adult males have produced diverging abundance trends between sexes. Despite constraints in recent years, both biological (whales' distribution changing) and logistical (fewer resources available to collect individual photo‐identifications), it is still possible to detect this relatively recent, small change in the population's trajectory. This is thanks to the massive dataset of individual North Atlantic right whale identifications accrued over the past three decades. Photo‐identification data provide biological information that allows more informed inference on the status of this species.

Estimates of Abundance and Trend of Chilean Blue Whales off Isla de Chiloé, Chile

Since 1970, blue whales (Balaenoptera musculus) have been seen feeding in the waters off southern Chile during the summer and autumn (December to May). Investigation of the genetic, acoustic and morphological characteristics of these blue whales shows that they are a distinct but unnamed subspecies, called the Chilean blue whales. Photo-identification surveys have been conducted in the waters off northwestern Isla Grande de Chiloé, southern Chile from 2004–2012 and Isla Chañaral, central Chile in 2012. Over this time, 1,070 blue whales were encountered yielding, after photo-quality control, 318 and 267 unique photographs of the left and right side of the flank respectively. Using mark-recapture analysis of left and right side photographs collected from Isla Grande de Chiloé (2004–2012), open population models estimate that ~570–760 whales are feeding seasonally in this region. POPAN superpopulation abundance estimates for the same feeding ground in 2012 are 762 (95% confidence intervals, CI = 638–933) and 570 (95% CI 475–705) for left and right side datasets respectively, very similar to results from closed population models. Estimates of trend revealed strong variation in abundance, peaking in 2009 and [suggesting] fluctuating use in the survey area over time, likely related to the density of their prey. High inter-annual return rates suggest a degree of site-fidelity of individuals to Isla Grande de Chiloé and that the number of whales using this feeding ground is relatively small.

An integrated approach to historical population assessment of the great whales: case of the New Zealand southern right whale

Accurate estimation of historical abundance provides an essential baseline for judging the recovery of the great whales. This is particularly challenging for whales hunted prior to twentieth century modern whaling, as population-level catch records are often incomplete. Assessments of whale recovery using pre-modern exploitation indices are therefore rare, despite the intensive, global nature of nineteenth century whaling. Right whales (Eubalaena spp.) were particularly exploited: slow swimmers with strong fidelity to sheltered calving bays, the species made predictable and easy targets. Here, we present the first integrated population-level assessment of the whaling impact and pre-exploitation abundance of a right whale, the New Zealand southern right whale (E. australis). In this assessment, we use a Bayesian population dynamics model integrating multiple data sources: nineteenth century catches, genetic constraints on bottleneck size and individual sightings histories informing abundance and trend. Different catch allocation scenarios are explored to account for uncertainty in the population's offshore distribution. From a pre-exploitation abundance of 28 800-47 100 whales, nineteenth century hunting reduced the population to approximately 30-40 mature females between 1914 and 1926. Today, it stands at less than 12% of pre-exploitation abundance. Despite the challenges of reconstructing historical catches and population boundaries, conservation efforts of historically exploited species benefit from targets for ecological restoration.

First Direct Evidence for Natal Wintering Ground Fidelity and Estimate of Juvenile Survival in the New Zealand Southern Right Whale Eubalaena australis

Juvenile survival and recruitment can be more sensitive to environmental, ecological and anthropogenic factors than adult survival, influencing population-level processes like recruitment and growth rate in long-lived, iteroparous species such as southern right whales. Conventionally, Southern right whales are individually identified using callosity patterns, which do not stabilise until 6–12 months, by which time the whale has left its natal wintering grounds. Here we use DNA profiling of skin biopsy samples to identify individual Southern right whales from year of birth and document their return to the species’ primary wintering ground in New Zealand waters, the Subantarctic Auckland Islands. We find evidence of natal fidelity to the New Zealand wintering ground by the recapture of 15 of 57 whales, first sampled in year of birth and available for subsequent recapture, during winter surveys to the Auckland Islands in 1995–1998 and 2006–2009. Four individuals were recaptured at the ages of 9 to 11, including two females first sampled as calves in 1998 and subsequently resampled as cows with calves in 2007. Using these capture-recapture records of known-age individuals, we estimate changes in survival with age using Cormack-Jolly-Seber models. Survival is modelled using discrete age classes and as a continuous function of age. Using a bootstrap method to account for uncertainty in model selection and fitting, we provide the first direct estimate of juvenile survival for this population. Our analyses indicate a high annual apparent survival for juveniles at between 0.87 (standard error (SE) 0.17, to age 1) and 0.95 (SE 0.05: ages 2–8). Individual identification by DNA profiling is an effective method for long-term demographic and genetic monitoring, particularly in animals that change identifiable features as they develop or experience tag loss over time.

Cultural traditions across a migratory network shape the genetic structure of southern right whales around Australia and New Zealand

Fidelity to migratory destinations is an important driver of connectivity in marine and avian species. Here we assess the role of maternally directed learning of migratory habitats, or migratory culture, on the population structure of the endangered Australian and New Zealand southern right whale. Using DNA profiles, comprising mitochondrial DNA (mtDNA) haplotypes (500 bp), microsatellite genotypes (17 loci) and sex from 128 individually-identified whales, we find significant differentiation among winter calving grounds based on both mtDNA haplotype (FST = 0.048, ΦST = 0.109, p < 0.01) and microsatellite allele frequencies (FST = 0.008, p < 0.01), consistent with long-term fidelity to calving areas. However, most genetic comparisons of calving grounds and migratory corridors were not significant, supporting the idea that whales from different calving grounds mix in migratory corridors. Furthermore, we find a significant relationship between δ(13)C stable isotope profiles of 66 Australian southern right whales, a proxy for feeding ground location, and both mtDNA haplotypes and kinship inferred from microsatellite-based estimators of relatedness. This indicates migratory culture may influence genetic structure on feeding grounds. This fidelity to migratory destinations is likely to influence population recovery, as long-term estimates of historical abundance derived from estimates of genetic diversity indicate the South Pacific calving grounds remain at <10% of pre-whaling abundance.

Maximum likelihood estimation for model Mt,α for capture-recapture data with misidentification

We investigate model Mt,α  for abundance estimation in closed-population capture-recapture studies, where animals are identified from natural marks such as DNA profiles or photographs of distinctive individual features. Model Mt,α  extends the classical model Mt  to accommodate errors in identification, by specifying that each sample identification is correct with probability α and false with probability 1-α. Information about misidentification is gained from a surplus of capture histories with only one entry, which arise from false identifications. We derive an exact closed-form expression for the likelihood for model Mt,α  and show that it can be computed efficiently, in contrast to previous studies which have held the likelihood to be computationally intractable. Our fast computation enables us to conduct a thorough investigation of the statistical properties of the maximum likelihood estimates. We find that the indirect approach to error estimation places high demands on data richness, and good statistical properties in terms of precision and bias require high capture probabilities or many capture occasions. When these requirements are not met, abundance is estimated with very low precision and negative bias, and at the extreme better properties can be obtained by the naive approach of ignoring misidentification error. We recommend that model Mt,α  be used with caution and other strategies for handling misidentification error be considered. We illustrate our study with genetic and photographic surveys of the New Zealand population of southern right whale (Eubalaena australis).

Two intense decades of 19th century whaling precipitated rapid decline of right whales around New Zealand and East Australia

Right whales (Eubalaena spp.) were the focus of worldwide whaling activities from the 16^th to the 20^th century. During the first part of the 19^th century, the southern right whale (E. australis) was heavily exploited on whaling grounds around New Zealand (NZ) and east Australia (EA). Here we build upon previous estimates of the total catch of NZ and EA right whales by improving and combining estimates from four different fisheries. Two fisheries have previously been considered: shore-based whaling in bays and ship-based whaling offshore. These were both improved by comparison with primary sources and the American offshore whaling catch record was improved by using a sample of logbooks to produce a more accurate catch record in terms of location and species composition. Two fisheries had not been previously integrated into the NZ and EA catch series: ship-based whaling in bays and whaling in the 20^th century. To investigate the previously unaddressed problem of offshore whalers operating in bays, we identified a subset of vessels likely to be operating in bays and read available extant logbooks. This allowed us to estimate the total likely catch from bay-whaling by offshore whalers from the number of vessels seasons and whales killed per season: it ranged from 2,989 to 4,652 whales. The revised total estimate of 53,000 to 58,000 southern right whales killed is a considerable increase on the previous estimate of 26,000, partly because it applies fishery-specific estimates of struck and loss rates. Over 80% of kills were taken between 1830 and 1849, indicating a brief and intensive fishery that resulted in the commercial extinction of southern right whales in NZ and EA in just two decades. This conforms to the global trend of increasingly intense and destructive southern right whale fisheries over time.

Characterization of class I- and class II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales

North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.