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In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS‐collected whale blow for conservation genetics from a remote location. see also the Perspective by Elena Valsecchi. [ABSTRACT FROM AUTHOR]

Context: Strandings are an important source of information for estimating marine mammal biodiversity, particularly in data-sparse ocean basins such as Oceania. Aims: Here, we report on knowledge acquired from 218 stranding events recorded in the waters of New Caledonia (1877–2022). Methods: We investigated spatio-temporal distribution, stable isotope signatures, trace element concentrations, biometry measurements, genetic diversity, and diet, for the four most commonly stranded taxa (dugongs, 35% of events; sperm whales, 19%; Delphinidae, 18%; pygmy and dwarf sperm whales, 14%). Key results: Beginning in 1991, reports of stranding events increased (183 events, 322 individuals, 20 species from seven families: Dugongidae, Physeteridae, Delphinidae, Kogiidae, Ziphiidae, Balaenopteridae, Otariidae), with hotspots identified on the west coast (Bourail, Ouano, Nouméa) and in Prony Bay. Causes of death were not determined in 84% of stranding events, but were identified in the majority of expert-led necropsies (24 of 29 individuals from 10 species). Yet, valuable information regarding the impact of anthropogenic activities was gathered for some species of concern, such as the endangered dugong (28% human-caused). Since 2016, training and outreach have been provided to rangers, veterinarians, and various public safety officers to support their engagement in the scientific monitoring of marine mammal strandings. A website (www.rescue.ird.nc) was developed to facilitate standardised data collection and storage, and to provide public access to stranding records. Conclusion: Although the number of individuals reported here remains modest, this study provides new information on poorly documented species in New Caledonia. Implications: Long-term monitoring of strandings can help design effective conservation measures. RESUME: Contexte: Les échouages constituent une source d'informations importante pour estimer la biodiversité des mammifères marins, en particulier dans les bassins océaniques pour lesquels les données sont rares, comme l'Océanie Objectif: Nous présentons ici les connaissances acquises à partir de 218 échouages enregistrés dans les eaux de Nouvelle-Calédonie (1877–2022). Méthodes: Nous avons étudié la distribution spatio-temporelle, les signatures isotopiques, les éléments traces, les mesures biométriques, la diversité génétique et le régime alimentaire des quatre taxons les plus fréquemment échoués (dugongs, 35% des échouages; cachalots, 19%; Delphinidae, 18% ; cachalots pygmées et nains, 14%). Principaux résultats: À partir de 1991, les signalements d'échouages ont augmenté (183 événements, 322 individus, 20 espèces de sept familles: Dugongidae, Physeteridae, Delphinidae, Kogiidae, Ziphiidae, Balaenopteridae, Otariidae), avec des points chauds identifiés sur la côte ouest de la Grande Terre (Bourail, Ouano, Nouméa) et dans la Baie de Prony. Les causes de décès n'ont pas été déterminées pour 84% des échouages, mais elles ont été identifiées dans la majorité des autopsies réalisées par des vétérinaires (24 des 29 individus de 10 espèces). Des informations précieuses concernant l'impact des activités anthropiques ont été recueillies pour certaines espèces préoccupantes, telles que le dugong, une espèce en voie de disparition (28% des échouages d'origine humaine). Depuis 2016, des formations et des activités de sensibilisation ont été dispensées aux gardes nature, aux vétérinaires et à divers agents publics pour soutenir leur engagement dans la surveillance scientifique des échouages de mammifères marins. Un site Web (www.rescue.ird.nc) a été développé pour faciliter la collecte et le stockage de données standardisées et pour fournir un accès public aux enregistrements d'échouages. Conclusion: Bien que le nombre d'individus signalés échoués ici reste modeste, cette étude apporte de nouvelles informations sur des espèces peu documentées en Nouvelle-Calédonie. Implications: La surveillance à long terme des échouages peut aider à concevoir des mesures de conservation efficaces. Map of strandings in New Caledonia; people gathered around a stranded whale; four commonly stranded species. Conservation of marine mammals in Oceania is limited by a lack of understanding of these relatively rare, yet emblematic species. Here, we report on significant biological and ecological data acquired from several decades of monitoring strandings in New Caledonia. This increased knowledge may help guide management measures locally and regionally. Photograph by Marine Mammal Stranding Center. This article belongs to the Collection Marine Mammals in the Pacific. [ABSTRACT FROM AUTHOR]

Although Hubbs' beaked whale (Mesoplodon carlhubbsi) was previously known from over 60 strandings on both sides of the North Pacific, it had been identified alive in the wild only once, off Oregon in 1994. In September 2021, we conducted a search effort for beaked whales off the coast of Oregon using a towed hydrophone array and a visual search team. Approximately 350 km off the Columbia River mouth, we detected the vocalizations of an unidentified mesoplodont whale; we stopped our vessel and waited in the area until two unidentified juvenile Mesoplodon surfaced and stayed near our vessel for almost 2 hr. During that time, we took numerous photographs and videos, made behavioral observations, and recorded their vocalizations. The DNA sequence from a biopsy sample identified them as M. carlhubbsi. In this paper, we discuss our biological observations, including color patterning and acquired markings, behavioral observations, and describe for the first time the acoustic characteristics of this species. We confirm that M. carlhubbsi is the source of a previously unidentified acoustic signal known as BW37V, and we update what is known about the at‐sea distribution of this species based on previous recordings and observational records. [ABSTRACT FROM AUTHOR]

The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere. [ABSTRACT FROM AUTHOR]

The age of an individual is an essential demographic parameter but is difficult to estimate without long‐term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including nonmodel organisms such as cetaceans. Māui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training data set, the optimal model required only eight methylation sites, provided an age correlation of.95, and had a median absolute age error of 1.54 years. A leave‐one‐out cross‐validation analysis with the same parameters resulted in an age correlation of.87 and median absolute age error of 2.09 years. To improve age estimation, we included previously published beluga whale (Delphinapterus leucas) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Māui dolphins revealed a shift from a median age of 8–9 years to a younger population aged 7–8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species. [ABSTRACT FROM AUTHOR]

Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville's beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville's beaked whales, suggested the potential for further resolution of differences between oceanic populations. [ABSTRACT FROM AUTHOR]

The krill surplus hypothesis of unlimited prey resources available for Antarctic predators due to commercial whaling in the 20th century has remained largely untested since the 1970s. Rapid warming of the Western Antarctic Peninsula (WAP) over the past 50 years has resulted in decreased seasonal ice cover and a reduction of krill. The latter is being exacerbated by a commercial krill fishery in the region. Despite this, humpback whale populations have increased but may be at a threshold for growth based on these human‐induced changes. Understanding how climate‐mediated variation in prey availability influences humpback whale population dynamics is critical for focused management and conservation actions. Using an 8‐year dataset (2013–2020), we show that inter‐annual humpback whale pregnancy rates, as determined from skin‐blubber biopsy samples (n = 616), are positively correlated with krill availability and fluctuations in ice cover in the previous year. Pregnancy rates showed significant inter‐annual variability, between 29% and 86%. Our results indicate that krill availability is in fact limiting and affecting reproductive rates, in contrast to the krill surplus hypothesis. This suggests that this population of humpback whales may be at a threshold for population growth due to prey limitations. As a result, continued warming and increased fishing along the WAP, which continue to reduce krill stocks, will likely impact this humpback whale population and other krill predators in the region. Humpback whales are sentinel species of ecosystem health, and changes in pregnancy rates can provide quantifiable signals of the impact of environmental change at the population level. Our findings must be considered paramount in developing new and more restrictive conservation and management plans for the Antarctic marine ecosystem and minimizing the negative impacts of human activities in the region. [ABSTRACT FROM AUTHOR]

Heteroplasmy in the mitochondrial genome offers a rare opportunity to track the evolution of a newly arising maternal lineage in populations of non-model species. Here, we identified a previously unreported mitochondrial DNA haplotype while assembling an integrated database of DNA profiles and photo-identification records from humpback whales in southeastern Alaska (SEAK). The haplotype, referred to as A8 , was shared by only 2 individuals, a mature female with her female calf, and differed by only a single base pair from a common haplotype in the North Pacific, referred to as A−. To investigate the origins of the A8 haplotype, we reviewed n = 1,089 electropherograms (including replicate samples) of n = 710 individuals with A− haplotypes from an existing collection. From this review, we found 20 individuals with clear evidence of heteroplasmy for A− / A8 (parental/derived) haplotypes. Of these, 15 were encountered in SEAK, 4 were encountered on the Hawaiian breeding ground (the primary migratory destination for whales in SEAK), and 1 was encountered in the northern Gulf of Alaska. We used genotype exclusion and likelihood to identify one of the heteroplasmic females as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. The mutation leading to this heteroplasmy and the fixation of the A8 haplotype provide an opportunity to document the population dynamics and regional fidelity of a newly arising maternal lineage in a population recovering from exploitation. [ABSTRACT FROM AUTHOR]

The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group. [ABSTRACT FROM AUTHOR]

The sei whale (Balaenopteraborealis) presents a disjointed geographic distribution. Significant genetic divergence between sei whales from the North Atlantic (NA) and North Pacific (NP) have been recorded; however, limited samples from the Southern Hemisphere (SH) have precluded a global analysis.The largest recorded mass mortality event occurred in Golfo de Penas, southern Chile, providing a primary source of SH samples. A global mitochondrial DNA phylogeographic study was undertaken including 111 SH samples (98 from Golfo de Penas), and new sequences from the NP.A marked phylogeographic structure was observed between the three ocean basins' populations, with the highest ΦST values between NA–NP and NA–SH, and a lower but still significant value between SH–NP. This structure, and the haplotype distribution pattern, suggest a more recent separation between SH–NP and an absence of recurrent gene flow among all three populations. Only one potential migratory event was detected from SH to NA.These results support an ongoing phylogeographic differentiation between all populations, highlighting the identity of each and the importance of independent management. Therefore, each population should represent a separate management unit, which is important in the development of conservation strategies.Demographic analyses detected a recent reduction of population size in the SH and NA, but not in the NP. For all populations, estimated effective population sizes were higher than estimated census sizes. This suggests that most of the genetic diversity of pre‐whaling populations is still retained; however, continued reduction in population sizes could lead to future loss of genetic diversity.This study highlights the necessity of local protection and systematic monitoring of the Golfo de Penas sei whale population. In such a remote area the use of remote sensing techniques could be a cost‐effective option for evaluating the threat, periodicity and magnitude of mortalities and their effect on the local whale population. The integration of genetic and demographic approaches improves the understanding of the dynamics of populations, which is particularly useful in endangered species. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) differences between humpback whales on different feeding grounds can reflect the cultural transmission of migration destinations over generations, and therefore represent one of the very few cases of gene-culture coevolution identified in the animal kingdom. In Russian Pacific waters, photo-identification (photo-ID) studies have shown minimal interchange between whales feeding off the Commander Islands and those feeding in the Karaginsky Gulf, regions that are separated by only 500 km and have previously been lumped together as a single Russian feeding ground. Here, we assessed whether genetic differentiation exists between these 2 groups of humpback whales. We discovered a strong mtDNA differentiation between the 2 feeding sites (F ST = 0.18, Φ ST = 0.14, P < 0.001). In contrast, nuclear DNA (nuDNA) polymorphisms, determined at 8 microsatellite loci, did not reveal any differentiation. Comparing our mtDNA results with those from a previous ocean-basin study reinforced the differences between the 2 feeding sites. Humpback whales from the Commanders appeared most similar to those of the western Gulf of Alaska and the Aleutian feeding grounds, whereas Karaginsky differed from all other North Pacific feeding grounds. Comparison to breeding grounds suggests mixed origins for the 2 feeding sites; there are likely connections between Karaginsky and the Philippines and to a lesser extent to Okinawa, Japan, whereas the Commanders are linked to the Mexican breeding grounds. The mtDNA differentiation between the Commander Islands and Karaginsky Gulf suggests a case of gene-culture coevolution, correlated to fidelity to a specific feeding site within a particular feeding ground. From a conservation perspective, our findings emphasize the importance of considering these 2 feeding sites as separate management units. [ABSTRACT FROM AUTHOR]

Humpback whales wintering in tropical waters along the Atlantic and Pacific coasts of the South American continent are thought to represent distinct populations or 'stocks.' Here we present the first analysis of genetic differentiation and estimates of gene flow between these breeding stocks, based on both mitochondrial DNA (mt DNA) control region sequences (465 bp) and 16 microsatellite loci from samples collected off Brazil ( n = 277) and Colombia ( n = 148), as well as feeding areas near the western Antarctic Peninsula ( n = 86). We found significant differentiation between Brazilian and Colombian breeding grounds at both mt DNA ( F ST = 0.058) and microsatellite ( F ST = 0.011) markers and corroborated previous studies showing genetic similarity between humpbacks from Colombia and those from Antarctic Peninsula feeding areas. Estimates of long-term gene flow between Brazil and Colombia were low to moderate, asymmetrical, and mostly mediated by males. Assignment procedures detected some cases of interchange and individuals of admixed ancestry between breeding grounds, indicating limited mixing of individuals between these stocks. Overall, results highlight the differentiation of humpback whale breeding populations with adjacent feeding grounds. This appears to be a remarkable example of fidelity to seasonal habitat in the absence of any contemporary barriers. [ABSTRACT FROM AUTHOR]

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mt DNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mt DNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394-bp mt DNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mt DNA diversity (π = 0.430%) reflecting an expansion event <80 000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male-mediated gene flow. A hierarchical amova showed that regions were important for explaining mt DNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mt DNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization. [ABSTRACT FROM AUTHOR]

We present genetic and morphological evidence supporting the recognition of a previously synonymized species of Mesoplodon beaked whale in the tropical Indo-Pacific, Mesoplodon hotaula. Although the new species is closely-related to the rare ginkgo-toothed beaked whale M. ginkgodens, we show that these two lineages can be differentiated by maternally (mitochondrial DNA), biparentally (autosomal), and paternally (Y chromosome) inherited DNA sequences, as well as by morphological features. The reciprocal monophyly of the mt DNA genealogies and the largely parapatric distribution of these lineages is consistent with reproductive isolation. The new lineage is currently known from at least seven specimens: Sri Lanka (1), Gilbert Islands, Republic of Kiribati (1+), Palmyra Atoll, Northern Line Islands, U.S.A. (3), Maldives (1), and Seychelles (1). The type specimen (Sri Lanka) was described as a new species, M. hotaula, in 1963, but later synonymized with M. ginkgodens. This discovery brings the total number of Mesoplodon species to 15, making it, by far, the most speciose yet least known genus of cetaceans. [ABSTRACT FROM AUTHOR]

To improve understanding of population structure, ecosystem relationships and predictive models of human impact in cetaceans and other marine megafauna, we developed gene GIS, a suite of GIS tools and a customized Arc Marine data model to facilitate visual exploration and spatial analyses of individual-based records from DNA profiles and photo-identification records. We used the open source programming language Python 2.7 and Arc GIS 10.1 software to create a user-friendly, menu-driven toolbar linked to a Python Toolbox containing customized geoprocessing scripts. For ease of sharing and installation, we compiled the gene GIS program into an Arc GIS Python Add- In, freely available for download from the website . We used the Lord- Castillo et al. (2009) Arc Marine data model customization as the starting point for our work and retained nine key base Arc Marine classes. We demonstrate the utility of gene GIS using an integrated database of more than 18,000 records of humpback whales ( Megaptera novaeangliae) in the North Pacific collected during the Structure of Populations, Levels of Abundance and Status of Humpback Whales in the North Pacific ( SPLASH) program. These records represent more than 8,000 naturally marked individuals and 2,700 associated DNA profiles, including 10 biparentally inherited microsatellite loci, maternally inherited mitochondrial DNA, and genetic sex. [ABSTRACT FROM AUTHOR]

Humpback whales undertake long-distance seasonal migrations between low latitude winter breeding grounds and high latitude summer feeding grounds. We report the first in-depth population genetic study of the humpback whales that migrate to separate winter breeding grounds along the northwestern and northeastern coasts of Australia, but overlap on summer feeding grounds around Antarctica. Weak but significant differentiation between eastern and western Australia was detected across ten microsatellite loci ( FST = 0.005, P = 0.001; DEST = 0.031, P = 0.001, n = 364) and mitochondrial control region sequences ( FST = 0.017 and Φ ST = 0.069, P = 0.001, n = 364). Bayesian clustering analyses using microsatellite data could not resolve any population structure unless sampling location was provided as a prior. This study supports the emerging evidence that weak genetic differentiation is characteristic among neighboring Southern Hemisphere humpback whale breeding populations. This may be a consequence of relatively high gene flow facilitated by overlapping summer feeding areas in Antarctic waters. [ABSTRACT FROM AUTHOR]

Historically, the range of the southern right whale ( SRW) included winter calving grounds around the North and South Islands (mainland) of New Zealand ( NZ) and in the NZ subantarctic Auckland and Campbell Islands. Due to extensive whaling in the 19th and 20th centuries, no SRW was seen around mainland NZ for nearly four decades (1928-1963). Here we present evidence for the regular use of the mainland NZ wintering ground, presumably from a remnant population that persisted in the NZ subantarctic Auckland and Campbell Islands. SRWs have been sighted every year around mainland NZ since 1988, with 125 sightings during the focus of this work: from 2003 to 2010. There were 28 cow-calf pairs sighted around mainland NZ from 2003 to 2010, compared with 11 sightings from 1991 to 2002. Furthermore, two females, identified by DNA profiles, were sighted with calves around mainland at 4 yr intervals: the first evidence of female site fidelity to the mainland NZ calving ground. Individual identification from photographs of natural markings and DNA profiles provided information on within-year movements and residency around the mainland, and further evidence for exchange between the mainland and subantarctic wintering grounds. Despite these promising signs, the distribution of NZ SRWs remains primarily concentrated in the NZ subantarctic. [ABSTRACT FROM AUTHOR]

In understanding the impact of commercial whaling, it is important to estimate the mixing of low latitude breeding populations on Antarctic feeding grounds, particularly the endangered humpback whale populations of Oceania. This paper estimates the degree of genetic differentiation among the putative populations of Oceania (New Caledonia, Tonga, the Cook Islands and French Polynesia) and Australia (western Australia and eastern Australia) using ten microsatellite loci and mtDNA, assesses the power of the data for a mixed-stock analysis, determines ways to improve statistical power for future studies and estimates the population composition of Antarctic samples collected in 2010 south of New Zealand and eastern Australia. A large proportion of individuals could not be assigned to a population of origin (> 52%) using a posterior probability threshold of > 0.90. The mixed-stock analysis simulations however, produced accurate results with humpback whales reapportioned to their population of origin above the 90% threshold for western Australia, New Caledonia and Oceania grouped using a combined mtDNA and microsatellite dataset. Removing the Cook Islands, considered a transient region for humpback whales, from the simulation analysis increased the ability to reapportion Tonga from 86% to 89% and French Polynesia from 89% to 92%. Breeding ground sample size was found to be a factor influencing the accuracy of population reapportionment whereas increasing the mixture or feeding ground sample size improved the precision of results. The mixed-stock analysis of our Antarctic samples revealed substantial contributions from both eastern Australia (53.2%, 6.8% SE) and New Caledonia (43.7%, 5.5% SE) [with Oceania contributing 46.8% (5.9% SE)] but not western Australia. Despite the need for more samples to improve estimates of population allocation, our study strengthens the emerging genetic and non-genetic evidence that Antarctic waters south of New Zealand and eastern Australia are used by humpback whales from both eastern Australia and the more vulnerable breeding population of New Caledonia, representing Oceania. [ABSTRACT FROM AUTHOR]

Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity. [ABSTRACT FROM AUTHOR]

The identification and characterization of reproductively isolated subpopulations or 'stocks' are essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and 'gametic recapture' to examine the reproductive autonomy of southern right whales ( Eubalaena australis) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother-calf pairs from skin biopsy samples, using sex-specific markers, 13 microsatellite loci and mtDNA haplotypes. We constructed DNA profiles for 314 adult males, representing 30% of the census male abundance of the NZ stock, previously estimated from genotypic mark-recapture modelling to be 1085 (95% CL 855, 1416). Under the hypothesis of demographic closure and the assumption of equal reproductive success among males, we predict: (i) the proportion of paternities assigned will reflect the proportion of the male population sampled and (ii) the gametic mark-recapture (GMR) estimate of male abundance will be equivalent to the census male estimate for the NZ stock. Consistent with these predictions, we found that the proportion of assigned paternities equalled the proportion of the census male population size sampled. Using the sample of males as the initial capture, and paternity assignment as the recapture, the GMR estimate of male abundance was 1001 (95% CL 542, 1469), similar to the male census estimate. These findings suggest that right whales returning to the NZ calving ground are reproductively autonomous on a generational timescale, as well as isolated by maternal fidelity on an evolutionary timescale, from others in the Indo-Pacific region. [ABSTRACT FROM AUTHOR]

The article discusses a study that analyzed the genetic identification of whale meat bought in sushi restaurants in Los Angeles, California in October 2009 and in Seoul, South Korea between June and September 2009. DNA extraction and amplification were carried. The study showed an exact match at seven microsatellite loci and mitochondrial (mt) DNA haplotype in fin whales from South Korea and Japan.

Pilot whales ( Globicephala spp.) provide an interesting example of recently diverged oceanic species with a complex evolutionary history. The two species have wide but largely non-overlapping ranges. Globicephala melas (long-finned pilot whale; LFPW) has an antitropical distribution and is found in the cold-temperate waters of the North Atlantic and Southern Hemisphere, whereas Globicephala macrorhynchus (short-finned pilot whale; SFPW) has a circumglobal distribution and is found mainly in the tropics and subtropics. To investigate pilot whale evolution and biogeography, we analysed worldwide population structure using mitochondrial DNA (mtDNA) control region sequences (up to 620 bp) from a variety of sources (LFPW = 643; SFPW = 150), including strandings in New Zealand and Tasmania, and whale-meat products purchased on the markets of Japan and Korea. Phylogenetic reconstructions failed to support a reciprocal monophyly of the two species, despite six diagnostic substitutions, possibly because of incomplete lineage sorting or inadequate phylogenetic information. Both species had low haplotype and nucleotide diversity compared to other abundant widespread cetaceans (LFPW, π = 0.35%; SFPW, π = 0.87%) but showed strong mtDNA differentiation between oceanic basins. Strong levels of structuring were also found at the regional level. In LFPW, phylogeographic patterns were suggestive either of a recent demographic expansion or selective sweep acting on the mtDNA. For SFPW, the waters around Japan appear to represent a centre of diversity, with two genetically-distinct forms, as well as a third population of unknown origin. The presence of multiple unique haplotypes among SFPW from South Japan, together with previously documented morphological and ecological differences, suggests that the southern form represents a distinct subspecies and/or evolutionary significant unit. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 729–744. [ABSTRACT FROM AUTHOR]

The article discusses the importance of the approach known as DNA taxonomy. It was revealed that DNA sequence data enable not only the inference of evolutionary relationships and population histories but also represent a powerful tool for uncovering hidden biodiversity. Accordingly, the application of DNA taxonomy to beaked whales, the least known of all cetacean families had led to some significant discoveries in recent years. Moreover, these include the description of a new species from the North Pacific, the resurrection of a long-forgotten species in the Southern Hemisphere. Furthermore, the framework for these findings was provided by comprehensive data sets of DNA reference sequences for two mitochondrial genes and cytochrome.

Obtaining direct measurements to characterise ecosystem function can be hindered by remote or inaccessible regions. Next-generation satellite tags that inform increasingly sophisticated movement models, and the miniaturisation of animal-borne loggers, have enabled the use of animals as tools to collect habitat data in remote environments, such as the Southern Ocean. Research on the distribution, habitat use and recovery of Oceania’s humpback whales ( Megaptera novaeangliae ) has been constrained by the inaccessibility to their Antarctic feeding grounds and the limitations of technology. In this multi-disciplinary study, we combine innovative analytical tools to comprehensively assess the distribution and population structure of this marine predator throughout their entire migratory range. We used genotype and photo-identification matches and conducted a genetic mixed-stock analysis to identify the breeding ground origins of humpback whales migrating past the Kermadec Islands, New Zealand. Satellite tracking data and a state-space model were then used to identify the migratory paths and behaviour of 18 whales, and to reveal their Antarctic feeding ground destinations. Additionally, we conducted progesterone assays and epigenetic aging to determine the pregnancy rate and age-profile of the population. Humpback whales passing the Kermadec Islands did not assign to a single breeding ground origin, but instead came from a range of breeding grounds spanning ∼3500 km of ocean. Sampled whales ranged from calves to adults of up to 67 years of age, and a pregnancy rate of 57% was estimated from 30 adult females. The whales migrated to the Southern Ocean (straight-line distances of up to 7000 km) and spanned ∼4500 km across their Antarctic feeding grounds. All fully tracked females with a dependent calf (n = 4) migrated to the Ross Sea region, while 70% of adults without calves (n = 7) travelled further east to the Amundsen and Bellingshausen Seas region. By combining multiple research and analytical tools we obtained a comprehensive understanding of this wide-ranging, remote population of whales. Our results indicate a population recovering from exploitation, and their feeding ground distribution serves as an indicator of the resources available in these environments. The unexpected Kermadec Islands migratory bottle-neck of whales from several breeding grounds, variable distribution patterns by life history stage and high pregnancy rates will be important in informing conservation and management planning, and for understanding how this, as well as other whale populations, might respond to emerging threats such as climate change. [ABSTRACT FROM AUTHOR]

Abstract: The conservation of rare or cryptic species in inaccessible habitats represents a particular challenge to biologists. Since 1991, a collaborative research program involving members of the public, indigenous communities, the Museum of New Zealand Te Papa Tongarewa (NMNZ) and the Department of Conservation has provided tissue samples for genetic analysis of stranded, or beach-cast cetaceans. The New Zealand Cetacean Tissue Archive (NZCeTA), initiated and maintained by the University of Auckland, is now one of the largest archives of its kind in the world, with tissue samples or extracted DNA from 1982 individuals. Species identity has been confirmed by DNA barcoding, using mtDNA control region sequences for 65% of the samples representing 35 species, 11 of which are from the poorly known beaked whale family, Ziphiidae. Although these animals regularly strand around the coastline of New Zealand there are no known areas at sea where they can be reliably found and very few reported live sightings. Samples collected from strandings of three species: Gray’s (Mesoplodon grayi); straptoothed (Mesoplodon layardii) and Cuvier’s beaked whale (Ziphius cavirostris), represent 83% (n =225) of all ziphiids in the NZCeTA (n =272). As an example of the archives utility, we used the spatial and temporal distribution of these records to provide new evidence for key habitat of these cryptic species and for seasonal and sex-biased patterns of stranding mortality. As beaked whales are known to be threatened by anthropogenic activity in other parts of the world, these records provide a critical baseline for understanding the future impacts of planned development in New Zealand’s near and offshore waters. [Copyright &y& Elsevier]