Primers for the amplification of tri- and tetramer microsatellite loci in baleen whales

Wild pedigrees inform mutation rates and historic abundance in baleen whales

Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.

Variation in blubber cortisol levels in a recovering humpback whale population inhabiting a rapidly changing environment

Glucocorticoids are regularly used as biomarkers of relative health for individuals and populations. Around the Western Antarctic Peninsula (WAP), baleen whales have and continue to experience threats, including commercial harvest, prey limitations and habitat change driven by rapid warming, and increased human presence via ecotourism. Here, we measured demographic variation and differences across the foraging season in blubber cortisol levels of humpback whales (Megaptera novaeangliae) over two years around the WAP. Cortisol concentrations were determined from 305 biopsy samples of unique individuals. We found no significant difference in the cortisol concentration between male and female whales. However, we observed significant differences across demographic groups of females and a significant decrease in the population across the feeding season. We also assessed whether COVID-19-related reductions in tourism in 2021 along the WAP correlated with lower cortisol levels across the population. The decline in vessel presence in 2021 was associated with a significant decrease in humpback whale blubber cortisol concentrations at the population level. Our findings provide critical contextual data on how these hormones vary naturally in a population over time, show direct associations between cortisol levels and human presence, and will enable comparisons among species experiencing different levels of human disturbance.

Demography of an ice-obligate mysticete in a region of rapid environmental change

Antarctic minke whales (Balaenoptera bonaerensis, AMW) are an abundant, ice-dependent species susceptible to rapid climatic changes occurring in parts of the Antarctic. Here, we used remote biopsy samples and estimates of length derived from unoccupied aircraft system (UAS) to characterize for the first time the sex ratio, maturity, and pregnancy rates of AMWs around the Western Antarctic Peninsula (WAP). DNA profiling of 82 biopsy samples (2013-2020) identified 29 individual males and 40 individual females. Blubber progesterone levels indicated 59% of all sampled females were pregnant, irrespective of maturity. When corrected for sexual maturity, the median pregnancy rate was 92.3%, indicating that most mature females become pregnant each year. We measured 68 individuals by UAS (mean = 8.04 m) and estimated that 66.5% of females were mature. This study provides the first data on the demography of AMWs along the WAP and represents the first use of non-lethal approaches to studying this species. Furthermore, these results provide baselines against which future changes in population status can be assessed in this rapidly changing marine ecosystem.

Evolution of the recombination regulator PRDM9 in minke whales

Background

PRDM9 is a key regulator of meiotic recombination in most metazoans, responsible for reshuffling parental genomes. During meiosis, the PRDM9 protein recognizes and binds specific target motifs via its array of C₂H₂ zinc-fingers encoded by a rapidly evolving minisatellite. The gene coding for PRDM9 is the only speciation gene identified in vertebrates to date and shows high variation, particularly in the DNA-recognizing positions of the zinc-finger array, within and between species. Across all vertebrate genomes studied for PRDM9 evolution, only one genome lacks variability between repeat types – that of the North Pacific minke whale. This study aims to understand the evolution and diversity of Prdm9 in minke whales, which display the most unusual genome reference allele of Prdm9 so far discovered in mammals.

Results

Minke whales possess all the features characteristic of PRDM9-directed recombination, including complete KRAB, SSXRD and SET domains and a rapidly evolving array of C₂H₂-type-Zincfingers (ZnF) with evidence of rapid evolution, particularly at DNA-recognizing positions that evolve under positive diversifying selection. Seventeen novel PRDM9 variants were identified within the Antarctic minke whale species, plus a single distinct PRDM9 variant in Common minke whales – shared across North Atlantic and North Pacific minke whale subspecies boundaries.

Conclusion

The PRDM9 ZnF array evolves rapidly, in minke whales, with at least one DNA-recognizing position under positive selection. Extensive PRDM9 diversity is observed, particularly in the Antarctic in minke whales. Common minke whales shared a specific Prdm9 allele across subspecies boundaries, suggesting incomplete speciation by the mechanisms associated with PRDM9 hybrid sterility.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08305-1.

Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean

Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.

Evidence of unidirectional hybridization and second-generation adult hybrid between the two largest animals on Earth, the fin and blue whales

Biodiversity in the oceans has dramatically declined since the beginning of the industrial era, with accelerated loss of marine biodiversity impairing the ocean's capacity to maintain vital ecosystem services. A few organisms epitomize the damaging and long-lasting effects of anthropogenic exploitation: Some whale species, for instance, were brought to the brink of extinction, with their population sizes reduced to such low levels that may have caused a significant disruption to their reproductive dynamics and facilitated hybridization events. The incidence of hybridization is nevertheless believed to be rare, and very little information exists on its directionality. Here, using genetic markers, we show that all but one whale hybrid sample collected in Icelandic waters originated from the successful mating of male fin whale and female blue whale, thus suggesting unidirectional hybridization. We also demonstrate for the first time the existence of a second-generation adult (male) hybrid resulting from a backcross between a female hybrid and a pure male fin whale. The incidence of hybridization events between fin and blue whales is likely underestimated and the observed unidirectional hybridization (for F1 and F2 hybrids) is likely to induce a reproductive loss in blue whale, which may represent an additional challenge to its recovery in the Atlantic Ocean compared to other rorquals.

Characterization of 25 new microsatellite markers for the fin whale (Balaenoptera physalus) and cross-species amplification in other cetaceans

Cetaceans are large mammals widely distributed on Earth. The fin whale, Balaenoptera physalus, is the second largest living animal. In the 20th century, commercial whaling reduced its global population by 70%, and in the Mediterranean Sea not only was their overall population depleted but the migration between the Mediterranean Sea and the Atlantic Ocean was reduced. Previous genetic studies identified isolation between these two regions, with a limited gene-flow between these adjacent populations based on nuclear and mitochondrial markers. However, only limited information exists for the Mediterranean population as genetic diversity and abundance trends are still unknown. In this study, 39 highly polymorphic microsatellite markers were tested, including 25 markers developed de novo together with 14 markers previously published. An average allelic diversity of 8.3 alleles per locus was reported, ranging from 3 to 15 alleles per locus, for B. physalus. Expected heterozygosity was variable among loci and ranged from 0.34 to 0.91. Only two markers in the new set were significantly deviant from the Hardy Weinberg equilibrium. Cross-species amplification was tested in four other cetacean species. A total of 27 markers were successfully amplified in the four species (Balaenoptera acutorostrata, Megaptera novaeangliae, Physeter macrocephalus and Globicephala melas). A multivariate analysis on the multilocus genotypes successfully discriminated the five species. This new set of microsatellite markers will not only provide a useful tool to identify and understand the genetic diversity and the evolution of the B. physalus population, but it will also be relevant for other cetacean species, and will allow further parentage analyses. Eventually, this new set of microsatellite markers will provide critical data that will shed light on important biological data within a conservation perspective.

Searching for humpback whales in a historical whaling hotspot of the Coral Sea, South Pacific

Humpback whales Megaptera novaeangliae were severely depleted by commercial whaling. Understanding key factors in their recovery is a crucial step for their conservation worldwide. In Oceania, the Chesterfield-Bellona archipelago was a primary whaling site in the 19th century, yet has been left almost unaffected by anthropogenic activities since. We present the results of the first multidisciplinary dedicated surveys in the archipelago assessing humpback whale populations 2 centuries post-whaling. We encountered 57 groups during 24 survey days (2016-2017), among which 35 whales were identified using photographs of natural markings (photo-ID), 38 using genotyping and 22 using both. Humpback whales were sparsely distributed (0.041 whales km-1): most sightings concentrated in shallow inner-reef waters and neighbouring offshore shallow banks. The recently created marine protected area covers most of the areas of high predicted habitat suitability and high residence time from satellite-tracked whales. Surprisingly for a breeding area, sex ratios skewed towards females (1:2.4), and 45% of females were with calf. Connectivity was established with the New Caledonia breeding area to the east (mtDNA FST = 0.001, p > 0.05, 12 photo-ID and 10 genotype matches) and with the Australian Great Barrier Reef breeding area to the west (mtDNA FST = 0.006, p > 0.05). Movement of satellite-tracked whales and photo-ID matches also suggest connections with the east Australian migratory corridor. This study confirms that humpback whales still inhabit the Chesterfield-Bellona archipelago 2 centuries post whaling, and that this pristine area potentially plays a role in facilitating migratory interchange among breeding grounds of the western South Pacific.

Global phylogeography and genetic diversity of the long-finned pilot whale Globicephala melas, with new data from the southeastern Pacific

The matrilineal long-finned pilot whale presents an antitropical distribution and is divided into two subspecies, one in the temperate seas of the Southern Hemisphere and the other restricted to the North Atlantic and Mediterranean. Until now, population genetic and phylogeographic studies have included localities of most of its Northern Hemisphere distribution, while only the southwestern Pacific has been sampled in the Southern Hemisphere. We add new genetic data from the southeastern Pacific to the published sequences. Low mitochondrial and nuclear diversity was encountered in this new area, as previously reported for other localities. Four haplotypes were found with only one new for the species. Fifteen haplotypes were detected in the global dataset, underlining the species’ low diversity. As previously reported, the subspecies shared two haplotypes and presented a strong phylogeographic structure. The extant distribution of this species has been related to dispersal events during the Last Glacial Maximum. Using the genetic data and Approximate Bayesian Calculations, this study supports this historical biogeographic scenario. From a taxonomic perspective, even if genetic analyses do not support the subspecies category, this study endorses the incipient divergence process between hemispheres, thus maintaining their status and addressing them as Demographically Independent Populations is recommended.

Cultural Transmission of Fine-Scale Fidelity to Feeding Sites May Shape Humpback Whale Genetic Diversity in Russian Pacific Waters

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 (FST = 0.18, ΦST = 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.

Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales

The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (N_em between 0.89-1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

Multidisciplinary studies on a sick-leader syndrome-associated mass stranding of sperm whales (Physeter macrocephalus) along the Adriatic coast of Italy

Mass strandings of sperm whales (Physeter macrocephalus) are rare in the Mediterranean Sea. Nevertheless, in 2014 a pod of 7 specimens stranded alive along the Italian coast of the Central Adriatic Sea: 3 individuals died on the beach after a few hours due to internal damages induced by prolonged recumbency; the remaining 4 whales were refloated after great efforts. All the dead animals were genetically related females; one was pregnant. All the animals were infected by dolphin morbillivirus (DMV) and the pregnant whale was also affected by a severe nephropathy due to a large kidney stone. Other analyses ruled out other possible relevant factors related to weather conditions or human activities. The results of multidisciplinary post-mortem analyses revealed that the 7 sperm whales entered the Adriatic Sea encountering adverse weather conditions and then kept heading northward following the pregnant but sick leader of the pod, thereby reaching the stranding site. DMV infection most likely played a crucial role in impairing the health condition and orientation abilities of the whales. They did not steer back towards deeper waters, but eventually stranded along the Central Adriatic Sea coastline, a real trap for sperm whales.

High pregnancy rates in humpback whales (Megaptera novaeangliae) around the Western Antarctic Peninsula, evidence of a rapidly growing population

Antarctic humpback whales are recovering from near extirpation from commercial whaling. To understand the dynamics of this recovery and establish a baseline to monitor impacts of a rapidly changing environment, we investigated sex ratios and pregnancy rates of females within the Western Antarctic Peninsula (WAP) feeding population. DNA profiling of 577 tissue samples (2010-2016) identified 239 males and 268 females. Blubber progesterone levels indicated 63.5% of the females biopsied were pregnant. This proportion varied significantly across years, from 36% in 2010 to 86% in 2014. A comparison of samples collected in summer versus fall showed significant increases in the proportion of females present (50% to 59%) and pregnant (59% to 72%), consistent with demographic variation in migratory timing. We also found evidence of annual reproduction among females; 54.5% of females accompanied by a calf were pregnant. These high pregnancy rates are consistent with a population recovering from past exploitation, but appear inconsistent with recent estimates of WAP humpback population growth. Thus, our results will help to better understand population growth potential and set a current baseline from which to determine the impact of climate change and variability on fecundity and reproductive rates.

Effective population size and the genetic consequences of commercial whaling on the humpback whales (Megaptera novaeangliae) from Southwestern Atlantic Ocean

Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (N_e) and census (N_c) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant N_e was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation N_c (N_e multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term N_c in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.

Fin whales and microplastics: The Mediterranean Sea and the Sea of Cortez scenarios

The impact that microplastics have on baleen whales is a question that remains largely unexplored. This study examined the interaction between free-ranging fin whales (Balaenoptera physalus) and microplastics by comparing populations living in two semi-enclosed basins, the Mediterranean Sea and the Sea of Cortez (Gulf of California, Mexico). The results indicate that a considerable abundance of microplastics and plastic additives exists in the neustonic samples from Pelagos Sanctuary of the Mediterranean Sea, and that pelagic areas containing high densities of microplastics overlap with whale feeding grounds, suggesting that whales are exposed to microplastics during foraging; this was confirmed by the observation of a temporal increase in toxicological stress in whales. Given the abundance of microplastics in the Mediterranean environment, along with the high concentrations of Persistent Bioaccumulative and Toxic (PBT) chemicals, plastic additives and biomarker responses detected in the biopsies of Mediterranean whales as compared to those in whales inhabiting the Sea of Cortez, we believe that exposure to microplastics because of direct ingestion and consumption of contaminated prey poses a major threat to the health of fin whales in the Mediterranean Sea.

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.

The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

Investigating population genetic structure in a highly mobile marine organism: the minke whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic

Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007-2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K = 1. (4) When K = 2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile species, more markers will be required.

Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences

The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.

High genetic diversity in a small population: the case of Chilean blue whales

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population.

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

Superpopulation capture-recapture models are useful for estimating the abundance of long-lived, migratory species because they are able to account for the fluid nature of annual residency at migratory destinations. Here we extend the superpopulation POPAN model to explicitly account for heterogeneity in capture probability linked to reproductive cycles (POPAN-tau). This extension has potential application to a range of species that have temporally variable life stages (e.g., non-annual breeders such as albatrosses and baleen whales) and results in a significant reduction in bias over the standard POPAN model. We demonstrate the utility of this model in simultaneously estimating abundance and annual population growth rate (lamda) in the New Zealand (NZ) southern right whale (Eubalaena australis) from 1995 to 2009. DNA profiles were constructed for the individual identification of more than 700 whales, sampled during two sets of winter expeditions in 1995-1998 and 2006-2009. Due to differences in recapture rates between sexes, only sex-specific models were considered. The POPAN-tau models, which explicitly account for a decrease in capture probability in non-calving years, fit the female data set significantly better than do standard superpopulation models (deltaAIC > 25). The best POPAN-tau model (AIC) gave a super-population estimate of 1162 females for 1995-2009 (95% CL 921, 1467) and an estimated annual increase of 5% (95% CL--2%, 13%). The best model (AIC) gave a superpopulation estimate of 1007 males (95% CL 794, 1276) and an estimated annual increase of 7% (95% CL 5%, 9%) for 1995-2009. Combined, the total superpopulation estimate for 1995-2009 was 2169 whales (95% CL 1836, 2563). Simulations suggest that failure to account for the effect of reproductive status on the capture probability would result in a substantial positive bias (+19%) in female abundance estimates.

Genetic evidence of multiple matrilines and spatial disruption of kinship bonds in mass strandings of long-finned pilot whales, Globicephala melas

Mass strandings of whales and dolphins have puzzled biologists since Aristotle. Although environmental factors are often assumed to initiate strandings, social forces must also influence the dynamics of many of these events, particularly for the primary species involved in mass strandings, the long-finned pilot whales (Globicephala melas). Here, we test two hypotheses derived from common assumptions about the social dynamics of long-finned pilot whales by identifying maternal lineages from mtDNA haplotypes and inferring kinship from microsatellite genotypes of 490 individuals from 12 stranding events. Contrary to the "extended matriline" hypothesis, we found that multiple maternal lineages were present in at least 9 of the 12 mass strandings. Contrary to the "kinship cohesion" hypothesis, we found no correlation between spatial distribution and kinship along the stranding beach. Most notably, we documented the spatial disruption of the expected proximity between mothers and their dependent calves. These results challenge the common assumption that kinship-based behavior, such as care-giving, are a primary factor in these mass strandings. We suggest instead that disruption of kinship bonds could result from interactions among unrelated social groups during feeding or mating aggregations, perhaps playing a causal role in these events. Our finding that dependent calves were often spatially separated or absent from their mothers has important implications for humane management of rescue efforts. To improve our understanding of the social causes and consequences of mass strandings, future documentation of strandings should include exhaustive DNA sampling, with accompanying spatial and temporal records.

Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change?

Understanding the degree of genetic exchange between subspecies and populations is vital for the appropriate management of endangered species. Blue whales (Balaenoptera musculus) have two recognized Southern Hemisphere subspecies that show differences in geographic distribution, morphology, vocalizations and genetics. During the austral summer feeding season, the Antarctic blue whale (B. m. intermedia) is found in polar waters and the pygmy blue whale (B. m. brevicauda) in temperate waters. Here, we genetically analyzed samples collected during the feeding season to report on several cases of hybridization between the two recognized blue whale Southern Hemisphere subspecies in a previously unconfirmed sympatric area off Antarctica. This means the pygmy blue whales using waters off Antarctica may migrate and then breed during the austral winter with the Antarctic subspecies. Alternatively, the subspecies may interbreed off Antarctica outside the expected austral winter breeding season. The genetically estimated recent migration rates from the pygmy to Antarctic subspecies were greater than estimates of evolutionary migration rates and previous estimates based on morphology of whaling catches. This discrepancy may be due to differences in the methods or an increase in the proportion of pygmy blue whales off Antarctica within the last four decades. Potential causes for the latter are whaling, anthropogenic climate change or a combination of these and may have led to hybridization between the subspecies. Our findings challenge the current knowledge about the breeding behaviour of the world's largest animal and provide key information that can be incorporated into management and conservation practices for this endangered species.

Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia)

The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131° longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968±0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F(ST) = 0.032, p<0.005) and microsatellite alleles (F(ST) = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales.

How many genetic markers to tag an individual? An empirical assessment of false matching rates among close relatives

Genetic identification of individuals is now commonplace, enabling the application of tagging methods to elusive species or species that cannot be tagged by traditional methods. A key aspect is determining the number of loci required to ensure that different individuals have non-matching multi-locus genotypes. Closely related individuals are of particular concern because of elevated matching probabilities caused by their recent co-ancestry. This issue may be addressed by increasing the number of loci to a level where full siblings (the relatedness category with the highest matching probability) are expected to have non-matching multi-locus genotypes. However, increasing the number of loci to meet this "full-sib criterion" greatly increases the laboratory effort, which in turn may increase the genotyping error rate resulting in an upward-biased mark-recapture estimate of abundance as recaptures are missed due to genotyping errors. We assessed the contribution of false matches from close relatives among 425 maternally related humpback whales, each genotyped at 20 microsatellite loci. We observed a very low (0.5-4%) contribution to falsely matching samples from pairs of first-order relatives (i.e., parent and offspring or full siblings). The main contribution to falsely matching individuals from close relatives originated from second-order relatives (e.g., half siblings), which was estimated at 9%. In our study, the total number of observed matches agreed well with expectations based upon the matching probability estimated for unrelated individuals, suggesting that the full-sib criterion is overly conservative, and would have required a 280% relative increase in effort. We suggest that, under most circumstances, the overall contribution to falsely matching samples from close relatives is likely to be low, and hence applying the full-sib criterion is unnecessary. In those cases where close relatives may present a significant issue, such as unrepresentative sampling, we propose three different genotyping strategies requiring only a modest increase in effort, which will greatly reduce the number of false matches due to the presence of related individuals.

Migration of Antarctic minke whales to the Arctic

The Antarctic minke whale (Balaenoptera bonaerensis), and the common minke whale found in the North Atlantic (Balaenoptera acutorostrata acutorostrata), undertake synchronized seasonal migrations to feeding areas at their respective poles during spring, and to the tropics in the autumn where they overwinter. Differences in the timing of seasons between hemispheres prevent these species from mixing. Here, based upon analysis of mitochondrial and microsatellite DNA profiles, we report the observation of a single B. bonaerensis in 1996, and a hybrid with maternal contribution from B. bonaerensis in 2007, in the Arctic Northeast Atlantic. Paternal contribution was not conclusively resolved. This is the first documentation of B. bonaerensis north of the tropics, and, the first documentation of hybridization between minke whale species.

Population genetics and social organization of the sperm whale (Physeter macrocephalus) in the Azores inferred by microsatellite analyses

In the northeast Atlantic Ocean, the archipelago of the Azores is frequented by female–offspring groups of sperm whales ( Physeter macrocephalus L., 1758), as well as large males. The Azores apparently constitute both a feeding ground and a reproduction site. Little is known about the population and group structure of sperm whales in the area. We analysed 151 sloughed skin and biopsy samples collected from 2002 to 2004. Molecular analyses involved genetic tagging using 11 microsatellite loci and molecular sexing. Our objectives were to determine the population genetic structure, compare relatedness within and between social groups, infer kinship, and estimate the age of males at dispersal. Results suggest that individuals visiting the archipelago of the Azores belong to a single population. High genetic diversity and absence of inbreeding suggest that the population is recovering from whaling. Individuals sampled in close association are highly related, as well as those observed in the same area on the same day, suggesting that secondary social groups (i.e., the union of primary social units) are largely but not exclusively composed of relatives. Probable mother–offspring and full-sibling pairs were identified. Age of males at dispersal was estimated at 16.6 years, which was well above previous estimates for this species.