Interfamilial characterization of a region of the ZFX and ZFY genes facilitates sex determination in cetaceans and other mammals

Australia's east coast humpback whales: Satellite tag-derived movements on breeding grounds, feeding grounds and along the northern and southern migration

Background

Satellite tags were deployed on 50 east Australian humpback whales (breeding stock E1) between 2008 and 2010 on their southward migration, northward migration and feeding grounds in order to identify and describe migratory pathways, feeding grounds and possible calving areas. At the time, these movements were not well understood and calving grounds were not clearly identified. To the best of our knowledge, this dataset details all long-term, implantable tag deployments that have occurred to date on breeding stock E1. As such, these data provide researchers, regulators and industry with clear and valuable insights into the spatial and temporal nature of humpback whale movements along the eastern coastline of Australia and into the Southern Ocean. As this population of humpback whales navigates an increasingly complex habitat undergoing various development pressures and anthropogenic disturbances, in addition to climate-mediated changes in their marine environment, this dataset may also provide a valuable baseline.

New information

At the time these tracks were generated, these were the first satellite tag deployments intended to deliver long-term, detailed movement information on east Australian (breeding stock E1) humpback whales. The tracking data revealed previously unknown migratory pathways into the Southern Ocean, with 11 individuals tracked to their Antarctic feeding grounds. Once assumed to head directly south on their southern migration, five individuals initially travelled west towards New Zealand. Six tracks detailed the coastal movement of humpback whales migrating south. One tag transmitted a partial southern migration, then ceased transmissions only to begin transmitting eight months later as the animal was migrating north. Northern migration to breeding grounds was detailed for 13 individuals, with four tracks including turning points and partial southern migrations. Another 14 humpback whales were tagged in Antarctica, providing detailed Antarctic feeding ground movements.Broadly speaking, the tracking data revealed a pattern of movement where whales were at their northern limit in July and their southern limit in March. Migration north was most rapid across the months of May and June, whilst migration south was most rapid between November and December. Tagged humpback whales were located on their Antarctic feeding grounds predominantly between January and May and approached their breeding grounds between July and August. Tracking distances ranged from 68 km to 8580 km and 1 to 286 days. To the best of our knowledge, this dataset compiles all of the long-term tag deployments that have occurred to date on breeding stock E1.

Biological clocks as age estimation markers in animals: a systematic review and meta-analysis

Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.

Satellite tag derived data from two Antarctic blue whales (Balaenopteramusculusintermedia) tagged in the east Antarctic sector of the Southern Ocean

Background

Satellite tags were deployed on two Antarctic blue whales (Balaenopteramusculusintermedia) in the east Antarctic sector of the Southern Ocean as part of the International Whaling Commission's Southern Ocean Research Partnership initiative. The satellite tracks generated are the first and currently, the only, satellite telemetry data that exist for this critically endangered species. These data provide valuable insights into the movements of Antarctic blue whales on their Antarctic feeding ground. The data were collected between February and April 2013 and span a 110° longitudinal range.

New information

This dataset is the first and only detailed movement data that exist for this critically endangered species. As such, this dataset provides the first measures of movement rates (distances travelled, speeds) and movement behaviour (distinguishing transit behaviour from area restricted search behaviour) within the Southern Ocean. These movement-based measures are critical to the ongoing management of Antarctic blue whales as they recover from commercial whaling as they provide insight into foraging behaviour, habitat use, population structure and overlap with anthropogenic threats.

J, Jacobsen JK, Scordino JJ, Lang AR, Baugh KA, Bolton JL, Brüniche-Olsen A, Calambokidis J, Martínez-Aguilar S, Subbiah S, Gribble MO, Godard-Codding CAJ. Influence of Life-History Parameters on Persistent Organic Pollutant Concentrations in Blubber of Eastern North Pacific Gray Whales (Eschrichtius robustus)

Exposure to persistent organic pollutants (POPs) can significantly impact marine mammal health, reproduction, and fitness. This study addresses a significant 20-year gap in gray whale contaminant monitoring through analysis of POPs in 120 blubber biopsies. The scope of this substantial sample set is noteworthy in its range and diversity with collection between 2003 and 2017 along North America's west coast and across diverse sex, age, and reproductive parameters, including paired mothers and calves. Mean blubber concentrations of polychlorinated biphenyls (∑PCBs), dichlorodiphenyltrichloroethanes (∑DDTs), and chlordanes (∑CHLs) generally decreased since previous reports (1968-1999). This is the first report of polybrominated diphenyl ethers (PBDEs) and select hexachlorocyclohexanes (HCHs) in this species. Statistical modeling of the 19 most frequently detected compounds in this dataset revealed sex-, age-, and reproductive status-related patterns, predominantly attributed to maternal offloading. Mean POP concentrations differed significantly by sex in adults (17 compounds, up to 3-fold higher in males) but not in immatures (all 19 compounds). Mean POP concentrations were significantly greater in adults versus immatures in both males (17 compounds, up to 12-fold) and females (13 compounds, up to 3-fold). POP concentrations were detected with compound-specific patterns in nursing calves, confirming maternal offloading for the first time in this species.

A mammalian messenger RNA sex determination method from humpback whale (Megaptera novaeangliae) blubber biopsies

The large size of free-ranging mysticetes, such as humpback whales (Megaptera novaeangliae), make capture and release health assessments unfeasible for conservation research. However, individual energetic condition or reproductive health may be assessed from the gene expression of remotely biopsied tissue. To do this, researchers must reliably extract RNA and interpret gene expression measurements within the context of an individual's sex. Here, we outline an RNA extraction protocol from blubber tissue and describe a novel mammalian RNA sex determination method. Our method consists of a duplex reverse transcription-quantitative (real-time) polymerase chain reaction (RT-qPCR) with primer sets for a control gene (ACTB) and the X-chromosome inactivation gene (XIST). Products of each RT-qPCR had distinct melting temperature profiles based on the presence (female) or absence (male) of the XIST transcript. Using high-resolution melt analysis, reactions were sorted into one of two clusters (male/female) based on their melting profiles. We validated the XIST method by comparing results with a standard DNA-based method. With adequate quantities of RNA (minimum of approx. 9 ng µl^-1), the XIST sex determination method shows 100% agreement with traditional DNA sex determination. Using the XIST method, future cetacean health studies can interpret gene expression within the context of an individual's sex, all from a single extraction.

A simple sexing test for elephant species and its application to faecal DNA

We developed a novel real-time PCR assay for rapid sexing in all three elephant species, which amplifies small fragments of the orthologous sexual chromosome zinc finger protein genes ZFX/ZFY (65 bp). This assay is a simple, inexpensive and reliable tool that is suitable for non-invasive DNA samples and can be incorporated into larger SNP panels for individual identification and population genetic studies.

Genomic signatures of divergent selection are associated with social behaviour for spinner dolphin ecotypes

Understanding the genomic basis of adaptation is critical for understanding evolutionary processes and predicting how species will respond to environmental change. Spinner dolphins in the eastern tropical Pacific (ETP) present a unique system for studying adaptation. Within this large geographical region are four spinner dolphin ecotypes with weak neutral genetic divergence and no obvious barriers to gene flow, but strong spatial variation in morphology, behaviour and habitat. These ecotypes have large population sizes, which could reduce the effects of drift and facilitate selection. To identify genomic regions putatively under divergent selective pressures between ecotypes, we used genome scans with 8994 RADseq single nucleotide polymorphisms (SNPs) to identify population differentiation outliers and genotype-environment association outliers. Gene ontology enrichment analyses indicated that outlier SNPs from both types of analyses were associated with multiple genes involved in social behaviour and hippocampus development, including 15 genes associated with the human social disorder autism. Evidence for divergent selection on social behaviour is supported by previous evidence that these spinner dolphin ecotypes differ in mating systems and associated social behaviours. In particular, three of the ETP ecotypes probably have a polygynous mating system characterized by strong premating competition among males, whereas the fourth ecotype probably has a polygynandrous mating system characterized by strong postmating competition such as sperm competition. Our results provide evidence that selection for social behaviour may be an evolutionary force driving diversification of spinner dolphins in the ETP, potentially as a result of divergent sexual selection associated with different mating systems. Future studies should further investigate the potential adaptive role of the candidate genes identified here, and could probably find further signatures of selection using whole genome sequence data.

Isotope-based inferences of the seasonal foraging and migratory strategies of blue whales in the eastern Pacific Ocean

Migratory marine megafauna generally move vast distances between productive foraging grounds and environmentally stable breeding grounds, but characterizing how they use these habitats to maintain homeostasis and reproduce is difficult. We used isotope analysis of blue whale skin strata (n = 621) and potential prey (n = 300) to examine their migratory and foraging strategies in the eastern Pacific Ocean. Our results suggest that most whales in the northeast Pacific use a mixed income and capital breeding strategy, and use the California Current Ecosystem as their primary summer-fall foraging ground. A subset of individuals exhibited migratory plasticity and spend most of the year in the Gulf of California or Costa Rica Dome, two regions believed to be their primary winter-spring breeding grounds. Isotope data also revealed that whales in the southern Eastern Tropical Pacific generally do not forage in the northeast Pacific, which suggests a north-south population structure with a boundary near the equator.

Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana (Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes

The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseq^TM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.

Life history and social structure as drivers of persistent organic pollutant levels and stable isotopes in Hawaiian false killer whales (Pseudorca crassidens)

False killer whales are long-lived, slow to mature, apex predators, and therefore susceptible to bioaccumulation of persistent organic pollutants (POPs). Hawaiian waters are home to three distinct populations: pelagic; Northwestern Hawaiian Islands (NWHI) insular; and main Hawaiian Islands (MHI) insular. Following a precipitous decline over recent decades, the MHI population was listed as "endangered" under the Endangered Species Act in 2012. This study assesses the risk of POP exposure to these populations by examining pollutant concentrations and ratios from blubber samples (n = 56) related to life history characteristics and MHI social clusters. Samples were analyzed for PCBs, DDTs, PBDEs, and some organochlorine pesticides. Skin samples (n = 52) were analyzed for stable isotopes δ¹³C and δ¹⁵N to gain insight into MHI false killer whale foraging ecology. Pollutant levels were similar among populations, although MHI whales had a significantly higher mean ratio of DDTs/PCBs than NWHI whales. The ∑PCB concentrations of 28 MHI individuals (68%) sampled were equal to or greater than suggested thresholds for deleterious health effects in marine mammals. The highest POP values among our samples were found in four stranded MHI animals. Eight of 24 MHI adult females have not been documented to have given birth; whether they have yet to reproduce, are reproductive senescent, or are experiencing reproductive dysfunction related to high POP exposure is unknown. Juvenile/sub-adults had significantly higher concentrations of certain contaminants than those measured in adults, and may be at greater risk of negative health effects during development. Multivariate analyses, POP ratios, and stable isotope ratios indicate varying risk of POP exposure, foraging locations and potentially prey items among MHI social clusters. Our findings provide invaluable insight into the ongoing risk POPs pose to the MHI population's viability, as well as consideration of risk for the NWHI and pelagic stocks.

A novel swine sex-linked marker and its application across different mammalian species

Advances in genome editing tools have reduced barriers to the creation of animal models. Due to their anatomical and physiological similarities to humans, there has been a growing need for pig models to study human diseases, for xenotransplantation and translational research. The ability to determine the sex of genetically modified embryos, cells or fetuses is beneficial for every project involving the production of transgenic animals. This strategy can improve the time-efficiency and lower the production costs. Additionally, sex assessment is very useful for wildlife studies to understand population behavior and structure. Thus, we developed a simple and fast PCR-based protocol for sex determination in pigs by using a unique primer set to amplify either the DDX3X or DDX3Y gene. The sex was 100% correctly assigned when tail genomic DNA, Day-35 fetus and hair samples from pigs were used. For both blastocysts and oocytes (84.6% and 96.5% of efficacy, respectively) the unidentified samples were potentially due to a limitation in sample size. Our assay also worked for domestic sheep (Ovis aries), American bison (Bison bison) and European cattle (Bos taurus) samples and by in silico analysis we confirmed X-Y amplicon length polymorphisms for the DDX3 gene in 12 other mammalian species. This PCR protocol for determining sex in pig tissues and cells showed to be simple, specific, highly reproducible and less time consuming as well as an important tool for other livestock species and wildlife studies.

The Use of RNAi Technology to Interfere with Zfx Gene Increases the Male Rates of Red Deer (Cervus elaphus) Offspring

Zinc finger protein X-linked (Zfx) was regarded to be a sex determination factor and plays a critical role in spermatogenesis. RNAi is an effective method of silencing Zfx mRNA expression. However, there has been little research on the use of RNAi technology to control the sex of the offspring of red deer (Cervus elaphus). The objective of this study was first to explore an efficient method to alter the red deer offspring sex-ratio by silencing the gene Zfx during spermatogenesis. Three recombinant expression vectors pLL3.7/A, pLL3.7/B, and pLL3.7/C were constructed to interrupt the Zfx gene. The results showed that the expression of Zfx mRNA was significantly silenced by pLL3.7/A (P < 0.01), compared with the control group. The group injected with pLL3.7/A produced 94 red deer, including 68 males and 26 females. The male rates (72.34%) were significantly higher than the control groups (P < 0.01). Our result suggests that Zfx siRNA is a useful approach to control offspring sex in red deer. This study further confirms that the Zfx gene plays a significant role in the process of X spermatogenesis.

Blubber cortisol levels in humpback whales (Megaptera novaeangliae): A measure of physiological stress without effects from sampling

Baleen whales are vulnerable to environmental impacts due to low fecundity, capital breeding strategies, and their reliance on a large amount of prey resources over large spatial scales. There has been growing interest in monitoring health and physiological stress in these species but, to date, few measures have been validated. The purpose of this study was to examine whether blubber cortisol could be used as a measure of physiological stress in humpback whales. Cortisol concentrations were initially compared between live, presumably 'healthy' whales (n = 187) and deceased whales (n = 35), which had died after stranding or entanglement, or washed ashore as a carcass. Deceased whales were found to have significantly higher cortisol levels (mean ± SD; 5.47 ± 4.52 ng/g) than live whales (0.51 ± 0.14 ng/g; p < 0.001), particularly for those animals that had experienced prolonged trauma (e.g. stranding) prior to death. Blubber cortisol levels in live whales were then examined for evidence of life history-related, seasonal, or sampling-related effects. Life history group and sampling-related factors, such as encounter time and the number of biopsy sampling attempts per animal, were found to be poor predictors of blubber cortisol levels in live whales. In contrast, blubber cortisol levels varied seasonally, with whales migrating north towards the breeding grounds in winter having significantly higher levels (0.54 ± 0.21 ng/g, p = 0.016) than those migrating south towards the feeding grounds in spring (0.48 ± 1.23 ng/g). These differences could be due to additional socio-physiological stress experienced by whales during peaks in breeding activity. Overall, blubber cortisol appears to be a suitable measure of chronic physiological stress in humpback whales.

The influence of physiological status on the reproductive behaviour of humpback whales (Megaptera novaeangliae)

For most cetacean species, there is little known about how an individual's physiology influences its behaviour. Humpback whales (Megaptera novaeangliae) are a good candidate to examine such links as they have a well-described distribution and behaviour, can be consistently sampled using remote biopsy systems, and have been the subject of several previous endocrine studies. The objective here was to examine whether a female humpback whale's social state (i.e. escorted by a male or not) is related to her endocrine condition, and whether male dominance ranking is related to testosterone levels. Skin and blubber biopsies were collected from the east and west Australian humpback whale populations in 2010-2016 (n = 252) at multiple times throughout the winter-spring breeding season. Steroid hormones were extracted from blubber and concentrations of progesterone (a marker for pregnancy), testosterone (a marker of male testicular activity) and oestradiol (a potential marker of ovarian activity) measured using enzyme-immunoassays. Principal escorts-the dominant males in mixed sex groups-had significantly higher blubber testosterone levels (mean ± SE; 1.43 ± 0.20 ng/g wet weight) than subordinate, secondary escorts (0.69 ± 0.06 ng/g wet weight). Females that were escorted by males typically possessed elevated blubber oestradiol levels (1.96 ± 0.25 ng/g wet weight; p = 0.014); few were considered to be pregnant (p = 0.083). 'Unescorted' females displayed characteristically lower blubber oestradiol levels (0.56 ± 0.06 ng/g wet weight). Together, these results are consistent with 'challenge hypothesis' theory and suggest the existence of associated reproductive patterns in humpback whales.

A method for determining sex and chromosome copy number: sex-by-sequencing reveals the first two species of marine mammals with XXY chromosome condition

Molecular assays of sex determination typically rely on qualitative evaluation of sex-linked markers, which can lead to uncertainty when results contradict morphological identifiers of sex. To investigate whether disagreement between phenotypic and genotypic assays of sex could be underpinned by variation in sex chromosome copy number, we developed a quantitative genetic method to determine sex that is broadly applicable to mammals with XY sex determination. We sequenced a region of the zinc-finger gene ZF, which has fixed genetic differences between the X and Y chromosomes, and screened 173 cetacean specimens for ZFX–ZFY haplotype identity and read depth. Using a subset of 90 male specimens, we demonstrate that haplotype read depth is an accurate estimator of chromosome copy number. We identified three specimens representing two different cetacean species that had external female morphological traits, Y chromosome haplotypes, and ratios of ZFX:ZFY haplotypes that were above the 1:1 value expected for genetic males. These results provide the first evidence of XXY aneuploidy in cetaceans. Investigation of the reproductive tract of one specimen, a True’s beaked whale (Mesoplodon mirus), revealed an intersex phenotype; despite having external characteristics typically diagnostic for the female sex, a penis and testes were present. Our results suggest that intersex phenotypes may be associated with XXY aneuploidy, and that this phenomenon may be underestimated due to it not being detectable by qualitative assays for determining sex.

A genetic method for sex determination in Ovis spp. by interruption of the zinc finger protein, Y-linked (ZFY) gene on the Y chromosome

The mammalian Y chromosome plays a critical role in spermatogenesis. However, the exact functions of each gene on the Y chromosome have not been completely elucidated, due, in part, to difficulties in gene targeting analysis of the Y chromosome. The zinc finger protein, Y-linked (ZFY) gene was first proposed to be a sex determination factor, although its function in spermatogenesis has recently been elucidated. Nevertheless, ZFY gene targeting analysis has not been performed to date. In the present study, RNA interference (RNAi) was used to generate ZFY-interrupted Hu sheep by injecting short hairpin RNA (shRNA) into round spermatids. The resulting spermatozoa exhibited abnormal sperm morphology, including spermatozoa without tails and others with head and tail abnormalities. Quantitative real-time polymerase chain reaction analysis showed that ZFY mRNA expression was decreased significantly in Hu sheep with interrupted ZFY compared with wild-type Hu sheep. The sex ratio of lambs also exhibited a bias towards females. Together, the experimental strategy and findings of the present study reveal that ZFY also functions in spermatogenesis in Hu sheep and facilitate the use of RNAi in the control of sex in Hu sheep.

Molecular sexing assays in 114 mammalian species: In silico sequence reanalysis and a unified graphical visualization of diagnostic tests

Molecular-based methods for identifying sex in mammals have a wide range of applications, from embryo manipulation to ecological studies. Various sex-specific or homologous genes can be used for this purpose, PCR amplification being a common method. Over the years, the number of reported tests and the range of tested species have increased greatly. The aim of the present analysis was to retrieve PCR-based sexing assays for a range of mammalian species, gathering the gene sequences from either the articles or online databases, and visualize the molecular design in a uniform manner. For nucleotide alignment and diagnostic test visualization, the following genomic databases and tools were used: NCBI, Ensembl Nucleotide BLAST, ClustalW2, and NEBcutter V2.0. In the 45 gathered articles, 59 different diagnostic tests based on eight different PCR-based methods were developed for 114 mammalian species. Most commonly used genes for the analysis were ZFX, ZFY, AMELX, and AMELY. The tests were most commonly based on sex-specific insertions and deletions (SSIndels) and sex-specific sequence polymorphisms (SSSP). This review provides an overview of PCR-based sexing methods developed for mammals. This information will facilitate more efficient development of novel molecular sexing assays and reuse of previously developed tests. Development of many novel and improvement of previously developed tests is also expected with the rapid increase in the quantity and quality of available genetic information.

Humpback whale migrations to Antarctic summer foraging grounds through the southwest Pacific Ocean

Humpback whale (Megaptera novaeangliae) populations typically undertake seasonal migrations, spending winters in low latitude breeding grounds and summers foraging in high latitude feeding grounds. Until recently, a broad scale understanding of whale movement has been derived from whaling records, Discovery marks, photo identification and genetic analyses. However, with advances in satellite tagging technology and concurrent development of analytical methodologies we can now detail finer scale humpback whale movement, infer behavioural context and examine how these animals interact with their physical environment. Here we describe the temporal and spatial characteristics of migration along the east Australian seaboard and into the Southern Ocean by 30 humpback whales satellite tagged over three consecutive austral summers. We characterise the putative Antarctic feeding grounds and identify supplemental foraging within temperate, migratory corridors. We demonstrate that Antarctic foraging habitat is associated with the marginal ice zone, with key predictors of inferred foraging behaviour including distance from the ice edge, ice melt rate and variability in ice concentration two months prior to arrival. We discuss the highly variable ice season within the putative foraging habitat and the implications that this and other environmental factors may have on the continued strong recovery of this humpback whale population.

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques

The dermis of cetaceans is in constant contact with microbial species. Although the skin of the bottlenose dolphin provides adequate defense against most disease-causing microbes, it also provides an environment for microbial community development. Microbial community uniqueness and richness associated with bottlenose dolphin skin is a function of varying habitats and changing environmental conditions. The current study uses ribosomal DNA as a marker to identify bacteria found on the skin of coastal and offshore bottlenose dolphins off of Southern California. The unique microbial communities recovered from these dolphins suggest a greater microbial diversity on the skin of offshore ecotype bottlenose dolphins, while microbial populations associated with the coastal ecotype include species that are more closely related to each other and that suggest exposure to communities that are likely to be associated with terrestrial runoff.

Physiological, morphological, and ecological tradeoffs influence vertical habitat use of deep-diving toothed-whales in the Bahamas

Dive capacity among toothed whales (suborder: Odontoceti) has been shown to generally increase with body mass in a relationship closely linked to the allometric scaling of metabolic rates. However, two odontocete species tagged in this study, the Blainville’s beaked whale Mesoplodon densirostris and the Cuvier’s beaked whale Ziphius cavirostris, confounded expectations of a simple allometric relationship, with exceptionally long (mean: 46.1 min & 65.4 min) and deep dives (mean: 1129 m & 1179 m), and comparatively small body masses (med.: 842.9 kg & 1556.7 kg). These two species also exhibited exceptionally long recovery periods between successive deep dives, or inter-deep-dive intervals (M. densirostris: med. 62 min; Z. cavirostris: med. 68 min). We examined competing hypotheses to explain observed patterns of vertical habitat use based on body mass, oxygen binding protein concentrations, and inter-deep-dive intervals in an assemblage of five sympatric toothed whales species in the Bahamas. Hypotheses were evaluated using dive data from satellite tags attached to the two beaked whales (M. densirostris, n = 12; Z. cavirostris, n = 7), as well as melon-headed whales Peponocephala electra (n = 13), short-finned pilot whales Globicephala macrorhynchus (n = 15), and sperm whales Physeter macrocephalus (n = 27). Body mass and myoglobin concentration together explained only 36% of the variance in maximum dive durations. The inclusion of inter-deep-dive intervals, substantially improved model fits (R² = 0.92). This finding supported a hypothesis that beaked whales extend foraging dives by exceeding aerobic dive limits, with the extension of inter-deep-dive intervals corresponding to metabolism of accumulated lactic acid. This inference points to intriguing tradeoffs between body size, access to prey in different depth strata, and time allocation within dive cycles. These tradeoffs and resulting differences in habitat use have important implications for spatial distribution patterns, and relative vulnerabilities to anthropogenic impacts.

Estimating blue whale skin isotopic incorporation rates and baleen growth rates: Implications for assessing diet and movement patterns in mysticetes

Stable isotope analysis in mysticete skin and baleen plates has been repeatedly used to assess diet and movement patterns. Accurate interpretation of isotope data depends on understanding isotopic incorporation rates for metabolically active tissues and growth rates for metabolically inert tissues. The aim of this research was to estimate isotopic incorporation rates in blue whale skin and baleen growth rates by using natural gradients in baseline isotope values between oceanic regions. Nitrogen (δ¹⁵N) and carbon (δ¹³C) isotope values of blue whale skin and potential prey were analyzed from three foraging zones (Gulf of California, California Current System, and Costa Rica Dome) in the northeast Pacific from 1996–2015. We also measured δ¹⁵N and δ¹³C values along the lengths of baleen plates collected from six blue whales stranded in the 1980s and 2000s. Skin was separated into three strata: basale, externum, and sloughed skin. A mean (±SD) skin isotopic incorporation rate of 163±91 days was estimated by fitting a generalized additive model of the seasonal trend in δ¹⁵N values of skin strata collected in the Gulf of California and the California Current System. A mean (±SD) baleen growth rate of 15.5±2.2 cm y^-1 was estimated by using seasonal oscillations in δ¹⁵N values from three whales. These oscillations also showed that individual whales have a high fidelity to distinct foraging zones in the northeast Pacific across years. The absence of oscillations in δ¹⁵N values of baleen sub-samples from three male whales suggests these individuals remained within a specific zone for several years prior to death. δ¹³C values of both whale tissues (skin and baleen) and potential prey were not distinct among foraging zones. Our results highlight the importance of considering tissue isotopic incorporation and growth rates when studying migratory mysticetes and provide new insights into the individual movement strategies of blue whales.

Cytochrome P4501A1 expression in blubber biopsies of endangered false killer whales (Pseudorca crassidens) and nine other odontocete species from Hawai'i

Odontocetes (toothed whales) are considered sentinel species in the marine environment because of their high trophic position, long life spans, and blubber that accumulates lipophilic contaminants. Cytochrome P4501A1 (CYP1A1) is a biomarker of exposure and molecular effects of certain persistent organic pollutants. Immunohistochemistry was used to visualize CYP1A1 expression in blubber biopsies collected by non-lethal sampling methods from 10 species of free-ranging Hawaiian odontocetes: short-finned pilot whale, melon-headed whale, pygmy killer whale, common bottlenose dolphin, rough-toothed dolphin, pantropical spotted dolphin, Blainville's beaked whale, Cuvier's beaked whale, sperm whale, and endangered main Hawaiian Islands insular false killer whale. Significantly higher levels of CYP1A1 were observed in false killer whales and rough-toothed dolphins compared to melon-headed whales, and in general, trophic position appears to influence CYP1A1 expression patterns in particular species groups. No significant differences in CYP1A1 were found based on age class or sex across all samples. However, within male false killer whales, juveniles expressed significantly higher levels of CYP1A1 when compared to adults. Total polychlorinated biphenyl (∑PCBs) concentrations in 84% of false killer whales exceeded proposed threshold levels for health effects, and ∑PCBs correlated with CYP1A1 expression. There was no significant relationship between PCB toxic equivalent quotient and CYP1A1 expression, suggesting that this response may be influenced by agonists other than the dioxin-like PCBs measured in this study. No significant differences were found for CYP1A1 expression among social clusters of false killer whales. This work provides a foundation for future health monitoring of the endangered stock of false killer whales and other Hawaiian odontocetes.

Carbon and nitrogen isotopes from top predator amino acids reveal rapidly shifting ocean biochemistry in the outer California Current

Climatic variation alters biochemical and ecological processes, but it is difficult both to quantify the magnitude of such changes, and to differentiate long-term shifts from inter-annual variability. Here, we simultaneously quantify decade-scale isotopic variability at the lowest and highest trophic positions in the offshore California Current System (CCS) by measuring δ¹⁵N and δ¹³C values of amino acids in a top predator, the sperm whale (Physeter macrocephalus). Using a time series of skin tissue samples as a biological archive, isotopic records from individual amino acids (AAs) can reveal the proximate factors driving a temporal decline we observed in bulk isotope values (a decline of ≥1 ‰) by decoupling changes in primary producer isotope values from those linked to the trophic position of this toothed whale. A continuous decline in baseline (i.e., primary producer) δ¹⁵N and δ¹³C values was observed from 1993 to 2005 (a decrease of ∼4‰ for δ¹⁵N source-AAs and 3‰ for δ¹³C essential-AAs), while the trophic position of whales was variable over time and it did not exhibit directional trends. The baseline δ¹⁵N and δ¹³C shifts suggest rapid ongoing changes in the carbon and nitrogen biogeochemical cycling in the offshore CCS, potentially occurring at faster rates than long-term shifts observed elsewhere in the Pacific. While the mechanisms forcing these biogeochemical shifts remain to be determined, our data suggest possible links to natural climate variability, and also corresponding shifts in surface nutrient availability. Our study demonstrates that isotopic analysis of individual amino acids from a top marine mammal predator can be a powerful new approach to reconstructing temporal variation in both biochemical cycling and trophic structure.

Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)

False killer whales (Pseudorca crassidens) are large delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago, there are 2 resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear DNA (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation among the 2 island-associated populations and offshore animals from the central and eastern North Pacific. Both mtDNA and nucDNA exhibit highly significant differentiation between populations, confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a strong pattern of phylogeographic concordance, with island-associated populations sharing 3 closely related haplotypes not found elsewhere in the Pacific. However, nucDNA data suggest that NWHI animals are at least as differentiated from MHI animals as they are from offshore animals. The patterns of differentiation revealed by the 2 marker types suggest that the island-associated false killer whale populations likely share a common colonization history, but have limited contemporary gene flow.

Migratory movements of pygmy blue whales (Balaenoptera musculus brevicauda) between Australia and Indonesia as revealed by satellite telemetry

In Australian waters during the austral summer, pygmy blue whales (Balaenoptera musculus brevicauda) occur predictably in two distinct feeding areas off western and southern Australia. As with other blue whale subspecies, outside the austral summer their distribution and movements are poorly understood. In order to describe the migratory movements of these whales, we present the satellite telemetry derived movements of eleven individuals tagged off western Australia over two years. Whales were tracked from between 8 and 308 days covering an average distance of 3,009±892 km (mean ± se; range: 832 km–14,101 km) at a rate of 21.94±0.74 km per day (0.09 km–455.80 km/day). Whales were tagged during March and April and ultimately migrated northwards post tag deployment with the exception of a single animal which remained in the vicinity of the Perth Canyon/Naturaliste Plateau for its eight day tracking period. The tagged whales travelled relatively near to the Australian coastline (100.0±1.7 km) until reaching a prominent peninsula in the north-west of the state of Western Australia (North West Cape) after which they travelled offshore (238.0±13.9 km). Whales reached the northern terminus of their migration and potential breeding grounds in Indonesian waters by June. One satellite tag relayed intermittent information to describe aspects of the southern migration from Indonesia with the animal departing around September to arrive in the subtropical frontal zone, south of western Australia in December. Throughout their migratory range, these whales are exposed to impacts associated with industry, fishing and vessel traffic. These movements therefore provide a valuable tool to industry when assessing potential interactions with pygmy blue whales and should be considered by conservation managers and regulators when mitigating impacts of development. This is particularly relevant for this species as it continues to recover from past exploitation.

Epigenetic estimation of age in humpback whales

Age is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as 4 years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed based on age-induced changes in DNA methylation of specific genes. We used information on age-associated DNA methylation in human and mouse genes to identify homologous gene regions in humpbacks. Humpback skin samples were obtained from individuals with a known year of birth and employed to calibrate relationships between cytosine methylation and age. Seven of 37 cytosines assayed for methylation level in humpback skin had significant age-related profiles. The three most age-informative cytosine markers were selected for a humpback epigenetic age assay. The assay has an R(2) of 0.787 (P = 3.04e-16) and predicts age from skin samples with a standard deviation of 2.991 years. The epigenetic method correctly determined which of parent-offspring pairs is the parent in more than 93% of cases. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. This is the first epigenetic age estimation method for a wild animal species and the approach we took for developing it can be applied to many other nonmodel organisms.

Vertical distribution of lipids, fatty acids and organochlorine contaminants in the blubber of southern hemisphere humpback whales (Megaptera novaeangliae)

Persistent organic pollutants (POPs), such as toxic lipophilic organochlorine (OC) compounds, accumulate in the blubber tissue of marine mammals. Toxicological sampling methods most frequently target only the superficial blubber layer. Vertical distribution of these contaminants through the blubber mantle may, however, not be homogenous and could reflect any dissemination of lipids and fatty acids (FAs). It is therefore critical to assess stratification patterns in a species of interest as a quality control measure for interpretation of toxicological data. Here, we analysed and compared the distribution of lipids, FAs, and OCs in the outermost and innermost blubber layer of southern hemisphere humpback whales. FA stratification was evident for short-chain (≤18) monounsaturated fatty acids (SC-MUFA), which were concentrated in the outer layer, consistent with the thermoregulatory role of this blubber layer. This stratification was, however, not reflected in OC distribution, which was similar in the inner and outer blubber layers of male humpback whales. By comparison, a noticeable gradient in total blubber lipid from the outer to the inner layer was observed in two lactating females, which coincided with higher lipid normalised contaminant levels in the inner layer. This study contains the most comprehensive assessment of humpback whale blubber stratification to date, however, further investigation of biological and ecological influencing factors is required.

Study of methylation of histone H3 lysine 9 and H3 lysine 27 during X chromosome inactivation in three types of cells

Histone methylation is one epigenetic modification of an inactive X chromosome (Xi). Histone H3 lysine 9 dimethylation (H3K9me) and histone H3 lysine 27 trimethylation (H3K27me) are both associated with the chromatin of gene-silenced regions in the X chromosome and with X inactivation. Studies have shown that H3K9me is supposedly an early mark on the X chromosome during inactivation. Here, we examined the distribution and enrichment profiles of H3K9me and H3K27me by indirect immunofluorescence. We found that H3K9me appears to have a broad distribution throughout the whole genome, but is specific, to a certain extent, to the Xi in WI38 cells. In contrast, H3K27me is highly specific to the entire Xi, which differs significantly from other areas of the nucleus. Thus, H3K27me is more suitable as an epigenetic mark than H3K9me. The chromatin immunoprecipitation analyses also showed that H3K27me predominates on the inactive genes of the X chromosome. Additionally, we compared the levels of H3K9me and H3K27me in four X-linked genes and two autosomal genes between the normal cells (WI38) and the tumor cells (HeLa). The results revealed that the methylation levels of the inactive genes (POLA and OCRL) in tumor cells (HeLa) were lower than those in normal cells (WI38) and that the methylation levels of the Xi inactivation-avoidance genes (SMCX and ZFX) and autosomal genes (Myc and β-actin) varied widely in tumor cells (HeLa). These events may be significant for cancer cell development and contribute to the characteristics of tumor cells.

A PCR-RFLP assay for gender assignment in the three-toed sloths (Bradypus, Pilosa, Bradypodidae)

The three-toed sloths (Bradypus) are slow-moving arboreal neotropical mammals. Understanding demographic variables (such as sex ratio) of populations is a key for conservation purposes. Nevertheless, gender assignment of Bradypus is particularly challenging because of the lack of sexual dimorphism in infants and in adults, particularly B. torquatus, the most endangered of the three-toed sloths, in which sex is attributed by visual observation of the reproductively active males. Here, we standardized a method for sexing Bradypus individuals using PCR-RFLP of sex-linked genes ZFX/ZFY. This assay was validated with known-gender animals and proved accurate to assign gender on three Bradypus species.

Ancient DNA from marine mammals: studying long-lived species over ecological and evolutionary timescales

Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an opportunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes in distribution and range of marine mammal species; we review these studies and discuss the limitations of such 'presence only' studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also discuss studies reconstructing inter- and intra-specific phylogenies from aDNA sequences and discuss how aDNA sequences could be used to estimate mutation rates. Finally, we highlight some of the problems of aDNA studies on marine mammals, such as obtaining sufficient sample sizes and calibrating for the marine reservoir effect when radiocarbon-dating such wide-ranging species.

Cytochrome P450 isozyme protein verified in the skin of southern hemisphere humpback whales (Megaptera novaeangliae): implications for biochemical biomarker assessment

Large mysticete whales represent a unique challenge for chemical risk assessment. Few epidemiological investigations are possible due to the low incidence of adult stranding events. Similarly their often extreme life-history adaptations of prolonged migration and fasting challenge exposure assumptions. Molecular biomarkers offer the potential to complement information yielded through tissue chemical analysis, as well as providing evidence of a molecular response to chemical exposure. In this study we confirm the presence of cytochrome P450 reductase (CPR) and cytochrome P450 isoenzyme 1A1 (CYP1A1) in epidermal tissue of southern hemisphere humpback whales (Megaptera novaeangliae). The detection of CYP1A1 in the integument of the humpback whale affords the opportunity for further quantitative non-destructive investigations of enzyme activity as a function of chemical stress.

Mitochondrial DNA diversity and PCR-based sex determination of Irrawaddy dolphin (Orcaella brevirostris) from Chilika Lagoon, India

Of the only known two Lagoon populations of Irrawaddy dolphins (Orcaella) in the world, one is residing in the Chilika Lagoon in Orissa state, India. In addition to accidental deaths in gill net fishery and mechanized boat operations, there has been exploitation of the species for their oil. Extreme patchy distribution and vulnerability to becoming entangled in fishing gear has made it a focus of conservation concern. Information on genetic diversity of populations has considerable potential for informing conservation plans. The present paper reports the first genetic study of O. brevirostris from Chilika Lagoon based on mtDNA sequencing and PCR-based sex identification from 11 individuals. Control region sequence comparison showed two haplotypes and cytochrome b a single haplotype in the Chilika population of the species. Phylogenetic analysis indicated distinct clades within the Asian samples, with the Indian population showing closest genetic proximity to the haplotypes from Thailand. Sex of the animal was determined by PCR-based method. It is important to continue to examine the population discreteness and genetic variation of Irrawaddy dolphin in Chilika Lagoon vis-à-vis its global geographic distribution for formulating the conservation plans of the species.

Genetic variation and evidence for population structure in eastern North Pacific false killer whales (Pseudorca crassidens)

False killer whales ( Pseudorca crassidens (Owen, 1846)) are incidentally taken in the North Pacific pelagic long-line fishery, but little is known about their population structure to assess the impact of these takes. Using mitochondrial DNA (mtDNA) control region sequence data, we quantified genetic variation for the species and tested for genetic differentiation among geographic strata. Our data set of 124 samples included 115 skin-biopsy samples collected from false killer whales inhabiting the eastern North Pacific Ocean (ENP), and nine samples collected from animals sampled at sea or on the beach in the western North Pacific, Indian, and Atlantic oceans. Twenty-four (24) haplotypes were identified, and nucleotide diversity was low (π = 0.37%) but comparable with that of closely related species. Phylogeographic concordance in the distribution of haplotypes was revealed and a demographically isolated population of false killer whales associated with the main Hawaiian islands was identified (ΦST= 0.47, p < 0.0001). This result supports recognition of the existing management unit, which has geo-political boundaries corresponding to the USA’s exclusive economic zone (EEZ) of Hawai‘i. However, a small number of animals sampled within the EEZ but away from the near-shore island area, which is defined as <25 nautical miles (1 nautical mile = 1.852 km) from shore, had haplotypes that were the same or closely related to those found elsewhere in the ENP, which suggests that there may be a second management unit within the Hawaiian EEZ. Biologically meaningful boundaries for the population(s) cannot be identified until we better understand the distribution and ecology of false killer whales.

Fast and non-invasive PCR sexing of primates: apes, Old World monkeys, New World monkeys and Strepsirrhines

Background

One of the key tools for determining the social structure of wild and endangered primates is the ability to sex DNA from small amounts of non-invasive samples that are likely to include highly degraded DNA. Traditional markers for molecular sex determination of primates are developed on the basis of the human sequence and are often non-functional in distantly related primate species. Hence, it is highly desirable to develop markers that simultaneously detect Y- and X-chromosome specific sequences and also work across many species.

Results

A novel method for sex identification in primates is described using a triple primer PCR reaction and agarose gel electrophoresis of the sex-chromosomal isoforms of the ubiquitously transcribed tetratricopeptide repeat protein gene (UTX/UTY). By comparing genomic data from several mammals we identified the UTX/UTY locus as the best candidate for a universal primate sexing marker. Using data from several species we identified a XY-conserved region, a Y conserved region and an X conserved region. This enabled the design of a triple primer PCR setup that amplifies X and Y products of different length in a single PCR reaction.

Conclusion

This simple PCR amplification of X and Y fragments is useful for sexing DNA samples from all species of primates. Furthermore, since the amplified fragments are very short the method can be applied to fragmented DNA extracted from non-invasive samples.