Evaluating short- to medium-term effects of implantable satellite tags on southern right whales Eubalaena australis.

Improving our understanding of the effects of satellite tags on large whales is a critical step in ongoing tag development to minimise potential health effects whilst addressing important research questions that enhance conservation management policy. In 2014, satellite tags were deployed on 9 female southern right whales Eubalaena australis accompanied by a calf off Australia. Photo-identification resights (n = 48) of 4 photo-identified individuals were recorded 1 to 2894 d (1-8 yr) post-tagging. Short-term (<22 d) effects observed included localised and regional swelling, depression at the tag site, blubber extrusion, skin loss and pigmentation colour change. Broad swelling observable from lateral but not aerial imagery (~1.2 m diameter or ~9% of body length) and depression at the tag site persisted up to 1446 d post-tagging for 1 individual, indicating a persistent foreign-body response or infection. Two tagged individuals returned 4 yr post-tagging in 2018 with a calf, and the medium-term effects were evaluated by comparing body condition of tagged whales with non-tagged whales. These females calved in a typical 4 yr interval, suggesting no apparent immediate impact of tagging on reproduction for these individuals, but longer-term monitoring is needed. There was no observable difference in the body condition between the 2 tagged and non-tagged females. Ongoing monitoring post-tagging is required to build on the sample size and statistical power. We demonstrate the value of long-term monitoring programmes and a collaborative approach for evaluating effects from satellite-tagging cetaceans to support species management.

Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere.

The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].

Molecular markers of telomere dysfunction and senescence are common findings in the usual interstitial pneumonia pattern of lung fibrosis.

AIMS: Idiopathic pulmonary fibrosis (IPF) is a genetically mediated, age-associated, progressive form of pulmonary fibrosis characterised pathologically by a usual interstitial pneumonia (UIP) pattern of fibrosis. The UIP pattern is also found in pulmonary fibrosis attributable to clinical diagnoses other than IPF (non-IPF UIP), whose clinical course is similarly poor, suggesting common molecular drivers. This study investigates whether IPF and non-IPF UIP lungs similarly express markers of telomere dysfunction and senescence. METHODS AND RESULTS: To test whether patients with IPF and non-IPF UIP share molecular drivers, lung tissues from 169 IPF patients and 57 non-IPF UIP patients were histopathologically and molecularly compared. Histopathological changes in both IPF and non-IPF UIP patients included temporal heterogeneity, microscopic honeycombing, fibroblast foci, and dense collagen fibrosis. Non-IPF UIP lungs were more likely to have lymphocytic infiltration, non-caseating granulomas, airway-centred inflammation, or small airways disease. Telomeres were shorter in alveolar type II (AECII) cells of both IPF and non-IPF UIP lungs than in those of age-similar, unused donor, controls. Levels of molecular markers of senescence (p16 and p21) were elevated in lysates of IPF and non-IPF UIP lungs. Immunostaining localised expression of these proteins to AECII cells. The mucin 5B (MUC5B) gene promoter variant minor allele frequency was similar between IPF and non-IPF UIP patients, and MUC5B expression was similar in IPF and non-IPF UIP lungs. CONCLUSIONS: Molecular markers of telomere dysfunction and senescence are pathologically expressed in both IPF and non-IPF UIP lungs. These findings suggest that common molecular drivers may contribute to the pathogenesis of UIP-associated pulmonary fibrosis, regardless of the clinical diagnosis.

Co-occurrence of beaked whale strandings and naval sonar in the Mariana Islands, Western Pacific.

Mid-frequency active sonar (MFAS), used for antisubmarine warfare (ASW), has been associated with multiple beaked whale (BW) mass stranding events. Multinational naval ASW exercises have used MFAS offshore of the Mariana Archipelago semi-annually since 2006. We report BW and MFAS acoustic activity near the islands of Saipan and Tinian from March 2010 to November 2014. Signals from Cuvier's (Ziphius cavirostris) and Blainville's beaked whales (Mesoplodon densirostris), and a third unidentified BW species, were detected throughout the recording period. Both recorders documented MFAS on 21 August 2011 before two Cuvier's beaked whales stranded on 22-23 August 2011. We compared the history of known naval operations and BW strandings from the Mariana Archipelago to consider potential threats to BW populations. Eight BW stranding events between June 2006 and January 2019 each included one to three animals. Half of these strandings occurred during or within 6 days after naval activities, and this co-occurrence is highly significant. We highlight strandings of individual BWs can be associated with ASW, and emphasize the value of ongoing passive acoustic monitoring, especially for beaked whales that are difficult to visually detect at sea. We strongly recommend more visual monitoring efforts, at sea and along coastlines, for stranded cetaceans before, during and after naval exercises.

Genomics of Population Differentiation in Humpback Dolphins, Sousa spp. in the Indo-Pacific Ocean.

Speciation is a fundamental process in evolution and crucial to the formation of biodiversity. It is a continuous and complex process, which can involve multiple interacting barriers leading to heterogeneous genomic landscapes with various peaks of divergence among populations. In this study, we used a population genomics approach to gain insights on the speciation process and to understand the population structure within the genus Sousa across its distribution in the Indo-Pacific region. We found 5 distinct clusters, corresponding to S. plumbea along the eastern African coast and the Arabian Sea, the Bangladesh population, S. chinensis off Thailand and S. sahulensis off Australian waters. We suggest that the high level of differentiation found, even across geographically close areas, is likely determined by different oceanographic features such as sea surface temperature and primary productivity.

Significance of bronchiolocentric fibrosis in patients with histopathological usual interstitial pneumonia.

AIMS: To evaluate the clinical significance of bronchiolocentric fibrosis (BCF) in patients with a histopathological pattern of usual interstitial pneumonia (UIP). METHODS AND RESULTS: Two hundred and fifty-two patients with pathological UIP pattern were identified. Two hundred and fifteen of these patients (215 of 252) had the multidisciplinary diagnosis of idiopathic pulmonary fibrosis (IPF). Prospectively defined clinical, radiological and pathological features (including BCF) were recorded, and peripheral blood MUC5B genotype and telomere length were measured. BCF was observed in 38% (96 of 252) of all patients and 33% (72 of 215) of IPF patients; its presence was associated with a non-IPF diagnosis on multivariate analysis (odds ratio = 3.71, 95% confidence interval = 1.68-8.19). BCF was not significantly associated with environmental exposures, gastroesophageal reflux, cigarette smoking or radiological patterns. There was no significant association of BCF with MUC5B genotype or telomere length. BCF has no significant impact on survival time. CONCLUSIONS: Most patients with BCF and a histopathological pattern of UIP have IPF. However, this combined fibrotic pattern is associated with a non-IPF multidisciplinary diagnosis, with approximately one-quarter of these patients being diagnosed as chronic hypersensitivity pneumonia or unclassifiable interstitial fibrosis. The presence of BCF in these patients is not significantly associated with presumed clinical risk factors for bronchiolocentric involvement, radiological findings, MUC5B genotype, telomere length or survival time.

Fecal steroid hormones reveal reproductive state in female blue whales sampled in the Gulf of California, Mexico.

Steroid hormone assessment using non-invasive sample collection techniques can reveal the reproductive status of aquatic mammals and the physiological mechanisms by which they respond to changes in their environment. A portion of the eastern North Pacific blue whale (Balaenoptera musculus) population that seasonally visits the Gulf of California, Mexico has been monitored using photo-identified individuals for over 30 years. The whales use the area in winter-early spring for nursing their calves and feeding and it therefore is well suited for fecal sample collection. Using radioimmunoassays in 25 fecal samples collected between 2009 and 2012 to determine reproductive state and stress, we validated three steroid hormones (progesterone, corticosterone and cortisol) in adult female blue whales. Females that were categorized as pregnant had higher mean fecal progesterone metabolite concentrations (1292.6 ±â€¯415.6 ng·g-1) than resting and lactating females (14.0 ±â€¯3.7 ng·g-1; 23.0 ±â€¯5.4 ng·g-1, respectively). Females classified as pregnant also had higher concentrations of corticosterone metabolites (37.5 ±â€¯9.9 ng·g-1) than resting and lactating females (17.4 ±â€¯2.0 ng·g-1; 16.8 ±â€¯2.8 ng·g-1, respectively). In contrast, cortisol metabolite concentrations showed high variability between groups and no significant relationship to reproductive state. We successfully determined preliminary baseline parameters of key steroid hormones by reproductive state in adult female blue whales. The presence of pregnant or with luteal activity and known lactating females confirms that the Gulf of California is an important winter-spring area for the reproductive phase of these blue whales. The baseline corticosterone levels we are developing will be useful for assessing the impact of the increasing coastal development and whale-watching activities on the whales in the Gulf of California.

The use of pretest probability increases the value of high-resolution CT in diagnosing usual interstitial pneumonia.

BACKGROUND: Recent studies have suggested that non-definitive patterns on high-resolution CT (HRCT) scan provide sufficient diagnostic specificity to forgo surgical lung biopsy in the diagnosis of idiopathic pulmonary fibrosis (IPF). The objective of this study was to determine test characteristics of non-definitive HRCT patterns for identifying histopathological usual interstitial pneumonia (UIP). METHODS: Patients with biopsy-proven interstitial lung disease (ILD) and non-definitive HRCT scans were identified from two academic ILD centres. Test characteristics for HRCT patterns as predictors of UIP on surgical lung biopsy were derived and validated in independent cohorts. RESULTS: In the derivation cohort, 64/385 (17%) had possible UIP pattern on HRCT; 321/385 (83%) had inconsistent with UIP pattern. 113/385 (29%) patients had histopathological UIP pattern in the derivation cohort. Possible UIP pattern had a specificity of 91.2% (95% CI 87.2% to 94.3%) and a positive predictive value (PPV) of 62.5% (95% CI 49.5% to 74.3%) for UIP pattern on surgical lung biopsy. The addition of age, sex and total traction bronchiectasis score improved the PPV. Inconsistent with UIP pattern demonstrated poor PPV (22.7%, 95% CI 18.3% to 27.7%). HRCT pattern specificity was nearly identical in the validation cohort (92.7%, 95% CI 82.4% to 98.0%). The substantially higher prevalence of UIP pattern in the validation cohort improved the PPV of HRCT patterns. CONCLUSIONS: A possible UIP pattern on HRCT has high specificity for UIP on surgical lung biopsy, but PPV is highly dependent on underlying prevalence. Adding clinical and radiographic features to possible UIP pattern on HRCT may provide sufficient probability of histopathological UIP across prevalence ranges to change clinical decision-making.

Precision Medicine: The New Frontier in Idiopathic Pulmonary Fibrosis.

Precision medicine is defined by the National Institute of Health's Precision Medicine Initiative Working Group as an approach to disease treatment that takes into account individual variability in genes, environment, and lifestyle. There has been increased interest in applying the concept of precision medicine to idiopathic pulmonary fibrosis, in particular to search for genetic and molecular biomarker-based profiles (so called endotypes) that identify mechanistically distinct disease subgroups. The relevance of precision medicine to idiopathic pulmonary fibrosis is yet to be established, but we believe that it holds great promise to provide targeted and highly effective therapies to patients. In this manuscript, we describe the field's nascent efforts in genetic/molecular endotype identification and how environmental and behavioral subgroups may also be relevant to disease management.

Population differentiation of 2 forms of Bryde's whales in the Indian and Pacific Oceans.

Accurate identification of units for conservation is particularly challenging for marine species as obvious barriers to gene flow are generally lacking. Bryde's whales (Balaenoptera spp.) are subject to multiple human-mediated stressors, including fisheries bycatch, ship strikes, and scientific whaling by Japan. For effective management, a clear understanding of how populations of each Bryde's whale species/subspecies are genetically structured across their range is required. We conducted a population-level analysis of mtDNA control region sequences with 56 new samples from Oman, Maldives, and Bangladesh, plus published sequences from off Java and the Northwest Pacific. Nine diagnostic characters in the mitochondrial control region and a maximum parsimony phylogenetic analysis identified 2 genetically recognized subspecies of Bryde's whale: the larger, offshore form, Balaenoptera edeni brydei, and the smaller, coastal form, Balaenoptera edeni edeni. Genetic diversity and differentiation indices, combined with a reconstructed maximum parsimony haplotype network, indicate strong differences in the genetic diversity and population structure within each subspecies. Discrete population units are identified for B. e. brydei in the Maldives, Java, and the Northwest Pacific and for B. e. edeni between the Northern Indian Ocean (Oman and Bangladesh) and the coastal waters of Japan.

Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator.

Hybridization is widespread and constitutes an important source of genetic variability and evolution. In animals, its role in generating novel and independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis is a marine apex predator of Pacific and Atlantic waters, with a disjunct set of populations in Peru and Northern Chile [Peruvian fur seal (Pfs)] with controversial taxonomic status. We demonstrate, using complete genome and reduced representation sequencing, that the Pfs is a genetically distinct species with an admixed genome that originated from hybridization between the SAfs and the Galapagos fur seal (Arctocephalus galapagoensis) ~400,000 years ago. Our results strongly support the origin of Pfs by homoploid hybrid speciation over alternative introgression scenarios. This study highlights the role of hybridization in promoting species-level biodiversity in large vertebrates.

The world's smallest whale population?

The North Pacific right whale (Eubalaena japonica) was heavily exploited by both nineteenth century whaling and recent (1960s) illegal Soviet catches. Today, the species remains extremely rare especially in the eastern North Pacific. Here, we use photographic and genotype data to calculate the first mark-recapture estimates of abundance for right whales in the Bering Sea and Aleutian Islands. The estimates were very similar: photographic = 31 (95% CL 23-54), genotyping = 28 (95% CL 24-42). We also estimated the population contains eight females (95% CL 7-18) and 20 males (95% CL 17-37). Although these estimates may relate to a Bering Sea subpopulation, other data suggest that the total eastern North Pacific population is unlikely to be much larger. Its precarious status today-the world's smallest whale population for which an abundance estimate exists-is a direct consequence of uncontrolled and illegal whaling, and highlights the past failure of international management to prevent such abuses.

Vaquitas (Phocoena sinus) continue to die from bycatch not pollutants.

BACKGROUND: The vaquita of Mexico is critically endangered, with a population less than 19 individuals in 2018. The population continues to decline and gillnet use continues in vaquita habitat. METHODS: Nine vaquita carcases were examined from 2016 to 2018 to establish cause of death. Concentrations of polychlorinated biphenyls (PCBs), DDTs and polybrominated diphenyl ethers (PBDEs) in blubber (n=3) were determined using gas chromatography/mass spectrometry and faeces tested for domoic acid and saxitoxin. RESULTS: Carcases were in good nutritional status and had lesions and full stomachs consistent with fisheries bycatch. PCB, DDT and PBDE concentrations ranged between 94 and 180 ng/g, 500 and 1200 ng/g and 97 and 210 ng/g lipid weight, respectively, which are low compared with other marine mammals. No saxitoxin or domoic acid was detected. CONCLUSION: These findings support the conclusion that bycatch is the primary source of vaquita population decline and emphasise the need for stronger measures to eliminate gillnets from the Upper Gulf of California, Mexico.

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 (Nem 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.

Concentrations of organotin compounds in the stranded killer whales from Rausu, Hokkaido, Japan.

We measured the concentrations of butyltin (BT) and phenyltin (PT) compounds in blubber, liver, lung, and muscle of seven stranded killer whales (Orcinus orca) collected from Rausu, Hokkaido, Japan. BTs in blubber (n = 6), liver (n = 4), lung (n = 1), and muscle (n = 4) of adult whale were in the range of 37-90, 385-676, 15, and 26-53 microg kg(-1) wet weight, respectively. Concentrations of PTs in blubber, liver, lung, and muscle were <1 to 58, <1 to 14, 7 and <1 to 4 microg kg(-1) wet weight, respectively. Detected frequencies of PTs were low in all tissues. Higher percentages of monobutyltin (MBT) in blubber, lung, and muscle were observed, while the percentage of dibutyltin (DBT) was high in liver. Detected frequencies of triphenyltin (TPT) were highest among tissues. Total BT concentrations in blubber and liver of a whale calf were lower than those in adult whales. MBT and DBT in the liver of the calf were the same (42%). MBT in blubber was the dominant compound among BTs.

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

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

Utility of North Atlantic Right Whale Museum Specimens for Assessing Changes in Genetic Diversity.

We examined six historical specimens of the endangered North Atlantic right whale (Eubalaena glacialis) using DNA isolated from documented baleen plates from the late nineteenth and early twentieth centuries. Sequences from the mitochondrial DNA (mtDNA) control region from these samples were compared with those from a near-exhaustive survey (269 of approximately 320 individuals) of the remaining right whales in the western North Atlantic Ocean. Our results suggest that there has been only relatively modest change in maternal lineage diversity over the past century in the North Atlantic right whale population. Any significant reduction in genetic variation in the species most likely occurred prior to the late nineteenth century. One historical specimen was from the last documented female capable of propagating one of the maternal lineages in the population today; no females in the existing population have been found to carry this mtDNA haplotype. Analysis of the only specimens from the eastern North Atlantic right whale population ever to be examined revealed that eastern and western North Atlantic right whales may not have been genetically differentiated populations. Loss of gene diversity experienced by North Atlantic right whales over the last century has been modest, and the six decades of protection have been successful in maintaining much of the maternal lineage diversity that was present in the late nineteenth century.

RESUMEN: Examinamos seis especímenes históricos de la ballena franca septentrional Eubalaena glacialis del Atlántico Norte, usando ADN aislado de placas de las barbas documentadas de finales de siglo diecinueve y principios del siglo veinte. Las secuencias del ADN mitocondrial (mtADN) de la región control de estas muestras comparadas con aquéllas de una muestra casi exhaustiva (269 de aproximadamente 320 individuos) de las ballenas francas remanentes en el océano Atlántico Norte Occidental. Nuestros resultados sugieren que solo ha habido ligeros cambios en la diversidad del linaje materno a lo largo del siglo pasado. Probablemente, cualquier reducción en la variación genética en las especies ocurrió antes del final del siglo diecinueve. Uno de los especímenes históricos fue de la última hembra documentada capaz de propagar uno de los linajes maternos en la población actual. Ninguna de las hembras en las poblaciones existentes ha sido identificada como portadora de este haplotipo de mtADN. El análisis de los especímenes de la población de ballenas del Atlántico Norte Oriental examinados revelan que las ballenas francas del este y del oeste del Atlántico Norte podrían no haber sido poblaciones genéticamente diferentes. La pérdida de diversidad genética experimentada en las poblaciones de ballena franca del Atlántico Norte a lo largo del siglo pasado ha sido modesta y las seis décadas de protección han sido exitosas en el mantenimiento de la mayoría de la diversidad del linaje materno que estaba presente a finales del siglo diecinueve.

Chemical contaminants in juvenile gray whales (Eschrichtius robustus) from a subsistence harvest in Arctic feeding grounds.

Gray whales are coastal migratory baleen whales that are benthic feeders. Most of their feeding takes place in the northern Pacific Ocean with opportunistic feeding taking place during their migrations and residence on the breeding grounds. The concentrations of organochlorines and trace elements were determined in tissues and stomach contents of juvenile gray whales that were taken on their Arctic feeding grounds in the western Bering Sea during a Russian subsistence harvest. These concentrations were compared to previously published data for contaminants in gray whales that stranded along the west coast of the US during their northbound migration. Feeding in coastal waters during their migrations may present a risk of exposure to toxic chemicals in some regions. The mean concentration (standard error of the mean, SEM) of sigmaPCBs [1400 (130) ng/g, lipid weight] in the blubber of juvenile subsistence whales was significantly lower than the mean level [27,000 (11,000) ng/g, lipid weight] reported previously in juvenile gray whales that stranded in waters off the west coast of the US. Aluminum in stomach contents of the subsistence whales was high compared to other marine mammal species, which is consistent with the ingestion of sediment during feeding. Furthermore, the concentrations of potentially toxic chemicals in tissues were relatively low when compared to the concentrations in tissues of other marine mammals feeding at higher trophic levels. These chemical contaminant data for the subsistence gray whales substantially increase the information available for presumably healthy animals.