Bellwethers of change: population modelling of North Pacific humpback whales from 2002 through 2021 reveals shift from recovery to climate response.

For the 40 years after the end of commercial whaling in 1976, humpback whale populations in the North Pacific Ocean exhibited a prolonged period of recovery. Using mark-recapture methods on the largest individual photo-identification dataset ever assembled for a cetacean, we estimated annual ocean-basin-wide abundance for the species from 2002 through 2021. Trends in annual estimates describe strong post-whaling era population recovery from 16 875 (± 5955) in 2002 to a peak abundance estimate of 33 488 (± 4455) in 2012. An apparent 20% decline from 2012 to 2021, 33 488 (± 4455) to 26 662 (± 4192), suggests the population abruptly reached carrying capacity due to loss of prey resources. This was particularly evident for humpback whales wintering in Hawai'i, where, by 2021, estimated abundance had declined by 34% from a peak in 2013, down to abundance levels previously seen in 2006, and contrasted to an absence of decline in Mainland Mexico breeding humpbacks. The strongest marine heatwave recorded globally to date during the 2014-2016 period appeared to have altered the course of species recovery, with enduring effects. Extending this time series will allow humpback whales to serve as an indicator species for the ecosystem in the face of a changing climate.

Inbreeding depression explains killer whale population dynamics.

Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often address extrinsic threats, such as environmental degradation and overexploitation, that can limit the recovery of endangered populations. Genetic factors such as inbreeding depression can also affect population dynamics but these effects are rarely measured in the wild and thus often neglected in conservation efforts. Here we show that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, despite genomic signatures of purging of deleterious alleles via natural selection. We find that the 'Southern Residents', which are currently endangered despite nearly 50 years of conservation efforts, exhibit strong inbreeding depression for survival. Our population models suggest that this inbreeding depression limits population growth and predict further decline if the population remains genetically isolated and typical environmental conditions continue. The Southern Residents also had more inferred homozygous deleterious alleles than three other, growing, populations, further suggesting that inbreeding depression affects population fitness. These results demonstrate that inbreeding depression can substantially limit the recovery of endangered populations. Conservation actions focused only on extrinsic threats may therefore fail to account for key intrinsic genetic factors that also limit population growth.

DNA methylation-based biomarkers for ageing long-lived cetaceans.

Epigenetic approaches for estimating the age of living organisms are revolutionizing studies of long-lived species. Molecular biomarkers that allow age estimates from small tissue biopsies promise to enhance studies of long-lived whales, addressing a fundamental and challenging parameter in wildlife management. DNA methylation (DNAm) can affect gene expression, and strong correlations between DNAm patterns and age have been documented in humans and nonhuman vertebrates and used to construct "epigenetic clocks". We present several epigenetic clocks for skin samples from two of the longest-lived cetaceans, killer whales and bowhead whales. Applying the mammalian methylation array to genomic DNA from skin samples we validate four different clocks with median errors of 2.3-3.7 years. These epigenetic clocks demonstrate the validity of using cytosine methylation data to estimate the age of long-lived cetaceans and have broad applications supporting the conservation and management of long-lived cetaceans using genomic DNA from remote tissue biopsies.

Large-scale design and refinement of stable proteins using sequence-only models.

Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be tested computationally and experimentally in order to find stable ones, which is expensive in terms of time and resources. Here we use a high-throughput, low-fidelity assay to experimentally evaluate the stability of approximately 200,000 novel proteins. These include a wide range of sequence perturbations, providing a baseline for future work in the field. We build a neural network model that predicts protein stability given only sequences of amino acids, and compare its performance to the assayed values. We also report another network model that is able to generate the amino acid sequences of novel stable proteins given requested secondary sequences. Finally, we show that the predictive model-despite weaknesses including a noisy data set-can be used to substantially increase the stability of both expert-designed and model-generated proteins.

Passive acoustic monitoring of killer whales (Orcinus orca) reveals year-round distribution and residency patterns in the Gulf of Alaska.

Killer whales (Orcinus orca) are top predators throughout the world's oceans. In the North Pacific, the species is divided into three ecotypes-resident (fish-eating), transient (mammal-eating), and offshore (largely shark-eating)-that are genetically and acoustically distinct and have unique roles in the marine ecosystem. In this study, we examined the year-round distribution of killer whales in the northern Gulf of Alaska from 2016 to 2020 using passive acoustic monitoring. We further described the daily acoustic residency patterns of three killer whale populations (southern Alaska residents, Gulf of Alaska transients, and AT1 transients) for one year of these data. Highest year-round acoustic presence occurred in Montague Strait, with strong seasonal patterns in Hinchinbrook Entrance and Resurrection Bay. Daily acoustic residency times for the southern Alaska residents paralleled seasonal distribution patterns. The majority of Gulf of Alaska transient detections occurred in Hinchinbrook Entrance in spring. The depleted AT1 transient killer whale population was most often identified in Montague Strait. Passive acoustic monitoring revealed that both resident and transient killer whales used these areas much more extensively than previously known and provided novel insights into high use locations and times for each population. These results may be driven by seasonal foraging opportunities and social factors and have management implications for this species.

Investigating the formation and diagnostic value of ω-(o-alkylphenyl)alkanoic acids in ancient pottery.

Long-chain ω-(o-alkylphenyl)alkanoic acids (APAAs) derived from the heating of unsaturated fatty acids have been widely used for the identification of aquatic products in archaeological ceramic vessels. To date, little attention has been paid to the diagnostic potential of shorter chain (< C20) APAAs, despite their frequent occurrence. Here, a range of laboratory and field experiments and analyses of archaeological samples were undertaken to investigate whether APAAs could be used to further differentiate different commodities. The results provide new insights about the conditions for the formation of APAAs and enable the proposition of novel criteria to distinguish different natural products.

Concentrations and profiles of organochlorine contaminants in North Pacific resident and transient killer whale (Orcinus orca) populations.

Organochlorine (OC) profiles have been used as chemical "fingerprints" to infer an animal's foraging area. North Pacific killer whale (Orcinus orca) populations are exposed to different levels and patterns of OCs based on their prey, distribution, and amount of time spent in a particular area. To characterize concentrations and profiles of OCs found in various populations of North Pacific killer whales, polychlorinated biphenyls (PCBs), including dioxin-like congeners, DDTs, and hexachlorobenzene (HCB), were measured in biopsy blubber samples of photo-identified resident (fish-eating) and transient (mammal-eating) killer whales collected from 1994 through 2002 from Russian Far East waters to the waters of the west coast of the United States, representing 10 populations. We compared blubber OC concentrations based on ecotype (resident vs. transient), sex and reproductive maturity, and geographic area. We also examined OC mixtures to determine if we could detect segregated geographical areas (foraging areas) among the six populations with sufficient sample sizes. Transients had significantly higher OC concentrations than residents and adult male whales had consistently higher OC levels compared to adult females, regardless of ecotype. Our OC profile findings indicate segregated foraging areas for the North Pacific killer whales, consistent with observations of their geographic distributions. Several potential health risks have also been associated with exposure to high levels of contaminants in top-level predators including reproductive impairment, immune suppression, skeletal deformities, and carcinoma. The results of this baseline study provide information on the geographic distribution of OCs found in North Pacific killer whales, results which are crucial for assessing the potential health risks associated with OC exposure in this species.

Protein structural motifs in prediction and design.

The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information from the PDB has been used to generate models ranging from specific structural mechanisms to general statistical potentials. With accumulating structural data, it has become possible to mine for more complete and complex structural observations, deducing more accurate generalizations. Motif libraries, which capture recurring structural features along with their sequence preferences, have exposed modularity in the structural universe and found successful application in various problems of structural biology. Here we summarize recent achievements in this arena, focusing on subdomain level structural patterns and their applications to protein design and structure prediction, and suggest promising future directions as the structural database continues to grow.

Physical constraints of cultural evolution of dialects in killer whales.

Odontocete sounds are produced by two pairs of phonic lips situated in soft nares below the blowhole; the right pair is larger and is more likely to produce clicks, while the left pair is more likely to produce whistles. This has important implications for the cultural evolution of delphinid sounds: the greater the physical constraints, the greater the probability of random convergence. In this paper the authors examine the call structure of eight killer whale populations to identify structural constraints and to determine if they are consistent among all populations. Constraints were especially pronounced in two-voiced calls. In the calls of all eight populations, the lower component of two-voiced (biphonic) calls was typically centered below 4 kHz, while the upper component was typically above that value. The lower component of two-voiced calls had a narrower frequency range than single-voiced calls in all populations. This may be because some single-voiced calls are homologous to the lower component, while others are homologous to the higher component of two-voiced calls. Physical constraints on the call structure reduce the possible variation and increase the probability of random convergence, producing similar calls in different populations.

Tertiary alphabet for the observable protein structural universe.

Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective mapping between sequence and structure. We demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones. Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Finally, locations of TERMs in protein chains can be predicted from sequence alone based on sequence signatures emergent from TERM instances in the PDB. For multisegment motifs, this method identifies spatially adjacent fragments that are not contiguous in sequence-a major bottleneck in structure prediction. Although all TERMs recur in diverse proteins, some appear specialized for certain functions, such as interface formation, metal coordination, or even water binding. Structural biology has benefited greatly from previously observed degeneracies in structure. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities toward better understanding, design, and prediction of protein structure.

Evidence based management of polyps of the gall bladder: A systematic review of the risk factors of malignancy.

BACKGROUND: There are no evidence-based guidelines to dictate when Gallbladder Polyps (GBPs) of varying sizes should be resected. AIM: To identify factors that accurately predict malignant disease in GBP; to provide an evidence-based algorithm for management. METHODS: A systematic review following PRISMA guidelines was performed using terms "gallbladder polyps" AND "polypoid lesion of gallbladder", from January 1993 and September 2013. Inclusion criteria required histopathological report or follow-up of 2 years. RTI-IB tool was used for quality analysis. Correlation with GBP size and malignant potential was analysed using Euclidean distance; a logistics mixed effects model was used for assessing independent risk factors for malignancy. RESULTS: Fifty-three articles were included in review. Data from 21 studies was pooled for analysis. Optimum size cut-off for resection of GBPs was 10 mm. Probability of malignancy is approximately zero at size <4.15 mm. Patient age >50 years, sessile and single polyps were independent risk factors for malignancy. For polyps sized 4 mm-10 mm, a risk assessment model was formulated. CONCLUSIONS: This review and analysis has provided an evidence-based algorithm for the management of GBPs. Longitudinal studies are needed to better understand the behaviour of polyps <10 mm, that are not at a high risk of malignancy, but may change over time.

Debating LGBT Workplace Protections in the Bible Belt: Social Identities in Legislative and Media Discourse.

This article reports a case study of the legislative and media discourse surrounding the addition of sexual orientation and gender identity language to the employment nondiscrimination ordinance of a city in the heart of the Bible Belt. The purpose of the study is to uncover how different identities were constructed and contested at city council meetings and in the news media on the way to passing legal protection for LGBT city employees in a region that is often characterized by anti-gay prejudice. This debate over the nondiscrimination ordinance centered on the question of whether LGBT identities are equivalent to identity categories based on race, gender, or religious belief, and it was shaped by various intergroup communication dynamics, specifically between members of the LGBT minority and the straight majority, between LGBT and Christian identities, and between "true" and "false" Christian identities.

Killer whale call frequency is similar across the oceans, but varies across sympatric ecotypes.

Killer whale populations may differ in genetics, morphology, ecology, and behavior. In the North Pacific, two sympatric populations ("resident" and "transient") specialize on different prey (fish and marine mammals) and retain reproductive isolation. In the eastern North Atlantic, whales from the same populations have been observed feeding on both fish and marine mammals. Fish-eating North Pacific "residents" are more genetically related to eastern North Atlantic killer whales than to sympatric mammal-eating "transients." In this paper, a comparison of frequency variables in killer whale calls recorded from four North Pacific resident, two North Pacific transient, and two eastern North Atlantic populations is reported to assess which factors drive the large-scale changes in call structure. Both low-frequency and high-frequency components of North Pacific transient killer whale calls have significantly lower frequencies than those of the North Pacific resident and North Atlantic populations. The difference in frequencies could be related to ecological specialization or to the phylogenetic history of these populations. North Pacific transient killer whales may have genetically inherited predisposition toward lower frequencies that may shape their learned repertoires.

Geographic and temporal dynamics of a global radiation and diversification in the killer whale.

Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.

Direct evidence of milk consumption from ancient human dental calculus.

Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein ß-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15(th) century CE.

Improved visual performance in letter perception through edge orientation encoding in a retinal prosthesis simulation.

Objective. Stimulation strategies for retinal prostheses predominately seek to directly encode image brightness values rather than edge orientations. Recent work suggests that the generation of oriented elliptical phosphenes may be possible by controlling interactions between neighboring electrodes. Based on this, we propose a novel stimulation strategy for prosthetic vision that extracts edge orientation information from the intensity image and encodes it as oriented elliptical phosphenes. We test the hypothesis that encoding edge orientation via oriented elliptical phosphenes leads to better alphabetic letter recognition than standard intensity-based encoding. Approach. We conduct a psychophysical study with simulated phosphene vision with 12 normal-sighted volunteers. The two stimulation strategies were compared with variations of letter size, electrode drop-out and spatial offsets of phosphenes. Main results. Mean letter recognition accuracy was significantly better with the new proposed stimulation strategy (65%) compared to direct grayscale encoding (47%). All examined parameters-stimulus size, phosphene dropout, and location shift-were found to influence the performance, with significant two-way interactions between phosphene dropout and stimulus size as well as between phosphene dropout and phosphene location shift. The analysis delivers a model of perception performance. Significance. Displaying available directional information to an implant user may improve their visual performance. We present a model for designing a stimulation strategy under the constraints of existing retinal prostheses that can be exploited by retinal implant developers to strategically employ oriented phosphenes.

An alternative certification examination ("ACE") in surgery.

BACKGROUND: Medical graduates are required to be competent in many domains of professional practice when joining the health care workforce. Current undergraduate examination methods robustly assess up to 5 of these 8 required skills. This study sought to evaluate an alternative certification examination ("ACE") in assessing all of the 8 required domains in surgical cases. METHODS: A total of 143 final-year medical students were invited to participate in an "ACE" in February 2013. In total, 137 students, 95.8% of the class, agreed to participate. The "ACE" format consisted of 4 sequential patient encounters observed by 2 independent examiners. It assessed all the 8 required domains of professional practice. The examiners and the students evaluated this examination format using a Likert scale and free-text comments. RESULTS: The "ACE" assessed all the 8 domains. The inclusion of a patient safety measure to avoid an egregious error in the pass criteria resulted in 27 (18.9%) students failing to meet them. The correlation of grades between the independent examiners in the "ACE" was strong at a Cronbach α of 0.907 (CI: 0.766-1). The "ACE" format was reported as an acceptable examination methodology by the examiners for formative or summative assessment of surgical cases at the end of a primary medical degree. CONCLUSION: The "ACE" format is standardized, is integrative, and has excellent interrater reliability. Inclusion of a patient safety measure as pass criteria appears to increase specificity. The "ACE" shows potential as an alternative examination to the traditional long case examination and objective structured clinical examination in assessing all the 8 domains of professional practice.

Embracing the irregular: a patient-specific image processing strategy for visual prostheses.

We propose a stimulation strategy for retinal prostheses that makes use of irregular shapes of elicited phosphenes. It is patient specific and thus relies on prior psychophysical measurements. Visual perceptions are stored in a phosphene map that relates stimulation parameters to the visual stimulus elicited. Based on this map, stimulation parameters are chosen in such a way that the edges of the target image are optimally represented through the shape of the phosphene. In a psychophysical pilot study, we compare this approach to one in which we choose phosphenes to match the brightness of the target image. We find that participants perform similarly well with both strategies overall. However, the results indicate that each strategy may have advantages for different stimulus sizes. Both of the proposed strategies are novel in using only previously recorded phosphenes rather than a model based on idealized assumptions about the relationship between stimulation parameters and phosphene properties.

Geographic patterns of genetic differentiation among killer whales in the northern North Pacific.

The difficulties associated with detecting population boundaries have long constrained the conservation and management of highly mobile, wide-ranging marine species, such as killer whales (Orcinus orca). In this study, we use data from 26 nuclear microsatellite loci and mitochondrial DNA sequences (988bp) to test a priori hypotheses about population subdivisions generated from a decade of killer whale surveys across the northern North Pacific. A total of 462 remote skin biopsies were collected from wild killer whales primarily between 2001 and 2010 from the northern Gulf of Alaska to the Sea of Okhotsk, representing both the piscivorous "resident" and the mammal-eating "transient" (or Bigg's) killer whales. Divergence of the 2 ecotypes was supported by both mtDNA and microsatellites. Geographic patterns of genetic differentiation were supported by significant regions of genetic discontinuity, providing evidence of population structuring within both ecotypes and corroborating direct observations of restricted movements of individual whales. In the Aleutian Islands (Alaska), subpopulations, or groups with significantly different mtDNA and microsatellite allele frequencies, were largely delimited by major oceanographic boundaries for resident killer whales. Although Amchitka Pass represented a major subdivision for transient killer whales between the central and western Aleutian Islands, several smaller subpopulations were evident throughout the eastern Aleutians and Bering Sea. Support for seasonally sympatric transient subpopulations around Unimak Island suggests isolating mechanisms other than geographic distance within this highly mobile top predator.

Earliest evidence for the use of pottery.

Pottery was a hunter-gatherer innovation that first emerged in East Asia between 20,000 and 12,000 calibrated years before present (cal bp), towards the end of the Late Pleistocene epoch, a period of time when humans were adjusting to changing climates and new environments. Ceramic container technologies were one of a range of late glacial adaptations that were pivotal to structuring subsequent cultural trajectories in different regions of the world, but the reasons for their emergence and widespread uptake are poorly understood. The first ceramic containers must have provided prehistoric hunter-gatherers with attractive new strategies for processing and consuming foodstuffs, but virtually nothing is known of how early pots were used. Here we report the chemical analysis of food residues associated with Late Pleistocene pottery, focusing on one of the best-studied prehistoric ceramic sequences in the world, the Japanese Jomon. We demonstrate that lipids can be recovered reliably from charred surface deposits adhering to pottery dating from about 15,000 to 11,800 cal bp (the Incipient Jomon period), the oldest pottery so far investigated, and that in most cases these organic compounds are unequivocally derived from processing freshwater and marine organisms. Stable isotope data support the lipid evidence and suggest that most of the 101 charred deposits analysed, from across the major islands of Japan, were derived from high-trophic-level aquatic food. Productive aquatic ecotones were heavily exploited by late glacial foragers, perhaps providing an initial impetus for investment in ceramic container technology, and paving the way for further intensification of pottery use by hunter-gatherers in the early Holocene epoch. Now that we have shown that it is possible to analyse organic residues from some of the world's earliest ceramic vessels, the subsequent development of this critical technology can be clarified through further widespread testing of hunter-gatherer pottery from later periods.