Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic.

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

Synthesising 2D Video from 3D Motion Data for Machine Learning Applications.

To increase the utility of legacy, gold-standard, three-dimensional (3D) motion capture datasets for computer vision-based machine learning applications, this study proposed and validated a method to synthesise two-dimensional (2D) video image frames from historic 3D motion data. We applied the video-based human pose estimation model OpenPose to real (in situ) and synthesised 2D videos and compared anatomical landmark keypoint outputs, with trivial observed differences (2.11−3.49 mm). We further demonstrated the utility of the method in a downstream machine learning use-case in which we trained and then tested the validity of an artificial neural network (ANN) to estimate ground reaction forces (GRFs) using synthesised and real 2D videos. Training an ANN to estimate GRFs using eight OpenPose keypoints derived from synthesised 2D videos resulted in accurate waveform GRF estimations (r > 0.9; nRMSE < 14%). When compared with using the smaller number of real videos only, accuracy was improved by adding the synthetic views and enlarging the dataset. The results highlight the utility of the developed approach to enlarge small 2D video datasets, or to create 2D video images to accompany 3D motion capture datasets to make them accessible for machine learning applications.

Relationship Between Mechanical Effectiveness in Sprint Running and Force-Velocity Characteristics of a Countermovement Jump in Australian Rules Football Athletes.

ABSTRACT: Morris, CG, Weber, JA, and Netto, KJ. Relationship between mechanical effectiveness in sprint running and force-velocity characteristics of a countermovement jump in Australian rules football athletes. J Strength Cond Res 36(3): e59-e65, 2022-This study evaluated the mechanical determinants of 40-m sprint performance in elite Australian Rules Football (ARF) athletes and identified variables of countermovement jumps (CMJs) that related to the sprint. Fourteen elite male ARF athletes (age = 22.7 ± 3.6 years; height = 1.88 ± 0.08 m; mass = 88.2 ± 9.38 kg) completed two 40-m sprints and 3 CMJs. Sprint mechanics were calculated using inverse dynamic methods from sprint times, anthropometric and spatiotemporal data, whereas CMJ variables were obtained from in-ground force plates. Associations between sprint mechanics, sprint performance, and CMJ variables were identified using Pearson's correlation coefficient. A p-value of <0.036 was considered statistically significant for all analyses after performing Bonferroni correction adjustment. Relative peak running power was significantly correlated (p < 0.036, r = -0.781 to -0.983) with sprint split times across all distances (5-40 m). Relative maximum horizontal force significantly correlated with acceleration performance (0-20 m, p < 0.036, r = -0.887 to -0.989). Maximum running velocity was significantly correlated (p < 0.036, r = -0.714 to -0.970) with sprint times across 20-40 m. Relative peak force in the CMJ was significantly associated (p < 0.036, r = -0.589 to -0.630) with sprint kinetics (power and horizontal force) and 5-20-m sprint times. Jump height and concentric time in the CMJ were significantly (p < 0.036) correlated with sprint time at 20 m (r = -0.550 and r = 0.546), respectively. These results indicate emphasis should be placed on training protocols that improve relative peak power, particularly in time-constrained environments such as team sports, focusing on maximal force production or maximal running velocity ability. Furthermore, associations between CMJ variables and sprint performance provide practitioners with an approach to assess sprint performance in-season, monitor training adaptations and further individualize training interventions, without requiring maximal sprint testing.

Incursions of sea lamprey, Petromyzon marinus, and striped bass, Morone saxatilis, in Labrador waters: Episodic events or evidence of a northward range expansion?

We describe observations of sea lamprey (Petromyzon marinus) and striped bass (Morone saxatilis) incursions into Labrador, Canada. While P. marinus have been periodically observed in similar latitudes, their numbers have conspicuously increased in estuarine environments in 2020. In contrast, M. saxatilis were not observed from Labrador until 2017 but appear to be declining after the initial surge in abundance that peaked in 2018. It remains unclear whether spawning populations of either species exist. Given the potential to negatively affect species of commercial and cultural importance through predation, follow-up surveys are warranted.

Assessing auditory masking for management of underwater anthropogenic noise.

Masking is often assessed by quantifying changes, due to increasing noise, to an animal's communication or listening range. While the methods used to measure communication or listening ranges are functionally similar if used for vocalizations, they differ in their approaches: communication range is focused on the sender's call, while the listening range is centered on the listener's ability to perceive any signal. How these two methods differ in their use and output is important for management recommendations. Therefore it was investigated how these two methods may alter the conclusions of masking assessments based on Atlantic cod calls in the presence of a commercial air gun array. The two methods diverged with increasing distance from the masking noise source with maximum effects lasting longer between air gun pulses in terms of communication range than listening range. Reductions in the cod's communication ranges were sensitive to fluctuations in the call's source level. That instability was not observed for the listening range. Overall, changes to the cod's communication range were more conservative but very sensitive to the call source level. A high level of confidence in the call is therefore required, while confidence in the receiver's audiogram and soundscape is required for the listening range method.

Sound exposure level as a metric for analyzing and managing underwater soundscapes.

The auditory frequency weighted daily sound exposure level (SEL) is used in many jurisdictions to assess possible injury to the hearing of marine life. Therefore, using daily SEL to describe soundscapes would provide baseline information about the environment using the same tools used to measure injury. Here, the daily SEL from 12 recordings with durations of 18-97 days are analyzed to: (1) identify natural soundscapes versus environments affected by human activity, (2) demonstrate how SEL accumulates from different types of sources, (3) show the effects of recorder duty cycling on daily SEL, (4) make recommendations on collecting data for daily SEL analysis, and (5) discuss the use of the daily SEL as an indicator of cumulative effects. The autocorrelation of the one-minute sound exposure is used to help identify soundscapes not affected by human activity. Human sound sources reduce the autocorrelation and add low-frequency energy to the soundscapes. To measure the daily SEL for all marine mammal auditory frequency weighting groups, data should be sampled at 64 kHz or higher, for at least 1 min out of every 30 min. The daily autocorrelation of the one-minute SEL provides a confidence interval for the daily SEL computed with duty-cycled data.

Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic.

Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analysed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a nonmigratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11k single nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and nonmigratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and nonmigratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and nonmigratory ecotypes on both sides of the Atlantic Ocean.

Combating COVID-19 Vaccine Inequity During the Early Stages of the COVID-19 Pandemic.

Throughout the COVID-19 pandemic, populations of color have been disproportionately impacted, with higher rates of infection, hospitalization, and mortality, compared to non-Hispanic whites. These disparities in health outcomes are likely related to a combination of factors including underlying socioeconomic inequities, unequal access to healthcare, higher rates of employment in essential or public-facing occupations, language barriers, and COVID-19 vaccine inequities. In this manuscript the authors discuss strategies of how one local health department responded to vaccine inequities to better serve historically excluded communities throughout the early stages of the COVID-19 pandemic in 2021. These efforts helped increase vaccination rates in marginalized communities, primarily in the Black or African American population in Durham County, North Carolina.

Illusions of scientific legitimacy: misrepresented science in the direct-to-consumer genetic-testing marketplace.

Marketers of genetic tests often openly or implicitly misrepresent the utility of genetic information. Scientists who are well aware of the current limitations to the utility of such tests are best placed to publicly counter misrepresentations of the science.

The sources and prevalence of anthropogenic noise in Rockfish Conservation Areas with implications for marine reserve planning.

Underwater noise pollution is a recognized threat to marine life. In British Columbia, Canada, Pacific rockfish (Sebastes spp.) were historically overfished, prompting the establishment of Rockfish Conservation Areas (RCAs). However, there are no restrictions prohibiting vessel transits in RCAs. We hypothesized that RCAs do not protect rockfish from sub-lethal harm from noise. We compared noise levels at three RCAs with adjacent unprotected reference sites from August 2018-June 2019. While RCAs had lower levels of noise overall than reference sites, this trend was inconsistent; some RCA sites had higher levels of noise during certain time periods than non-RCA sites. A vessel noise detector was the best predictor of noise level over three frequency bands (20-100 Hz, 100-1000 Hz, 1-10 kHz), and predicted sound levels which could mask rockfish communication. We conclude that RCAs do not reliably protect rockfish from noise pollution, and recommend further study into potential impacts on stock recovery.

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature.

Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n=40) for which allele frequencies show parallel temperature-associated clines (p<0.001, r2=0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted 'neutral' loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.

A Redescription of the Bulla, Antennae, and Mouth Parts of Female Clavella sp. (Copepoda: Siphonostomatoida: Lernaeopodidae) Infesting Wild Gadus morhua Using Scanning Electron Microscopy (SEM).

Many members of the Copepod family Lernaeopodidae are well-known parasites of gadids. This study reports on the occurrence of a lernaeopodid infestation of wild-sourced Gadus morhua sampled from separate inshore (Gilbert Bay, NL) and offshore (Virgin Rocks, NL) populations from Newfoundland, Canada. The majority of the parasites were observed to be associated with the buccal cavity, gill filaments, gill arch, and occasionally near the outer edge of the operculum. Anatomical analysis and detailed redescriptions of the parasite's functional anatomy (mouth parts, antennae, and bulla complex) using high-resolution SEM indicated that the parasite was most likely of the genus Clavella. New morphological details of the second antennae ornamentation, first maxillae, bulla complex, and the oral cone are provided and discussed with regard to their potential in taxonomic applications.

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish.

Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod.

Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.

Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish.

As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.

Autotaxin-lysophosphatidic acid axis is a novel molecular target for lowering intraocular pressure.

Primary open-angle glaucoma is the second leading cause of blindness in the United States and is commonly associated with elevated intraocular pressure (IOP) resulting from diminished aqueous humor (AH) drainage through the trabecular pathway. Developing effective therapies for increased IOP in glaucoma patients requires identification and characterization of molecular mechanisms that regulate IOP and AH outflow. This study describes the identification and role of autotaxin (ATX), a secretory protein and a major source for extracellular lysophosphatidic acid (LPA), in regulation of IOP in a rabbit model. Quantitative proteomics analysis identified ATX as an abundant protein in both human AH derived from non-glaucoma subjects and in AH from different animal species. The lysophospholipase D (LysoPLD) activity of ATX was found to be significantly elevated (by ∼1.8 fold; n=20) in AH derived from human primary open angle glaucoma patients as compared to AH derived from age-matched cataract control patients. Immunoblotting analysis of conditioned media derived from primary cultures of human trabecular meshwork (HTM) cells has confirmed secretion of ATX and the ability of cyclic mechanical stretch of TM cells to increase the levels of secreted ATX. Topical application of a small molecular chemical inhibitor of ATX (S32826), which inhibited AH LysoPLD activity in vitro (by >90%), led to a dose-dependent and significant decrease of IOP in Dutch-Belted rabbits. Single intracameral injection of S32826 (∼2 µM) led to significant reduction of IOP in rabbits, with the ocular hypotensive response lasting for more than 48 hrs. Suppression of ATX expression in HTM cells using small-interfering RNA (siRNA) caused a decrease in actin stress fibers and myosin light chain phosphorylation. Collectively, these observations indicate that the ATX-LPA axis represents a potential therapeutic target for lowering IOP in glaucoma patients.

Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua.

The increasing use of single nucleotide polymorphisms (SNPs) in studies of nonmodel organisms accentuates the need to evaluate the influence of ascertainment bias on accurate ecological or evolutionary inference. Using a panel of 1641 expressed sequence tag-derived SNPs developed for northwest Atlantic cod (Gadus morhua), we examined the influence of ascertainment bias and its potential impact on assignment of individuals to populations ranging widely in origin. We hypothesized that reductions in assignment success would be associated with lower diversity in geographical regions outside the location of ascertainment. Individuals were genotyped from 13 locations spanning much of the contemporary range of Atlantic cod. Diversity, measured as average sample heterozygosity and number of polymorphic loci, declined (c. 30%) from the western (H(e) = 0.36) to eastern (H(e) = 0.25) Atlantic, consistent with a signal of ascertainment bias. Assignment success was examined separately for pools of loci representing differing degrees of reductions in diversity. SNPs displaying the largest declines in diversity produced the most accurate assignment in the ascertainment region (c. 83%) and the lowest levels of correct assignment outside the ascertainment region (c. 31%). Interestingly, several isolated locations showed no effect of assignment bias and consistently displayed 100% correct assignment. Contrary to expectations, estimates of accurate assignment range-wide using all loci displayed remarkable similarity despite reductions in diversity. Our results support the use of large SNP panels in assignment studies of high geneflow marine species. However, our evidence of significant reductions in assignment success using some pools of loci suggests that ascertainment bias may influence assignment results and should be evaluated in large-scale assignment studies.

Centromere assembly and propagation.

Centromere assembly provides a unique example of how elaborate protein structures can be assembled onto DNA, independent of sequence, and then stably propagated through numerous cell divisions. Here, we review the possible epigenetic strategies that organisms ranging from yeast to human use to assemble and propagate active centromeres.

Identification of cis-regulatory elements from the C. elegans Hox gene lin-39 required for embryonic expression and for regulation by the transcription factors LIN-1, LIN-31 and LIN-39.

Expression of the Caenorhabditis elegans Hox gene lin-39 begins in the embryo and continues in multiple larval cells, including the P cell lineages that generate ventral cord neurons (VCNs) and vulval precursor cells (VPCs). lin-39 is regulated by several factors and by Wnt and Ras signaling pathways; however, no cis-acting sites mediating lin-39 regulation have been identified. Here, we describe three elements controlling lin-39 expression: a 338-bp upstream fragment that directs embryonic expression in P5-P8 and their descendants in the larva, a 247-bp intronic region sufficient for VCN expression, and a 1.3-kb upstream cis-regulatory module that drives expression in the VPC P6.p in a Ras-dependent manner. Three trans-acting factors regulate expression via the 1.3-kb element. A single binding site for the ETS factor LIN-1 mediates repression in VPCs other than P6.p; however, loss of LIN-1 decreases expression in P6.p. Therefore, LIN-1 acts both negatively and positively on lin-39 in different VPCs. The Forkhead domain protein LIN-31 also acts positively on lin-39 in P6.p via this module. Finally, LIN-39 itself binds to this element, suggesting that LIN-39 autoregulates its expression in P6.p. Therefore, we have begun to unravel the cis-acting sites regulating lin-39 Hox gene expression and have shown that lin-39 is a direct target of the Ras pathway acting via LIN-1 and LIN-31.