Depth as a driver of evolution in the deep sea: Insights from grenadiers (Gadiformes: Macrouridae) of the genus Coryphaenoides

Here we consider the role of depth as a driver of evolution in a genus of deep-sea fishes. We provide a phylogeny for the genus Coryphaenoides (Gadiformes: Macrouridae) that represents the breadth of habitat use and distributions for these species. In our consensus phylogeny species found at abyssal depths (> 4000 m) form a well-supported lineage, which interestingly also includes two non-abyssal species, C. striaturus and C. murrayi, diverging from the basal node of that lineage. Biogeographic analyses suggest the genus may have originated in the Southern and Pacific Oceans where contemporary species diversity is highest. The abyssal lineage seems to have arisen secondarily and likely originated in the Southern/Pacific Oceans but diversification of this lineage occurred in the Northern Atlantic Ocean. All abyssal species are found in the North Atlantic with the exception of C. yaquinae in the North Pacific and C. filicauda in the Southern Oceans. Abyssal species tend to have broad depth ranges and wide distributions, indicating that the stability of the deep oceans and the ability to live across wide depths may promote population connectivity and facilitate large ranges. We also confirm that morphologically defined subgenera do not agree with our phylogeny and that the Giant grenadier (formally Albatrossia pectoralis) belongs to Coryphaenoides, indicating that a taxonomic revision of the genus is needed. We discuss the implications of our findings for understanding the radiation and diversification of this genus, and the likely role of adaptation to the abyss

COBRA Master Class: Providing deep-sea expedition leadership training to accelerate early career advancement

Leading deep-sea research expeditions requires a breadth of training and experience, and the opportunities for Early Career Researchers (ECRs) to obtain focused mentorship on expedition leadership are scarce. To address the need for leadership training in deep-sea expeditionary science, the Crustal Ocean Biosphere Research Accelerator (COBRA) launched a 14-week virtual Master Class with both synchronous and asynchronous components to empower students with the skills and tools to successfully design, propose, and execute deep-sea oceanographic field research. The Master Class offered customized and distributed training approaches and created an open-access syllabus with resources, including reading material, lectures, and on-line resources freely-available on the Master Class website (cobra.pubpub.org). All students were Early Career Researchers (ECRs, defined here as advanced graduate students, postdoctoral scientists, early career faculty, or individuals with substantial industry, government, or NGO experience) and designated throughout as COBRA Fellows. Fellows engaged in topics related to choosing the appropriate deep-sea research asset for their Capstone “dream cruise” project, learning about funding sources and how to tailor proposals to meet those source requirements, and working through an essential checklist of pre-expedition planning and operations. The Master Class covered leading an expedition at sea, at-sea operations, and ship-board etiquette, and the strengths and challenges of telepresence. It also included post-expedition training on data management strategies and report preparation and outputs. Throughout the Master Class, Fellows also discussed education and outreach, international ocean law and policy, and the importance and challenges of team science. Fellows further learned about how to develop concepts respectfully with regard to geographic and cultural considerations of their intended study sites. An assessment of initial outcomes from the first iteration of the COBRA Master Class reinforces the need for such training and shows great promise with one-quarter of the Fellows having submitted a research proposal to national funding agencies within six months of the end of the class. As deep-sea research continues to accelerate in scope and speed, providing equitable access to expedition training is a top priority to enable the next generation of deep-sea science leadership

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Table_1_COBRA Master Class: Providing deep-sea expedition leadership training to accelerate early career advancement.docx

Leading deep-sea research expeditions requires a breadth of training and experience, and the opportunities for Early Career Researchers (ECRs) to obtain focused mentorship on expedition leadership are scarce. To address the need for leadership training in deep-sea expeditionary science, the Crustal Ocean Biosphere Research Accelerator (COBRA) launched a 14-week virtual Master Class with both synchronous and asynchronous components to empower students with the skills and tools to successfully design, propose, and execute deep-sea oceanographic field research. The Master Class offered customized and distributed training approaches and created an open-access syllabus with resources, including reading material, lectures, and on-line resources freely-available on the Master Class website (cobra.pubpub.org). All students were Early Career Researchers (ECRs, defined here as advanced graduate students, postdoctoral scientists, early career faculty, or individuals with substantial industry, government, or NGO experience) and designated throughout as COBRA Fellows. Fellows engaged in topics related to choosing the appropriate deep-sea research asset for their Capstone “dream cruise” project, learning about funding sources and how to tailor proposals to meet those source requirements, and working through an essential checklist of pre-expedition planning and operations. The Master Class covered leading an expedition at sea, at-sea operations, and ship-board etiquette, and the strengths and challenges of telepresence. It also included post-expedition training on data management strategies and report preparation and outputs. Throughout the Master Class, Fellows also discussed education and outreach, international ocean law and policy, and the importance and challenges of team science. Fellows further learned about how to develop concepts respectfully with regard to geographic and cultural considerations of their intended study sites. An assessment of initial outcomes from the first iteration of the COBRA Master Class reinforces the need for such training and shows great promise with one-quarter of the Fellows having submitted a research proposal to national funding agencies within six months of the end of the class. As deep-sea research continues to accelerate in scope and speed, providing equitable access to expedition training is a top priority to enable the next generation of deep-sea science leadership.</p

Evolution of the immune system influences speciation rates in teleost fishes

Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9-39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification