Context-dependent changes in maritime traffic activity during the first year of the COVID-19 pandemic

Rapid implementation of human mobility restrictions during the COVID-19 pandemic dramatically reduced maritime activity in early 2020. But where and when activity rebounded, or remained low, during the full extent of 2020 restrictions remains unclear. Using global high-resolution datasets, we reveal a surprising degree of complexity in maritime activity patterns during 2020, yielding a more nuanced picture of how restrictions affected activity. Overall, shipping activity in Exclusive Economic Zones decreased (1.35 %), as expected, however high-seas activity increased (0.28 %). While these annual changes appear modest, there were striking spatially and temporally asynchronous variations in different vessel types’ activity in the second half of 2020, ranging from an > 80 % sustained reduction in passenger vessel activity to a 150 % increase in fishing activity. Results suggest systems-level responses were highly context-dependent, pinpointing areas that experienced significant reductions and spikes in activity, and providing hitherto missing details of COVID-19 impacts on economic and environmental sustainability

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

The relationships of passerines (such as the well-studied zebra finch) with non-passerine birds is one of the great enigmas of avian phylogenetic research, because decades of extensive morphological and molecular studies yielded highly inconsistent results between and within data sets. Here we show the first application of the virtually homoplasy-free retroposon insertions to this controversy. Our study examined ~200,000 retroposon-containing loci from various avian genomes and retrieved 51 markers resolving early bird phylogeny. Among these, we obtained statistically significant evidence that parrots are the closest and falcons the second-closest relatives of passerines, together constituting the Psittacopasserae and the Eufalconimorphae, respectively. Our new and robust phylogenetic framework has substantial implications for the interpretation of various conclusions drawn from passerines as model organisms. This includes insights of relevance to human neuroscience, as vocal learning (that is, birdsong) probably evolved in the psittacopasseran ancestor, >30 million years earlier than previously assumed

Singing in the Rain Forest: How a Tropical Bird Song Transfers Information

How information transmission processes between individuals are shaped by natural selection is a key question for the understanding of the evolution of acoustic communication systems. Environmental acoustics predict that signal structure will differ depending on general features of the habitat. Social features, like individual spacing and mating behavior, may also be important for the design of communication. Here we present the first experimental study investigating how a tropical rainforest bird, the white-browed warbler Basileuterus leucoblepharus, extracts various information from a received song: species-specific identity, individual identity and location of the sender. Species-specific information is encoded in a resistant acoustic feature and is thus a public signal helping males to reach a wide audience. Conversely, individual identity is supported by song features susceptible to propagation: this private signal is reserved for neighbors. Finally, the receivers can locate the singers by using propagation-induced song modifications. Thus, this communication system is well matched to the acoustic constraints of the rain forest and to the ecological requirements of the species. Our results emphasize that, in a constraining acoustic environment, the efficiency of a sound communication system results from a coding/decoding process particularly well tuned to the acoustic properties of this environment

Habitat-related birdsong divergence: a multi-level study on the influence of territory density and ambient noise in European blackbirds

Song plays an important role in avian communication and acoustic variation is important at both the individual and population level. Habitat-related variation between populations in particular can reflect adaptations to the environment accumulated over generations, but this may not always be the case. In this study, we test whether variation between individuals matches local conditions with respect to noise level and territory density to examine whether short-term flexibility could contribute to song divergence at the population level. We conducted a case study on an urban and forest population of the European blackbird and show divergence at the population level (i.e. across habitats) in blackbird song, anthropogenic noise level and territory density. Unlike in several other species, we found a lack of any correlation at the individual level (i.e. across individuals) between song features and ambient noise. This suggests species-specific causal explanations for noise-dependent song differentiation which are likely associated with variation in song-copying behaviour or feedback constraints related to variable singing styles. On the other hand, we found that at the level of individual territories, temporal features, but not spectral ones, are correlated to territory density and seasonality. This suggests that short-term individual variation can indeed contribute to habitat-dependent divergence at the population level. As this may undermine the potential role for song as a population marker, we conclude that more investigations on individual song flexibility are required for a better understanding of the impact of population-level song divergence on hybridisation and speciation

HIV infection of the male genital tract – consequences for sexual transmission and reproduction

Despite semen being the main vector of human immunodeficiency virus (HIV) dissemination worldwide, the origin of the virus in this bodily fluid remains unclear. It was recently shown that several organs of the male genital tract (MGT) are infected by HIV/simian immunodeficiency virus (SIV) and likely to contribute to semen viral load during the primary and chronic stages of the infection. These findings are important in helping answer the following questions: (i) does the MGT constitute a viral reservoir responsible for the persistence of virus release into the semen of a subset of HIV-infected men under antiretroviral therapy, who otherwise show an undetectable blood viral load? (ii) What is the aetiology of the semen abnormalities observed in asymptomatic HIV-infected men? (iii) What is the exact nature of the interactions between the spermatozoa, their testicular progenitors and HIV, an important issue in the context of assisted reproductive techniques proposed for HIV-seropositive (HIV+) men? Answers to these questions are crucial for the design of new therapeutic strategies aimed at eradicating the virus from the genital tract of HIV+ men – thus reducing its sexual transmission – and for improving the care of serodiscordant couples wishing to have children. This review summarizes the most recent literature on HIV infection of the male genital tract, discusses the above issues in light of the latest findings and highlights future directions of research

Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org)

Vocal Learning and Auditory-Vocal Feedback

Vocal learning is usually studied in songbirds and humans, species that can form auditory templates by listening to acoustic models and then learn to vocalize to match the template. Most other species are thought to develop vocalizations without auditory feedback. However, auditory input influences the acoustic structure of vocalizations in a broad distribution of birds and mammals. Vocalizations are dened here as sounds generated by forcing air past vibrating membranes. A vocal motor program may generate vocalizations such as crying or laughter, but auditory feedback may be required for matching precise acoustic features of vocalizations. This chapter discriminates limited vocal learning, which uses auditory input to fine-tune acoustic features of an inherited auditory template, from complex vocal learning, in which novel sounds are learned by matching a learned auditory template. Two or three songbird taxa and four or ve mammalian taxa are known for complex vocal learning. A broader range of mammals converge in the acoustic structure of vocalizations when in socially interacting groups, which qualifies as limited vocal learning. All birds and mammals tested use auditory-vocal feedback to adjust their vocalizations to compensate for the effects of noise, and many species modulate their signals as the costs and benefits of communicating vary. This chapter asks whether some auditory-vocal feedback may have provided neural substrates for the evolution of vocal learning. Progress will require more precise definitions of different forms of vocal learning, broad comparative review of their presence and absence, and behavioral and neurobiological investigations into the mechanisms underlying the skills.PostprintPeer reviewe

A Net Energy Analysis of the Global Agriculture, Aquaculture, Fishing and Forestry System

The global agriculture, aquaculture, fishing and forestry (AAFF) energy system is subject to three unsustainable trends: (1) the approaching biophysical limits of AAFF; (2) the role of AAFF as a driver of environmental degradation; and (3) the long-term declining energy efficiency of AAFF due to growing dependence on fossil fuels. In response, we conduct a net energy analysis for the period 1971–2017 and review existing studies to investigate the global AAFF energy system and its vulnerability to the three unsustainable trends from an energetic perspective. We estimate the global AAFF system represents 27.9% of societies energy supply in 2017, with food energy representing 20.8% of societies total energy supply. We find that the net energy-return-on-investment (net EROI) of global AAFF increased from 2.87:1 in 1971 to 4.05:1 in 2017. We suggest that rising net EROI values are being fuelled in part by ‘depleting natures accumulated energy stocks’. We also find that the net energy balance of AAFF increased by 130% in this period, with at the same time a decrease in both the proportion of rural residents and also the proportion of the total population working in AAFF—which decreased from 19.8 to 10.3%. However, this comes at the cost of growing fossil fuel dependency which increased from 43.6 to 62.2%. Given the increasing probability of near-term fossil fuel scarcity, the growing impacts of climate change and environmental degradation, and the approaching biophysical limits of global AAFF, ‘Odum’s hoax’ is likely soon to be revealed

Infection of Semen-Producing Organs by SIV during the Acute and Chronic Stages of the Disease

International audienceBACKGROUND: Although indirect evidence suggests the male genital tract as a possible source of persistent HIV shedding in semen during antiretroviral therapy, this phenomenon is poorly understood due to the difficulty of sampling semen-producing organs in HIV+ asymptomatic individuals. METHODOLOGY/PRINCIPAL FINDINGS: Using a range of molecular and cell biological techniques, this study investigates SIV infection within reproductive organs of macaques during the acute and chronic stages of the disease. We demonstrate for the first time the presence of SIV in the testes, epididymides, prostate and seminal vesicles as early as 14 days post-inoculation. This infection persists throughout the chronic stage and positively correlates with blood viremia. The prostate and seminal vesicles appear to be the most efficiently infected reproductive organs, followed by the epididymides and testes. Within the male genital tract, mostly T lymphocytes and a small number of germ cells harbour SIV antigens and RNA. In contrast to the other organs studied, the testis does not display an immune response to the infection. Testosteronemia is transiently increased during the early phase of the infection but spermatogenesis remains unaffected. CONCLUSIONS/SIGNIFICANCE: The present study reveals that SIV infection of the macaque male genital tract is an early event and that semen-producing organs display differential infection levels and immune responses. These results help elucidate the origin of HIV in semen and constitute an essential base to improving the design of antiretroviral therapies to eradicate virus from semen