Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae.

BACKGROUND: The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. RESULTS: We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. CONCLUSIONS: Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

Long-term analysis of microseism during extreme weather events: Medicanes and common storms in the Mediterranean Sea.

In this work, we analyze 12 meteorological events that occurred in the Mediterranean Sea during the period November 2011-November 2021 from a seismic point of view. In particular, we consider 8 Medicanes and 4 more common storms. Each of these events, in spite of the marked differences between them, caused heavy rainfall, strong wind gusts and violent storm surge with significant wave heights usually >3 m. We deal with the relationships between these meteorological events and the features of microseism (the most continuous and widespread seismic signal on Earth) in terms of spectral content, space-time variation of the amplitude and source locations tracked employing two different methods (amplitude decay-based grid search and array techniques). By comparing the positions of the microseism sources with the areas of significant storm surges, we observe that the microseism locations align with the actual locations of the storm surges for 10 out of 12 events analyzed (two Medicanes present very low intensity in terms of meteorological parameters and the microseism amplitude does not show significant variations during these two events). We also perform two analyses that allowed us to obtain both the seismic signature of these events, by using a method that exploits the coherence of continuous seismic noise, and their strength from a seismic point of view, called Microseism Reduced Amplitude. In addition, by integrating the results obtained from these two methods, we are able to "seismically" distinguish Medicanes and common storms. Consequently, we demonstrate the possibility of creating a novel monitoring system for Mediterranean meteorological events by incorporating microseism information alongside with other commonly employed techniques for studying meteorological phenomena. The integration of microseism with the data provided by routinely used techniques in sea state monitoring (e.g., wave buoy and HF radar) has the potential to offer valuable insights into the examination of historical extreme weather events within the context of climate change.

Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae.

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

Monitoring extreme meteo-marine events in the Mediterranean area using the microseism (Medicane Apollo case study).

Microseism is the continuous background seismic signal caused by the interaction between the atmosphere, the hydrosphere and the solid Earth. Several studies have dealt with the relationship between microseisms and the tropical cyclones, but none focused on the small-scale tropical cyclones that occur in the Mediterranean Sea, called Medicanes. In this work, we analysed the Medicane Apollo which impacted the eastern part of Sicily during the period 25 October-5 November 2021 causing heavy rainfall, strong wind gusts and violent sea waves. We investigated the microseism accompanying this extreme Mediterranean weather event, and its relationship with the sea state retrieved from hindcast maps and wave buoys. The spectral and amplitude analyses showed the space-time variation of the microseism amplitude. In addition, we tracked the position of Apollo during the time using two different methods: (i) a grid search method; (ii) an array analysis. We obtained a good match between the real position of Apollo and the location constraint by both methods. This work shows that it is possible to extract information on Medicanes from microseisms for both research and monitoring purposes.

Signals of adaptation to agricultural stress in the genomes of two European bumblebees.

Human-induced environmental impacts on wildlife are widespread, causing major biodiversity losses. One major threat is agricultural intensification, typically characterised by large areas of monoculture, mechanical tillage, and the use of agrochemicals. Intensification leads to the fragmentation and loss of natural habitats, native vegetation, and nesting and breeding sites. Understanding the adaptability of insects to these changing environmental conditions is critical to predicting their survival. Bumblebees, key pollinators of wild and cultivated plants, are used as model species to assess insect adaptation to anthropogenic stressors. We investigated the effects of agricultural pressures on two common European bumblebees, Bombus pascuorum and B. lapidarius. Restriction-site Associated DNA Sequencing was used to identify loci under selective pressure across agricultural-natural gradients over 97 locations in Europe. 191 unique loci in B. pascuorum and 260 in B. lapidarius were identified as under selective pressure, and associated with agricultural stressors. Further investigation suggested several candidate proteins including several neurodevelopment, muscle, and detoxification proteins, but these have yet to be validated. These results provide insights into agriculture as a stressor for bumblebees, and signal for conservation action in light of ongoing anthropogenic changes.

Hidden pressurized fluids prior to the 2014 phreatic eruption at Mt Ontake.

A large fraction of volcanic eruptions does not expel magma at the surface. Such an eruption occurred at Mt Ontake in 2014, claiming the life of at least 58 hikers in what became the worst volcanic disaster in Japan in almost a century. Tens of scientific studies attempted to identify a precursor and to unravel the processes at work but overall remain inconclusive. By taking advantage of continuous seismic recordings, we uncover an intriguing sequence of correlated seismic velocity and volumetric strain changes starting 5 months before the eruption; a period previously considered as completely quiescent. We use various novel approaches such as covariance matrix eigenvalues distribution, cutting-edge deep-learning models, and ascribe such velocity pattern as reflecting critically stressed conditions in the upper portions of the volcano. These, in turn, later triggered detectable deformation and earthquakes. Our results shed light onto previously undetected pressurized fluids using stations located above the volcano-hydrothermal system and hold great potential for monitoring.

Finding the Best Match: A Ranking Procedure of Fish Species Combinations for Polyculture Development.

Polyculture is a potentially interesting rearing practice for future aquaculture developments. Nevertheless, it may result in beneficial as well as detrimental consequences for fish production. One way to maximize the benefits of polyculture is to combine species with high levels of compatibility and complementarity. This requires the development of a ranking procedure, based on a multi-trait assessment, that highlights the most suitable species combinations for polyculture. Moreover, in order to ensure the relevance of such a procedure, it is important to integrate the socio-economic expectations by assigning relative weights to each trait according to the stakeholder priorities. Here, we proposed a ranking procedure of candidate fish polycultures (i.e., species combinations that could be potentially interesting for aquaculture) based on a multi-trait assessment approach and the stakeholder priorities. This procedure aims at successively (i) weighting evaluation results obtained for each candidate polyculture according to stakeholder priorities; (ii) assessing differentiation between candidate species combinations based on these weighted results; and (iii) ranking differentiated candidate polycultures. We applied our procedure on three test cases of fish polycultures in recirculated aquaculture systems. These test cases each focused on a target species (two on Sander lucioperca and one on Carassius auratus), which were reared in two or three different alternative candidate fish polycultures. For each test case, our procedure aimed at ranking alternative combinations according to their benefits for production and/or welfare of the target species. These benefits were evaluated based on survival rate as well as morphology, behavioral, and physiological traits. Three scenarios of stakeholder priorities were considered for weighting evaluation results: placing a premium on production, welfare, or both for the target species. A comparison of our procedure results between these scenarios showed that the ranking changed for candidate polycultures in two test cases. This highlights the need to carefully consider stakeholder priorities when choosing fish polycultures.

AquaDesign: A tool to assist aquaculture production design based on abiotic requirements of animal species.

Farming new species and promoting polyculture can enhance aquaculture sustainability. This implies to define the rearing conditions that meet the ecological requirements of a target species and/or to assess if different species can live in the same farming environment. However, there is a large number of rearing conditions and/or taxon combinations that can be considered. In order to minimise cumbersome and expensive empirical trials to explore all possibilities, we introduce a tool, AquaDesign. It is based on a R-script and package which help to determine farming conditions that are most likely suitable for species through in silico assessment. We estimate farming conditions potentially suitable for an aquatic organism by considering the species niche. We define the species n-dimensional niche hypervolume using a correlative approach in which the species niche is estimated by relating distribution data to environmental conditions. Required input datasets are mined from several public databases. The assistant tool allows users to highlight (i) abiotic conditions that are most likely suitable for species and (ii) combinations of species potentially able to live in the same abiotic environment. Moreover, it offers the possibility to assess if a particular set of abiotic conditions or a given farming location is potentially suitable for the monoculture or the polyculture of species of interest. Our tool provides useful pieces of information to develop freshwater aquacultures. Using the large amount of biogeographic and abiotic information available in public databases allows us to propose a pragmatic and operational tool even for species for which abiotic requirements are poorly or not available in literature such as currently non-produced species. Overall, we argue that the assistant tool can act as a stepping stone to promote new aquatic productions which are required to enhance aquaculture sustainability.

Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming.

The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.

Atmospheric waves and global seismoacoustic observations of the January 2022 Hunga eruption, Tonga.

The 15 January 2022 climactic eruption of Hunga volcano, Tonga, produced an explosion in the atmosphere of a size that has not been documented in the modern geophysical record. The event generated a broad range of atmospheric waves observed globally by various ground-based and spaceborne instrumentation networks. Most prominent was the surface-guided Lamb wave (≲0.01 hertz), which we observed propagating for four (plus three antipodal) passages around Earth over 6 days. As measured by the Lamb wave amplitudes, the climactic Hunga explosion was comparable in size to that of the 1883 Krakatau eruption. The Hunga eruption produced remarkable globally detected infrasound (0.01 to 20 hertz), long-range (~10,000 kilometers) audible sound, and ionospheric perturbations. Seismometers worldwide recorded pure seismic and air-to-ground coupled waves. Air-to-sea coupling likely contributed to fast-arriving tsunamis. Here, we highlight exceptional observations of the atmospheric waves.

Computer Vision Algorithms of DigitSeis for Building a Vectorised Dataset of Historical Seismograms from the Archive of Royal Observatory of Belgium.

Archived seismograms recorded in the 20th century present a valuable source of information for monitoring earthquake activity. However, old data, which are only available as scanned paper-based images should be digitised and converted from raster to vector format prior to reuse for geophysical modelling. Seismograms have special characteristics and specific featuresrecorded by a seismometer and encrypted in the images: signal trace lines, minute time gaps, timing and wave amplitudes. This information should be recognised and interpreted automatically when processing archives of seismograms containing large collections of data. The objective was to automatically digitise historical seismograms obtained from the archives of the Royal Observatory of Belgium (ROB). The images were originallyrecorded by the Galitzine seismometer in 1954 in Uccle seismic station, Belgium. A dataset included 145 TIFF images which required automatic approach of data processing. Software for digitising seismograms are limited and many have disadvantages. We applied the DigitSeis for machine-based vectorisation and reported here a full workflowof data processing. This included pattern recognition, classification, digitising, corrections and converting TIFFs to the digital vector format. The generated contours of signals were presented as time series and converted into digital format (mat files) which indicated information on ground motion signals contained in analog seismograms. We performed the quality control of the digitised traces in Python to evaluate the discriminating functionality of seismic signals by DigitSeis. We shown a robust approach of DigitSeis as a powerful toolset for processing analog seismic signals. The graphical visualisation of signal traces and analysis of the performed vectorisation results shown that the algorithms of data processing performed accurately and can be recommended in similar applications of seismic signal processing in future related works in geophysical research.

Split it up and see: using proxies to highlight divergent inter-populational performances in aquaculture standardised conditions.

BACKGROUND: Considering wild inter-populational phenotypic differentiation can facilitate domestication and subsequent production of new species. However, comparing all populations across a species range to identify those exhibiting suitable key traits for aquaculture (KTA; i.e. important for domestication and subsequent production) expressions is not feasible. Therefore, proxies highlighting inter-populational divergences in KTA are needed. The use of such proxies would allow to identify, prior to bioassays, the wild population pairs which are likely to present differentiations in KTA expressions in aquaculture conditions. Here, we assessed the relevance of three alternative proxies: (i) genetic distance, (ii) habitat divergence, and (iii) geographic/hydrologic distances. We performed this evaluation on seven allopatric populations of Perca fluviatilis for which divergences in KTA had already been shown. RESULTS: We showed differences in the correlation degree between the alternative proxy-based and KTA-based distance matrices, with the genetic proxy being correlated to the highest number of KTA. However, no proxy was correlated to all inter-populational divergences in KTA. CONCLUSION: For future domestication trials, we suggest using a multi-proxy assessment along with a prioritisation strategy to identify population pairs which are of interest for further evaluation in bioassays.

Global effects of extreme temperatures on wild bumblebees.

Climate plays a key role in shaping population trends and determining the geographic distribution of species because of limits in species' thermal tolerance. An evaluation of species tolerance to temperature change can therefore help predict their potential spatial shifts and population trends triggered by ongoing global warming. We assessed inter- and intraspecific variations in heat resistance in relation to body mass, local mean temperatures, and evolutionary relationships in 39 bumblebee species, a major group of pollinators in temperate and cold ecosystems, across 3 continents, 6 biomes, and 20 regions (2386 male specimens). Based on experimental bioassays, we measured the time before heat stupor of bumblebee males at a heatwave temperature of 40 °C. Interspecific variability was significant, in contrast to interpopulational variability, which was consistent with heat resistance being a species-specific trait. Moreover, cold-adapted species are much more sensitive to heat stress than temperate and Mediterranean species. Relative to their sensitivity to extreme temperatures, our results help explain recent population declines and range shifts in bumblebees following climate change.

Efectos Globales de las Temperaturas Extremas sobre Abejorros Silvestres Resumen El clima juega un papel importante en la configuración de las tendencias poblacionales y en la determinación de la distribución geográfica de las especies debido a los límites de la tolerancia térmica y al agua que tiene cada especie. Por lo tanto, una evaluación de la tolerancia de las especies al cambio térmico puede ayudar a predecir los potenciales cambios espaciales y las tendencias poblacionales detonadas por el calentamiento global en curso. Evaluamos las variaciones inter- e intraespecíficas de la resistencia al calor en relación con la masa corporal, temperaturas locales promedio y las relaciones evolutivas para 39 especies de abejorros, un grupo primordial de polinizadores en ecosistemas templados y fríos, en tres continentes, seis biomas y 20 regiones (2,386 especímenes machos). Con base en bioanálisis experimentales, medimos el tiempo previo al letargo por calor de los abejorros machos a temperaturas de 40 °C, típicas de una ola de calor. La variabilidad interespecífica fue significativa, en contraste con la variabilidad interpoblacional, lo cual fue consistente con el hecho de que la resistencia al calor sea una característica específica de la especie. Además, las especies adaptadas al frío son mucho más sensibles al estrés por calor que las especies de clima templado o Mediterráneo. En relación con la sensibilidad a las temperaturas extremas, nuestros resultados ayudan a explicar las recientes declinaciones poblacionales y cambios en la distribución de los abejorros posteriores al cambio climático.

When more is more: taking advantage of species diversity to move towards sustainable aquaculture.

Human population growth has increased demand for food products, which is expected to double in coming decades. Until recently, this demand has been met by expanding agricultural area and intensifying agrochemical-based monoculture of a few species. However, this development pathway has been criticised due to its negative impacts on the environment and other human activities. Therefore, new production practices are needed to meet human food requirements sustainably in the future. Herein, we assert that polyculture practices can ensure the transition of aquaculture towards sustainable development. We review traditional and recent polyculture practices (ponds, recirculated aquaculture systems, integrated multi-trophic aquaculture, aquaponics, integrated agriculture-aquaculture) to highlight how they improve aquaculture through the coexistence and interactions of species. This overview highlights the importance of species compatibility (i.e. species that can live in the same farming environment without detrimental interactions) and complementarity (i.e. complementary use of available resources and/or commensalism/mutualism) to achieve efficient and ethical aquaculture. Overall, polyculture combines aspects of productivity, environmental protection, resource sharing, and animal welfare. However, several challenges must be addressed to facilitate polyculture development across the world. We developed a four-step conceptual framework for designing innovative polyculture systems. This framework highlights the importance of (i) using prospective approaches to consider which species to combine, (ii) performing integrated assessment of rearing environments to determine in which farming system a particular combination of species is the most relevant, (iii) developing new tools and strategies to facilitate polyculture system management, and (iv) implementing polyculture innovation for relevant stakeholders involved in aquaculture transitions.

City-Scale Dark Fiber DAS Measurements of Infrastructure Use During the COVID-19 Pandemic.

Throughout the recent COVID-19 pandemic, real-time measurements about shifting use of roads, hospitals, grocery stores, and other public infrastructure became vital for government decision makers. Mobile phone locations are increasingly assimilated for this purpose, but an alternative, unexplored, natively anonymous, absolute method would be to use geophysical sensing to directly measure public infrastructure usage. In this paper, we demonstrate how fiber-optic distributed acoustic sensing (DAS) connected to a telecommunication cable beneath Palo Alto, CA, successfully monitored traffic over a 2-month period, including major reductions associated with COVID-19 response. Continuous DAS recordings of over 450,000 individual vehicles were analyzed using an automatic template-matching detection algorithm based on roadbed strain. In one commuter sector, we found a 50% decrease in vehicles immediately following the order, but near Stanford Hospital, the traffic persisted. The DAS measurements correlate with mobile phone locations and urban seismic noise levels, suggesting geophysics would complement future digital city sensing systems.

Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails.

In agriculture, diversifying production implies picking up, in the wild biodiversity, species or populations that can be domesticated and fruitfully produced. Two alternative approaches are available to highlight wild candidate(s) with high suitability for aquaculture: the single-trait (i.e. considering a single phenotypic trait and, thus, a single biological function) and multi-trait (i.e. considering multiple phenotypic traits involved in several biological functions) approaches. Although the former is the traditional and the simplest method, the latter could be theoretically more efficient. However, an explicit comparison of advantages and pitfalls between these approaches is lacking to date in aquaculture. Here, we compared the two approaches to identify best candidate(s) between four wild allopatric populations of Perca fluviatilis in standardised aquaculture conditions. Our results showed that the single-trait approach can (1) miss key divergences between populations and (2) highlight different best candidate(s) depending on the trait considered. In contrast, the multi-trait approach allowed identifying the population with the highest domestication potential thanks to several congruent lines of evidence. Nevertheless, such an integrative assessment is achieved with a far more time-consuming and expensive study. Therefore, improvements and rationalisations will be needed to make the multi-trait approach a promising way in the aquaculture development.

Global quieting of high-frequency seismic noise due to COVID-19 pandemic lockdown measures.

Human activity causes vibrations that propagate into the ground as high-frequency seismic waves. Measures to mitigate the coronavirus disease 2019 (COVID-19) pandemic caused widespread changes in human activity, leading to a months-long reduction in seismic noise of up to 50%. The 2020 seismic noise quiet period is the longest and most prominent global anthropogenic seismic noise reduction on record. Although the reduction is strongest at surface seismometers in populated areas, this seismic quiescence extends for many kilometers radially and hundreds of meters in depth. This quiet period provides an opportunity to detect subtle signals from subsurface seismic sources that would have been concealed in noisier times and to benchmark sources of anthropogenic noise. A strong correlation between seismic noise and independent measurements of human mobility suggests that seismology provides an absolute, real-time estimate of human activities.

TOFF, a database of traits of fish to promote advances in fish aquaculture.

Functional traits can be valuable pieces of information for aquaculture research and management. Although fish traits have been the focus of an abundant research, trait datasets for these organisms are difficult to access and often unpractical to achieve meta-analyses without a time-consuming extensive review. Already available large-scale compilations include trait information for many fish species but not as detailed as required for aquaculture purpose. Here, we introduce the TOFF (i.e. Traits OF Fish), a database focusing on fish functional traits that aims at bringing together behavioral, morphological, phenological, and physiological traits always coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. Here, we release data for 228 traits for 174 species extracted from 165 publications and present a collaborative platform. We ultimately aim at providing an inclusive and accessible data resource to facilitate advances in aquaculture development.

The cephalic labial gland secretions of two socially parasitic bumblebees Bombus hyperboreus (Alpinobombus) and Bombus inexspectatus (Thoracobombus) question their inquiline strategy.

Social parasitic Hymenopterans have evolved morphological, chemical, and behavioral adaptations to overcome the sophisticated recognition and defense systems of their social host to invade host nests and exploit their worker force. In bumblebees, social parasitism appeared in at least 3 subgenera independently: in the subgenus Psithyrus consisting entirely of parasitic species, in the subgenus Alpinobombus with Bombus hyperboreus, and in the subgenus Thoracobombus with B. inexspectatus. Cuckoo bumblebee males utilize species-specific cephalic labial gland secretions for mating purposes that can impact their inquiline strategy. We performed cephalic labial gland secretions in B. hyperboreus, B. inexspectatus and their hosts. Males of both parasitic species exhibited high species specific levels of cephalic gland secretions, including different main compounds. Our results showed no chemical mimicry in the cephalic gland secretions between inquilines and their host and we did not identify the repellent compounds already known in other cuckoo bumblebees.