Biology subjects

Mariani, S.

Publications and source records attributed to Mariani, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A quantitative approach to species occupancy across communities: the co-occurrence-occupancy curve

Species tolerating the same environmental conditions can potentially colonize and thrive in the same habitats and eco-regions. Are any pair of those species equally probable to co-occur in the same community? Can we quantify the propensity of two species to co-occur together? Here, we focus on a simple but largely overlooked community-level pattern: the co-occurrence-occupancy curve, which relates the tendency of species to co-occur with others to their total occupancy across sites. We first define this empirical curve and then derive its expected shape under a random null model that assumes site equivalence and species independence. Building on these results, we introduce the Species Association Index (SAI), an occupancy-standardized measure that quantifies the tendency of a species to associate with others independently of its overall frequency of occurrence. The SAI enables meaningful comparisons among species with contrasting occupancies and provides a transparent benchmark against which departures from neutrality can be assessed. We illustrate the approach using two contrasting systems--tropical rain forest trees on Barro Colorado Island and organisms from Mediterranean rocky shores--highlighting both the generality of the co-occurrence-occupancy framework and its limitations.

ecology↗

bioRxiv2025

Volatilized ammonia supports extremophilic cave ecosystems with unusual nitrogen isotopic signatures

The sulfidic Frasassi cave system hosts a robust, subterranean ecosystem based on microbial lithoautotrophy. Curiously, acidic biofilms forming above degassing sulfidic cave streams, and the invertebrates that feed on them, are extremely depleted in nitrogen-15 ({delta}15N values less than -20{per thousand}). In this study, we tested the hypothesis that these low {delta}15N values result from the volatilization, trapping, and uptake of ammonia degassed from the circumneutral streams. We found that dissolved ammonium in the streams had {delta}15N values near +3{per thousand}, whereas NH3(g) in the cave atmosphere above streams exhibited {delta}15N values as low as -27{per thousand}, consistent with fractionation by NH3 volatilization. Extremely acidic condensation droplets on cave walls efficiently trapped airborne NH3, accumulating up to 4 mM NH4+ with {delta}15N values as low as -29{per thousand}, thereby confirming volatilized and trapped ammonia as the primary N source to cave wall biofilms and the extensive subsurface ecosystem they support. Airborne ammonia trapping represents a novel mechanism for biological N acquisition and provides abundant N for growth in an extreme subsurface environment that otherwise receives very limited nutrient input. SignificanceNitrogen is one of the most abundant elements in organic molecules, and is a key limiting nutrient in many ecosystems. We showed that acidic microbial biofilms in sulfidic caves scavenge trace amounts of airborne ammonia, enabling microbial primary production and supporting associated food webs, including animals, in an environment where nitrogen is otherwise extremely scarce. This process represents a novel mechanism of biological nutrient acquisition and results in biomass and organic matter more depleted in the heavy isotope of nitrogen (15N) than almost all other biological materials on Earth. Extreme 15N isotope depletion is therefore a potential signature of acidic underground ecosystems on Earth and other planetary bodies.

microbiology↗

bioRxiv2025

Integrating citizen science and field sampling into next-generation early warning systems for vector surveillance: Twenty years of municipal detections of Aedes invasive mos-quito species in Spain

The spread of invasive mosquitoes Aedes albopictus, Aedes aegypti and Aedes japonicus in Spain represents an increasing public health risk due to their capacity to transmit arboviruses such as dengue, Zika and chikungunya among others. Traditional field entomological surveillance remains essential for tracking their spread, but it faces limitations in terms of cost, scalability and labor intensity. Since 2014, the Mosquito Alert citizen science project has enabled public participation in the surveillance through the submission of geolocated images via a mobile app, which are identified using AI in combination to expert validation. While field surveillance provides high accuracy, citizen science offers low-cost, large-scale real-time data collection aligned to open data managment principles. It is particularly useful for detecting long-distance dispersal events and has contributed up to one-third of the municipal detections of invasive mosquito species since 2014. This study assesses the value of integrating both surveillance systems to capitalize on their complementary strengths while compensating weaknesses in the areas of taxonomic accuracy, scalability, spatial detection patterns, data curation and validation systems, geographic precision, interoperability and real-time output. We present the listing of municipal detections of these species from 2004 to 2024, integrating data from both sources. Spains integrated approach demonstrates a pioneering model for cost-effective, scalable vector surveillance tailored to the dynamics of invasive species and emerging epidemiological threats. Simple SummarySpain, with its diverse ecological and climatic landscapes, represents a key area for the introduction and establishment of invasive mosquito species, posing threats to public health due to their capacity to transmit human diseases. Field entomological surveillance conducted by experts remains the primary tool for tracking their spread, though it is limited by geographical scales and cost factors. Advances in smartphone technology allows citizen science strategies of data collection such as submitting mosquito photos via the Mosquito Alert app. This type of information is of a different nature from the field sampling and still needs expert interpretation, but offers significantly broader and faster geographical coverage. Two decades have passed since the first detection of the Asian tiger mosquito in Spain in 2004, and following the Mosquito Alert creation in 2014, citizen science has contributed with one-third of the discoveries of this species at the municipal level in Spain. We discuss integration of both approaches in order to harness their respective strengths while compensating their drawbacks, to develop faster and more powerful early warning surveillance systems, and also returning value to the society by empowering citizenship.

ecology↗

bioRxiv2025

Opportunistic diver-assisted eDNA sampling unpicks fine-scale ecological and conservation signals in tropical reef fishes

Coral reefs are emblematic ecosystems of astonishing biological diversity and significant economic value for many countries, yet they are increasingly vulnerable to direct and indirect human-related threats, such as heavy tourism and global warming. To assess the biodiversity status, track assemblage changes and forecast future trends of these megadiverse ecosystems, there is pressing need for accurate, rapid and comprehensive assessments of fish communities. Here, we employed a versatile low-tech passive environmental DNA collector, the metaprobe, in association with the recreational activity of scuba divers to collect eDNA data from reefs in the Seychelles archipelago and assess both the taxonomic and functional fish diversity of the area. Using a fish-specific 12S marker on eDNA metaprobe samples collected during 18 dives, we detected 174 fish taxa, eight elasmobranchs and 166 teleosts, corresponding to 112 unique functional entities and including iconic tropical reef taxa, endangered elasmobranchs and commercially valuable species. Despite the geographic proximity of dive sites, we identified ecological patterns of fish composition and community structure influenced by both the presence of marine protected areas (MPAs) and the type of predominant substrate (i.e., coral vs rocky). Ecological differences between MPA/non-MPA and coral/rocky habitats involved both taxonomic and functional community elements, which returned very similar patterns of significantly higher fish diversity in protected and coral areas. We argue that simple, inexpensive eDNA-based collection tools in association with recreational activities, such as scuba diving, provide a promising approach for upscaling ecological data collection and expanding biodiversity monitoring, while engaging and empowering the public.

ecology↗

bioRxiv2025

Recovering historical fish eDNA from museum-preserved Antarctic filter feeders via non-destructive metabarcoding.

O_LIRecent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. C_LIO_LIIn this study, we evaluated the feasibility of extracting historical fish eDNA from the ethanol preservative used to store Antarctic museum specimens. We compared a variety of extraction methods - centrifugation, evaporation, filtration, and precipitation - using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a Bryozoa and two Porifera, i.e., Demospongiae and Hexactinellida. C_LIO_LIComparative analyses with tissue biopsies revealed that the total genomic DNA was significantly reduced for non-destructive approaches. However, 10 ml ethanol filtration performed equal to, or in some instances, outperformed tissue biopsies when investigating the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (-diversity) and community characterisation ({beta}-diversity). C_LIO_LIOur findings demonstrate the potential of ethanol preservative as a valuable, non-destructive source of historical fish eDNA from museum-stored filter-feeding specimens. These results highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic research. C_LI

ecology↗

bioRxiv2025

Refining a molecular tool kit to capture tropicalization in Mediterranean Marine Protected Areas

Tropicalization, the process by which tropical species expand their ranges poleward due to global ocean warming, is a prominent threat to Mediterranean marine ecosystems, challenging their effective management and conservation. The arrival of non-indigenous fish is exacerbated by the Suez Canal that allows Indo-Pacific species to enter the region from the Red Sea. While some non-indigenous species (NIS) have already changed the composition and function of native Mediterranean communities, many others continue to arrive but often go unnoticed without regular surveys or until they are strongly established. We conducted biodiversity surveys using underwater visual census (UVC), aqueous environmental DNA (eDNA) and sponge-derived eDNA (i.e., eDNA accumulated in sea sponge tissue) at two protected locations in Zakynthos, Greece. Seven NIS were detected by eDNA, but only one (dusky spinefoot, Siganus luridus) was detected with all three methods. The fish assemblages of the two locations could be distinguished based on both UVC and eDNA but not from sponge-derived eDNA data, perhaps given low filtration rates. Of the three methods, aqueous eDNA metabarcoding provided the most comprehensive species list including new NIS detected (with the red-toothed triggerfish, Odonus niger, and the houndfish, Tylosurus crocodilus, being the first and third record in the Mediterranean Sea, respectively). Our findings highlight the potential value of incorporating molecular methods into regular monitoring as early warning tools for detecting NIS in marine protected areas threatened by ocean warming.

ecology↗

bioRxiv2025

DNA Divers: volunteer-based eDNA capture for local and global marine biodiversity monitoring

Volunteer-based biodiversity recording is a powerful source of scalable data yet to be used to its full potential by the scientific community. Coastal ecosystems are varied and diverse, making it difficult for managers to identify flexible methods for monitoring biological components. Emerging technologies such as environmental DNA (eDNA) analysis are promising for measuring aquatic biodiversity, yet most management organizations lack personnel and capacity to collect molecular data. Here we investigate, together as professional and non-professional scientists, the efficacy of a quasi-passive eDNA capture technique. Volunteer SCUBA divers and snorkelers used low-cost materials, namely cotton medical gauze, to capture eDNA via swimming. We compared this method to conventional eDNA capture techniques in an aquarium and nature, collectively iterating the field and laboratory procedures to improve feasibility. With a small (< 30) network of volunteers, we detected 275 unique teleost and elasmobranch species from varied marine habitats spanning 90 degrees of latitude. The swimming motion of divers was more effective than stationary soaking and the fish communities sampled by divers were comparable to that of conventional eDNA samples. The ease of this technique matched by the eagerness and generosity of volunteers presents an untapped, viable approach for scaling multi-species marine eDNA monitoring as well as an avenue for improving science literacy. Data availabilityhttps://zenodo.org/records/14853820?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImYxMTlhODFiLTI3NGYtNDQ2Ni05MDYyLTIyOTlkNWVhY2FkNiIsImRhdGEiOnt9LCJyYW5kb20iOiIwYmZlMzJhMWU0YWZkM2ZhMWEwYTE0NmY0ZWM5YWZkNSJ9.0R7GJjVJLEuq-UJVKA1CcMT8LCTamv3GEvPl-5ItzP10pFRd-cAzAr_Q5ggjEewZUtByHjBu-eSegWWlLAx_Rw

ecology↗

bioRxiv2025

Complementary assessment of fish biodiversity across the upper/lower mesophotic interface in a subtropical coral reef using eDNA metabarcoding and baited cameras

Mesophotic Coral Ecosystems (MCEs) occur in the middle to lower photic zone ([~]30-150 m) of tropical and subtropical regions, are often extensions of shallow reef communities, and generally hold great importance for local commercial fisheries. Compared to their shallower counterpart, MCEs have been traditionally understudied, primarily due to their inaccessibility with traditional monitoring methodologies. In this study, we aim to provide an interdisciplinary assessment of the biodiversity of Bermudan reef fish communities from the upper/lower mesophotic interface (60 m) by utilising a combination of environmental DNA (eDNA) metabarcoding and baited remote underwater videos (BRUVs). In total, 155 species from 137 genera were detected by eDNA metabarcoding whilst a total of 85 species from 53 genera were detected by BRUVs. The combined species detections totalled 182 species with approximately half of those detections unique to this study when compared to previous studies. Both methodologies found differences in -diversity between study locations, with each method independently detecting the highest species richness at the same location. The species assemblage at each location was dominated ([~]80%) by species known to occur throughout the shallow reef system and the upper mesophotic, whilst species only known to inhabit mesophotic ecosystems accounted for [~]6% at each location. These findings suggest a high level of species continuity with the adjacent shallower reef systems. The complementary nature of eDNA metabarcoding and BRUVs allows for a more accurate characterisation of fish biodiversity at the upper/lower mesophotic interface, which can lead to a more comprehensive understanding of ecosystem structure and more informed management decisions.

ecology↗

bioRxiv2024

Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection

Ecosystem monitoring is a fundamental tool to avert biodiversity loss, gathering valuable information that can be used to develop conservation policies, evaluating management outcomes, and guiding science-based decision-making. The Mar Menor costal lagoon (South-East of Spain) has experienced episodes of eutrophication due to intensive agriculture and other human activities, causing mass mortalities of marine fauna. In this scenario, biodiversity monitoring is crucial to evaluate the status of fauna and flora and take appropriate measures. Here, our main objective was to assess faunal composition and its spatial and temporal structure associated with the pillars used to support the built recreational well-being facilities along the Mar Menor. We capitalised on the many sea sponges that settle on these structures by collecting tissue samples for subsequent extraction of filtered environmental DNA (i.e. natural sampler DNA, nsDNA) in northern and southern areas of the lagoon, both in spring and summer. We metabarcoded all samples at the cytochrome oxidase subunit I gene (COI), and reliably identified 76 taxa belonging to nine different phyla, with annelids, poriferans, molluscs and cnidarians being the richest groups. We detected emblematic species of threatened status, such as pipefishes (genus Syngnathus) and the piddock clam, Pholas dactylus, and others known to become invasive, such as the ascidians Styela canopus and Botrylloides niger, the barnacle Amphibalanus amphitrite, and the polychaetes Branchiomma bairdi and Branchiomma boholense. The use of common and widely distributed sponges as natural eDNA samplers allowed us to characterise both spatial and temporal diversity, further emphasizing the importance of this low-cost approach to monitoring biological communities in shallow coastal ecosystems.

ecology↗

bioRxiv2024

Unlocking Antarctic molecular time-capsules - recovering historical environmental DNA from museum-preserved sponges

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA (heDNA), trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

molecular biology↗

bioRxiv2022

Shark-dust: High-throughput DNA sequencing of processing residues unveils widespread trade in threatened sharks and rays

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g. fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded shark-dust samples from seven processing plants in the worlds biggest shark landing site (Java, Indonesia), and identified 54 shark and ray taxa (representing half of all chondrichthyan orders), half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded. One-Sentence SummaryShark-dust, the traces of biological material left behind from the processing of shark products, can now be DNA-sequenced in bulk to accurately reconstruct the biodiversity underlying trade.

genetics↗

bioRxiv2022

Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots

Trade restrictions for many endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, the variety of products and the complexity of import/export routes make trade monitoring challenging. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitate in-situ monitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 species (including 22 CITES-listed species) commonly encountered in landing sites and export hubs to test a recently developed real-time PCR single-assay originally developed for screening bony fish. We employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine learning assignment methods, we distinguished 25 out of 28 species, 20 of which were CITES-listed. With further refinement, this method can provide a practical tool for monitoring elasmobranch trade worldwide, without the need for a lab or the bespoke design of species-specific assays. HighlightsO_LIWe applied a portable, universal, closed-tube DNA barcoding approach originally developed for bony fishes to distinguish between shark and ray species traded in Indonesia. C_LIO_LIWe built a deep machine learning model to automatically assign species from the qPCR fluorescence spectra produced by two barcodes C_LIO_LIThe model achieved 79.41% accuracy for classifying 28 elasmobranch species, despite the barcode regions being designed for teleost species C_LIO_LIThis tool can serve as a potent single-assay in-situ diagnostic tool to regulate trade operations and it will be significantly enhanced by further optimisation of the barcode regions to fit elasmobranch DNA sequence variation C_LI

genetics↗

bioRxiv2022

Multiple invasions, Wolbachia and human-aided transport drive the genetic variability of Aedes albopictus in the Iberian Peninsula

The Asian tiger mosquito, Aedes albopictus, is a highly invasive species that has been spreading rapidly throughout tropical and temperate regions worldwide since the late 1970s. On the Iberian Peninsula, it was first recorded in 2004 near Barcelona. Since then, the species has spread along the Mediterranean coast and is now colonising the Peninsulas inner territories. As with other species of the genus Aedes, the spread of the tiger mosquito has been linked to global shipping routes and road networks. In particular, the transport of adult mosquitoes by car has been shown to augment its natural spreading capacity by orders of magnitude. Much remains unknown, however, about the impact of human-mediated dispersal on the genetic variability of this species. This study aimed to ascertain the factors that have contributed to the spread and the current genetic variation of Ae. albopictus across the Iberian Peninsula, through complex dispersal mechanisms and endosymbiosis with bacteria like Wolbachia. We do so through population genetic analysis of mitochondrial (COI) and nuclear (ITS2) DNA sequences. Overall, both COI and ITS2 markers showed a lack of genetic structure among sampled regions and the presence of worldwide dominant haplotypes, suggesting a pattern of multiple introductions from abroad. We found extremely low levels of variation in COI compared to ITS2, and this lack of mitochondrial polymorphism is likely explained by high Wolbachia prevalence (79%). Multilevel models revealed that greater mosquito fluxes (estimated from commuting patterns and tiger mosquito population distribution) and spatial proximity between sampling sites were associated with lower ITS2 genetic distance, suggesting that rapid short- and medium-distance dispersal is facilitated by humans through vehicular traffic. This study highlights the significant role of human transportation in shaping the genetic attributes of Ae. albopictus and promoting regional gene flow, and underscores the need for a territorially integrated surveillance across scales of this disease-carrying mosquito. Author SummaryThe tiger mosquito, Aedes albopictus, is one of the most invasive species in the world. Native to the tropical forests of Southeast Asia, over the past 30 years it has rapidly spread throughout tropical and temperate regions of the world. Its dramatic expansion has resulted in public health concerns as a consequence of its vector competence for at least 16 viruses. Previous studies showed that Ae. albopictus spread has been facilitated by human-mediated transportation, but much remains unknown about how this has affected its genetic attributes. Here we examined the factors that contributed to shaping the current genetic constitution of Ae. albopictus in the Iberian Peninsula, where the species was first found in 2004, by combining population genetics and Bayesian modelling. We found that both mitochondrial and nuclear DNA markers showed a lack of genetic structure and the presence of worldwide dominant haplotypes, suggesting regular introductions from abroad. Mitochondrial DNA showed little genetic diversity compared to nuclear DNA, likely explained by infection with maternally transmitted bacteria of the genus Wolbachia. Our models indicated that human transportation plays a role in shaping Ae. albopictus nuclear genetic structure by means of passive dispersal of adult tiger mosquitoes through the road network.

genetics↗

bioRxiv2022

Optimised DNA isolation from marine sponges for natural sampler DNA (nsDNA) metabarcoding

Marine sponges have recently been recognised as natural samplers of environmental DNA (eDNA) due to their effective water filtration and their ubiquitous, sessile and regenerative nature. However, laboratory workflows for metabarcoding of sponge tissue have not been optimised to ensure that these natural samplers achieve their full potential for community survey. We used a phased approach to investigate the influence of DNA isolation procedures on the biodiversity information recovered from sponges. In Phase 1, we compared three treatments of residual ethanol preservative in sponge tissue alongside five DNA extraction protocols. The results of Phase 1 informed which ethanol treatment and DNA extraction protocol should be used in Phase 2, where we assessed the effect of starting tissue mass on extraction success and whether homogenisation of sponge tissue is required. Phase 1 results indicated that ethanol preservative may contain unique and/or additional biodiversity information to that present in sponge tissue, but blotting tissue dry generally recovered more taxa and generated more sequence reads from the wild sponge species. Tissue extraction protocols performed best in terms of DNA concentration, taxon richness and proportional read counts, but the non-commercial tissue protocol was selected for Phase 2 due to cost-efficiency and greater recovery of target taxa. In Phase 2 overall, we found that homogenisation may not be required for sponge tissue and more starting material does not necessarily improve taxon detection. These results combined provide an optimised DNA isolation procedure for sponges to enhance marine biodiversity assessment using natural sampler DNA metabarcoding.

molecular biology↗

bioRxiv2022

Environmental DNA persistence and fish detection in captive sponges

Large and hyper-diverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as natural samplers of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the journey of eDNA particles in the sponge tissues, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA from three encrusting sponge species and how these compare with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the chosen natural samplers in certain habitats and regions.

ecology↗

bioRxiv2021

Estuarine molecular bycatch as a landscape-wide biomonitoring tool

Environmental DNA analysis is rapidly transforming biodiversity monitoring and bolstering conservation applications worldwide. This approach has been assisted by the development of metabarcoding PCR primers that are suited for detection of a wide range of taxa. However, little effort has gone into exploring the value of the non-target DNA sequences that are generated in every survey, but subsequently discarded. Here we demonstrate that fish-targeted markers widely employed in aquatic biomonitoring can also detect birds and mammals present in the surrounding habitats. We showcase this feature in three temperate estuaries over multiple seasons, where dozens of bird and mammal species offer valuable insights into spatial and temporal faunal variation. Our results indicate that existing metabarcode sequence data sets are suitable for mining and exploration of this molecular by-catch, and that any future eDNA-based surveys can be designed to accommodate this enhanced property of this widely applicable tool.

ecology↗

bioRxiv2020

Disentangling the shark and ray trade in Indonesia to reconcile conservation with food security

Indonesian marine resources are among the richest on the planet, sustaining highly diverse fisheries and includes the largest elasmobranch landings in the world, making Indonesia one of the worlds largest exporters of shark and ray products. Socio-economic and food security considerations pertaining to Indonesian communities add further layers of complexity to the management and conservation of these vulnerable species. This study investigates how shark and ray trade flows in and out of Indonesia and attempts to examine patterns and drivers of the current scenario. We identify substantial discrepancies between reported landings and declared exports, and between Indonesian exports in shark fin and meat products and the corresponding figures reported by importing countries. These mismatches are estimated to amount to over $43.6M and $20.9M for fins and meat, respectively, for the period between 2012 and 2018. Although the declared exports are likely to be an underestimation because of significant unreported or illegal trading activities, we find that domestic consumption of shark and ray products plays a significant role in explaining these discrepancies due to the increasing local demand for meat. The study also unearths a general scenario of unsystematic data collection and lack of granularity of product terminology, which is inadequate to meet the challenges of over-exploitation, illegal trade and food security in Indonesia. We discuss how to improve data transparency to support trade regulations and governance actions, by improving inspection measures, and conserving elasmobranch populations without neglecting the socio-economic dimension of this complex system.

scientific communication and education↗

bioRxiv2020

Unexpected redundancy of Gpr56 and Gpr97 during hematopoietic cell development and differentiation

Integrated molecular signals regulate cell fate during embryonic hematopoietic stem cell (HSC) generation. The G-protein coupled receptor 56 (Gpr56) is the most highly-upregulated receptor gene in cells that take on hematopoietic fate and it is expressed by adult bone marrow HSCs. Although Gpr56 is required for hematopoietic stem/progenitor cell (HS/PC) generation in zebrafish embryos, its function in mammalian hematopoiesis remains unclear. Here we examine the role of Gpr56 in HS/PC development in Gpr56 conditional knockout (cKO) mouse embryos and Gpr knockout (KO) embryonic stem cell (ESC) hematopoietic differentiation cultures. Our results show a myeloid bias of Gpr56 cKO fetal liver HSCs and an increased definitive myeloid progenitor cell frequency in Gpr56KO ESC differentiation cultures. Surprisingly, we find that mouse Gpr97 rescues Gpr56 morphant zebrafish hematopoietic generation, and that Gpr97 expression is upregulated in mouse Gpr56 deletion models. When both Gpr56 and Gpr97 are deleted in ESCs, no/few HS/PCs are generated upon ESC differentiation. Together, our results reveal novel and redundant functions for these two G-protein coupled receptors in normal mammalian hematopoietic cell development and differentiation.

developmental biology↗