Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness ...of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict (
R
² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
•Environmental DNA samples were taken seasonally in a Marine Protected Area.•Vulnerable species were mostly detected in the Fully Protected Area.•eDNA metabarcoding revealed seasonal changes in ...community composition.•Fish composition changes were detected along a depth gradient.•eDNA is useful for frequent monitoring in MPAs to guide management strategies.
Marine fish communities suffer from anthropogenic pressures and climate change, which influence their spatio-temporal dynamics. Marine Protected Areas (MPAs) have been established worldwide to preserve these communities, while mesophotic ecosystems could provide natural refugia. Assessing the extent to which MPAs and deeper ecosystems can mitigate human and climate change impacts requires regular monitoring of temporal community dynamics. Environmental DNA (eDNA) surveys – being time- and cost-effective – can provide valuable insights on biodiversity change. Here, we initiated a long-term study based on eDNA monitoring in an MPA in the north-western Mediterranean Sea that includes areas with various protection levels. Specifically, from June 2021 to January 2023, we collected eDNA samples during the summer, fall, and winter seasons from shallow water (20 m depth), at 40 m depth, and from the mesophotic zone (80 m depth) in a Fully Protected Area (FPA) and in a nearby Lightly Protected Area (LPA) in the Riou archipelago (France). In this short period and relatively small area, we detected a total of 113 actinopterygian and chondrichthyan taxa. Species with high fishing vulnerability had higher detection rates in the FPA than in the LPA, suggesting a positive impact of FPAs on the conservation of these threatened species. A marked seasonal signal in species detections, including significantly lower detections of several species in winter, indicated a combined effect of species biological changes and migration behavior. The seasonality trend was stronger in the FPA than in the LPA, indicating that such areas may modify sub-yearly patterns in communities and ecosystem processes. Fish composition was associated with water depth, with marked species dissimilarities between shallow waters and the mesophotic zone, implying that multiple depths should be considered in MPA monitoring to fully capture the response of biodiversity to management. Our results point to the importance of temporal information combined with extensive sampling across depths and protection levels to fully understand the ecological dynamics and structure of coastal fish communities.
Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing ...subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual‐based surveys. However, eDNA‐based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling‐theory methods to estimate species richness in under‐sampled and hyper‐diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the ‘Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower‐bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies.
Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled ...about the diversity and evolutionary history of these 'living fossils' using new molecular data, including the possibility of 'cryptic' species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.
The link between biodiversity and ecosystem functioning has been the topic of considerable research, but it remains unclear how biodiversity decline is compromising ecosystem functionality, ...particularly in the pelagic realm. Here, we explore how pelagic fish species diversity relates to functional diversity by sampling two locations, which, on the basis of biogeography, environmental conditions and human pressures, were expected to host pronounced differences in species composition and abundances and therefore functionality. Strings of five drifting mid-water Baited Remote Underwater Video Systems were used to survey pelagic vertebrate diversity and abundance in two isolated oceanic island systems, the Malpelo Fauna and Flora Sanctuary—a large, 25-year-old marine protected area—and an unprotected area in Cape Verde. Functional diversity, which offers insight into a community’s resilience against disturbance, was analysed using six key functional traits of marine fishes. Abundance was recorded as Max
N
, the maximum number of individuals of a given species in a single frame during the 2-h deployment time. Cape Verde showed high overall abundance (Total Max
N
873) and low biomass (3559 kg), with a predominance of smaller fishes. Malpelo showed high biomass (7839 kg) but lower abundance (Total Max
N
465), with a predominance of large species. Species and functional diversity were marginally different between locations. Multivariate analysis of species relative abundances showed significant divergence between locations, although community functional traits overlapped strongly, suggesting that both communities share a similar structure and vulnerability. The existence of a common functional ‘backbone’ in diverging species communities across the oceans, under different productivity regimes, and under different protection levels, suggests that although pelagic communities may differ considerably in terms of species composition, this does not translate into a differing functional structure and resilience potential. Whether this vulnerability is a common feature of pelagic communities and how this contrasts with benthic systems warrants further research.
Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and ...nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long‐term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
Uso de ADN Ambiental en la Evaluación de la Diversidad Funcional y Filogenética de los Peces
Resumen
La evaluación del impacto de los cambios globales y la efectividad de la protección es un paso fundamental para el monitoreo de peces marinos. La mayoría de los métodos tradicionales de censos son demandantes o destructivos, por lo que las estrategias no letales y no intrusivas basadas en videograbaciones y en el ADN ambiental (ADNa) son alternativas a los censos visuales submarinos y a la pesca. Sin embargo, todavía no se conoce la habilidad que tienen estos métodos para detectar diferentes factores de la biodiversidad más allá de la diversidad taxonómica. Para los peces óseos y los elasmobranquios, comparamos el desempeño de la caracterización genética con ADNa y del video remoto de larga duración para evaluar la diversidad funcional y filogenética de las especies. Usamos diez muestras de ADNa tomadas de 30 litros de agua cada una y 25 horas de vídeos submarinos grabados durante cuatro días en la Isla Malpelo (costa del Pacífico de Colombia), un área marina protegida remota. La caracterización genética con el ADNa detectó 66% más unidades taxonómicas moleculares operacionales (UTMOs) que el video. Encontramos 66 y 43 entidades funcionales con un solo marcador de ADNa y con el video, respectivamente, y una riqueza funcional más alta para el ADNa que el video. A pesar de los vacíos en las bases de datos genéticos usadas como referencia, el ADNa también detectó una diversidad filogenética más alta que aquella en los videos; las curvas de acumulación mostraron cómo un solo transecto de ADNa detectó tanta diversidad filogenética como 25 horas de video. La caracterización genética con ADN ambiental puede usarse para censar los factores de biodiversidad de manera asequible, eficiente y certera en los sistemas marinos. Aunque las atribuciones taxonómicas todavía están limitadas por la cobertura de especies en las bases de datos genéticos de referencia, el uso de los UTMOs resalta el potencial que tiene la caracterización genética con ADNa una vez que las bases de datos de referencia sean expandidas.
摘要
评估全球变化影响及保护有效性是海洋鱼类监测的关键步骤。然而, 大多数传统种群调查方法都有较高的要求或具有破坏性。基于视频和环境 DNA 的非干扰性、非致死性方法则是水下视觉调查或鱼类捕捞的替代方法。然而, 这些方法检测传统分类学多样性之外其它生物多样性因子的能力尚不清楚。本研究关注硬骨鱼类和软骨鱼类, 比较了环境 DNA宏条形码和长期远程视频监测在评估物种的系统发育多样性和功能多样性中的表现情况。我们在一个偏远的海洋保护区——马尔佩洛岛 (哥伦比亚太平洋海岸) , 收集了10个分别取自 30 升水体的环境 DNA 样品, 以及4天共25小时的水下视频。结果发现, 环境 DNA 宏条形码比水下视频多检测出66%的分子操作分类单元 (MOTUs) 。我们利用单一环境DNA标记或视频分别发现了66个和 43 个功能实体, 利用环境 DNA 检测出的功能丰富度高于水下视频。尽管遗传参考数据库仍存在一些空缺, 但环境DNA 还是比视频检测出更高的鱼类系统发育多样性;累积曲线展示了1个环境 DNA 样带检测到的系统发育多样性相当于25小时的水下视频。环境 DNA 宏条形码可以经济、有效且准确地用于调查海洋系统中的生物多样性因子。尽管分类学鉴定仍受到遗传参考数据库中物种覆盖范围的限制, 但 MOTUs 的使用显现了在参考数据库得到扩充后环境 DNA 宏条形码所具备的潜力。【翻译:胡怡思;审校:聂永刚】
The intensification of warming-induced mass-mortalities in invertebrate populations including in temperate regions is a critical global issue. Mesophotic zones (30–150 m depth) have been suggested as ...potential refuges from climate change for gorgonian populations, offering hope for reseeding damaged shallow populations. Using a proteomic approach, we investigated the responses and acclimatization ability of the yellow gorgonian
Eunicella cavolini
along an environmental gradient following reciprocal transplantations between shallow (20 m) and mesophotic (70 m) zones. Our findings indicate that yellow gorgonians from mesophotic waters exhibit a greater plasticity when transplanted to shallow waters, compared to shallow gorgonians transplanted to the mesophotic zone at 70 m. Transplanted colonies from mesophotic to shallow waters showed an increasing level of proteins involved in immune response but displayed no signs of necrosis or apoptosis, highlighting the acclimation potential of mesophotic populations. These results suggest that
Eunicella cavolini
populations may exhibit physiological plasticity in response to future climate change, allowing natural colonization from mesophotic populations. This analysis offers valuable insights into gorgonians' cellular and molecular responses to environmental changes.
DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA ...barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA‐based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo‐Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA‐based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA‐based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo‐Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.
Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose ...biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
in Spanish is available with online material.
Resumen
Los estuarios se caracterizan por un régimen de mareas y están fuertemente influenciados por la hidrodinámica, albergando hábitats diversos y muy dinámicos, desde agua dulce, salobre o salada hasta terrestre, cuya biodiversidad es especialmente difícil de monitorear. Aquí investigamos el potencial del metabarcoding del ADN ambiental (eDNA), con tres pares de marcadores dirigidos a diferentes regiones del gen 12S del ADN mitocondrial en el ARN ribosomal, para detectar la diversidad de vertebrados en el estuario del río Don Diego en Colombia. Con el eDNA, detectamos no sólo organismos acuáticos, incluyendo peces, anfibios y reptiles, sino también una gran diversidad de vertebrados terrestres, arborícolas y voladores, incluyendo mamíferos y aves, que viven en los alrededores del estuario. Además, la señal de eDNA se mantuvo relativamente localizada a lo largo del curso de agua. Un transecto desde la sección exterior profunda del estuario, a través de la desembocadura del río hacia la sección interior del mismo, mostró un marcado cambio taxonómico desde los típicos peces marinos a los de agua dulce, mientras que el eDNA de las especies terrestres y arborícolas se encontró principalmente en la sección interior del estuario. Nuestros resultados indican que el eDNA permite detectar una gran diversidad de vertebrados y podría convertirse en una herramienta importante para el seguimiento de la biodiversidad en los estuarios, donde el agua integra la información de todo el ecosistema.
eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, ...amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non‐overlapping assemblages rather than subsets of one another. As a result, non‐saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false‐negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
Biodiversity estimates from eDNA metabarcoding often uncover only a portion of the diversity in a location. We discover that for species‐rich areas, such as coral reefs, we may need more samples than previously thought to recover and monitor biodiversity in a local area.
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