Riverine distribution of mussel environmental DNA reflects a balance among density,transport, and removal processes

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Assessment of fish communities using environmental DNA: Effect of spatial sampling design in lentic systems of different sizes

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)‐based methods have been shown to be highly sensitive and cost‐efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA‐detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA‐based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.     

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA‐based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water‐limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus‐specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non‐African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over‐representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100‐fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.     

The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding

Environmental DNA (eDNA) is a promising tool for rapid and noninvasive biodiversity monitoring. eDNA density is low in environmental samples, and a capture method, such as filtration, is often required to concentrate eDNA for downstream analyses. In this study, six treatments, with differing filter types and pore sizes for eDNA capture, were compared for their efficiency and accuracy to assess fish community structure with known fish abundance and biomass via eDNA metabarcoding. Our results showed that different filters (with the exception of 20‐μm large‐pore filters) were broadly consistent in their DNA capture ability. The 0.45‐μm filters performed the best in terms of total DNA yield, probability of species detection, repeatability within pond and consistency between ponds. However performance of 0.45‐μm filters was only marginally better than for 0.8‐μm filters, while filtration time was significantly longer. Given this trade‐off, the 0.8‐μm filter is the optimal pore size of membrane filter for turbid, eutrophic and high fish density ponds analysed here. The 0.45‐μm Sterivex enclosed filters performed reasonably well and are suitable in situations where on‐site filtration is required. Finally, prefilters are applied only if absolutely essential for reducing the filtration time or increasing the throughput volume of the capture filters. In summary, we found encouraging similarity in the results obtained from different filtration methods, but the optimal pore size of filter or filter type might strongly depend on the water type under study.     

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding

Environmental DNA (eDNA) is the DNA suspended in the environment (e.g., water column), which includes cells, gametes, and other material derived from but not limited to shedding of tissue, scales, mucus, and fecal matter. Amplifying and sequencing marker genes (i.e., metabarcoding) from eDNA can reveal the wide range of taxa present in an ecosystem through analysis of a single water sample. Metabarcoding of eDNA provides higher resolution data than visual surveys, aiding in assessments of ecosystem health. This study conducted eDNA metabarcoding of two molecular markers (cytochrome c oxidase I (COI) and 18S ribosomal RNA (rRNA) genes) to survey eukaryotic diversity across multiple trophic levels in surface water samples collected at three sites along the coral reef tract within the Florida Keys National Marine Sanctuary (FKNMS) during four research cruises in 2015. The 18S rRNA gene sequences recovered 785 genera while the COI gene sequences recovered 115 genera, with only 33 genera shared between the two datasets, emphasizing the complementarity of these marker genes. Community composition for both genetic markers clustered by month of sample collection, suggesting that temporal variation has a larger effect on biodiversity than spatial variability in the FKNMS surface waters. Sequences from both marker genes were dominated by copepods, but each marker recovered distinct phytoplankton groups, with 18S rRNA gene sequences dominated by dinoflagellates and COI sequences dominated by coccolithophores. Although eDNA samples were collected from surface waters, many benthic species such as sponges, crustaceans, and corals were identified. These results show the utility of eDNA metabarcoding for cataloging biodiversity to establish an ecosystem baseline against which future samples can be compared in order to monitor community changes.     

Geographic variation and environmental correlates of apparent survival rates in adult tree swallows Tachycineta bicolor

Determining demographic rates in wild animal populations and understanding why rates vary are important challenges in population ecology and conservation. Whereas reproductive success is reported frequently for many songbird species, there are relatively few corresponding estimates of annual survival for widespread populations of the same migratory species. We incorporated mark–recapture data into Cormack–Jolly–Seber models to estimate annual apparent survival and recapture rates of adult male and female tree swallows Tachycineta bicolor in eight local breeding populations across North America for periods of 7–33 yr. We found strong site‐specific and annual variation in apparent survival rates of adult swallows, and evidence of higher survival or site fidelity among males than females. There were no strong associations between putative overwintering region and survival. Strength and patterns of winter climate‐apparent survival relationships varied across four sites monitored for >15 yr; at one site, spring pond conditions, local spring precipitation and, to a lesser extent, winter North Atlantic Oscillation Index were credible predictors of annual apparent survival. Further work is needed to evaluate how survival is related to environmental conditions throughout the annual cycle and how these factors affect population dynamics of swallows and related species of conservation concern.     

Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure

The distribution of guanine and cytosine nucleotides throughout a genome, or the GC content, is associated with numerous features in mammals; understanding the pattern and evolutionary history of GC content is crucial to our efforts to annotate the genome. The local GC content is decaying toward an equilibrium point, but the causes and rates of this decay, as well as the value of the equilibrium point, remain topics of debate. By comparing the results of 2 methods for estimating local substitution rates, we identify 620 Mb of the human genome in which the rates of the various types of nucleotide substitutions are the same on both strands. These strand-symmetric regions show an exponential decay of local GC content at a pace determined by local substitution rates. DNA segments subjected to higher rates experience disproportionately accelerated decay and are AT rich, whereas segments subjected to lower rates decay more slowly and are GC rich. Although we are unable to draw any conclusions about causal factors, the results support the hypothesis proposed by Khelifi A, Meunier J, Duret L, and Mouchiroud D (2006. GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol. 62:745-752.) that the isochore structure has been reshaped over time. If rate variation were a determining factor, then the current isochore structure of mammalian genomes could result from the local differences in substitution rates. We predict that under current conditions strand-symmetric portions of the human genome will stabilize at an average GC content of 30% (considerably less than the current 42%), thus confirming that the human genome has not yet reached equilibrium.     

Responses of foraminifera communities to aquaculture‐derived organic enrichment as revealed by environmental DNA metabarcoding

Current monitoring methods to assess benthic impacts of marine finfish aquaculture are based on complex biological indices and/or geochemistry data. The former requires benthic macrofauna morpho‐taxonomic characterization that is time‐ and cost‐intensive, while the latter provides rapid assessment of the organic enrichment status of sediments but does not directly measure biotic impacts. In this study, sediment samples were collected from seven stations at six salmon farms in British Columbia, Canada, and analyzed for geochemical parameters and by eDNA metabarcoding to investigate linkages between geochemistry and foraminifera. Sediment texture across farm sites ranged from sand to silty loam, while the maximum sediment pore‐water sulphide concentration at each site ranged from 1,000 to 13,000 μM. Foraminifera alpha diversity generally increased with distance from cage edge. Adonis analyses revealed that farm site explained the most variation in foraminifera community, followed by sediment type, enrichment status, and distance from cage edge. Farm‐specific responses were observed in diversity analyses, taxonomic difference analyses, and correlation analyses. Results demonstrated that species diversity and composition of foraminifera characterized by eDNA metabarcoding generated signals consistent with benthic biodiversity being impacted by finfish farming activities. This substantiates the validity of eDNA metabarcoding for augmenting current approaches to benthic impact assessments by providing more cost‐effective and practicable biotic measures than traditional morpho‐taxonomy. To capitalize on this potential, further work is needed to design a new nomogram that combines eDNA metabarcoding data and geochemistry data to enable accurate monitoring of benthic impacts of fish farming in a time‐ and cost‐efficient way.     

Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016–0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.     

Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90–0.99) vs. 0.58 (CI = 0.50–0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.     

Biomass encounter rates limit the size scaling of feeding interactions

The rate that consumers encounter resources in space necessarily limits the strength of feeding interactions that shape ecosystems. To explore the link between encounters and feeding, we first compiled the largest available dataset of interactions in the marine benthos by extracting data from published studies and generating new data. These data indicate that the size‐scaling of feeding interactions varies among consumer groups using different strategies (passive or active) to encounter different resource types (mobile or static), with filter feeders exhibiting the weakest feeding interactions. Next, we used these data to develop an agent‐based model of resource biomass encounter rates, underpinned by consumer encounter strategy and resource biomass density. Our model demonstrates that passive strategies for encountering small, dispersed resources limits biomass encounter rates, necessarily limiting the strength of feeding interactions. Our model is based on generalisable assumptions, providing a framework to assess encounter‐based drivers of consumption and coexistence across systems.     

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.     

Life history influences rates of climatic niche evolution in flowering plants

Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.     

基于环境DNA技术的赤水河秋季鱼类多样性分布特征

赤水河是长江上游少有的仍保持自然流态的大型一级支流,是长江鱼类重要的繁衍场和珍稀物种的保护地,摸清其鱼类多样性现状及鱼类群落结构特征对赤水河水生态恢复评估极为重要。于2021年9月对赤水河流域开展了鱼类多样性、分布及其特征调查,全流域共设置52个采样点,采用环境DNA技术采集并研究了赤水河鱼类的组成及其分布。结果显示通过环境DNA方法共调查到鱼类6目18科62属77种,包含16种长江特有鱼类。以鲤形目为主,占总数的87.87%。赤水河鱼类食性以杂食性和肉食性鱼类为主,群落结构上,处于下层水环境鱼类较多;赤水河鱼类优势种为宽鳍鱲(Y=0.205)、西昌华吸鳅(Y=0.085)、麦穗鱼(Y=0.068)、乌苏拟鲿(Y=0.033)、云南光唇鱼(Y=0.027);赤水河上游和下游鱼类群落(P<0.01)和Shannon-Wiener指数差异均显著(P<0.05)。海拔、流速、pH、电导率和温度是影响赤水河鱼类多样性的主要环境因素。为环境DNA技术在赤水河鱼类多样性调查中的应用提供了探索性研究,将有助于赤水河生物多样性的保护。     

环境DNA技术在宜昌江段四大家鱼自然繁殖中的应用

本研究通过环境DNA(eDNA)技术的样品采集及DNA提取方法,采用微滴式数字PCR(ddPCR)技术检测了长江干流宜昌江段不同水层、不同断面四大家鱼的eDNA浓度,分析了eDNA浓度变化与卵苗密度的关系,探讨了利用eDNA技术监测四大家鱼自然繁殖情况的可行性.结果 表明:与传统调查结果相比,四大家鱼的eDNA浓度与卵...     

Sampling large geographic areas for rare species using environmental DNA: a study of bull trout Salvelinus confluentus occupancy in western Montana

This study tested the efficacy of environmental DNA (eDNA) sampling to delineate the distribution of bull trout Salvelinus confluentus in headwater streams in western Montana, U.S.A. Surveys proved fast, reliable and sensitive: 124 samples were collected across five basins by a single crew in c. 8 days. Results were largely consistent with past electrofishing, but, in a basin where S. confluentus were known to be scarce, eDNA samples indicated that S. confluentus were more broadly distributed than previously thought.     

基于环境DNA宏条形码技术的辽东湾典型围海养殖池塘内水母多样性研究

研究使用环境DNA宏条形码技术(eDNA metabarcoding)检测辽东湾东北部河口区围海养殖池塘水母种类多样性,探索适用于水母种类物种鉴定和监测的新方法。利用环境DNA宏条形码技术,分别基于18S rDNA和COI宏条形码检测了辽东湾东北部河口区围海养殖池塘水母种类多样性,通过水样采集、过滤、eDNA提取、遗传标记扩增、测序与生物信息分析的环境DNA宏条形码标准化分析流程,从围海养殖池塘7个采样点中获得可检测的采样点数据。结果显示,基于18S rDNA宏条形码检测出8种水母种类,其中钵水母纲大型水母2种、水螅水母总纲小型水母6种;基于COI宏条形码技术共检测出19种水母种类,其中钵水母纲大型水母5种、水螅水母总纲小型水母14种;两种DNA条形码标记都显示养殖种类海蜇(Rhopilema esculentum)为优势种。研究结果表明,环境DNA宏条形码技术作为一种新兴的生物多样性监测手段可用于快速检测水母种类多样性,在水母类物种鉴定、监测及早期预警中有较大的应用潜能。     

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.     

Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding is an increasingly popular tool for measuring and cataloguing biodiversity. Because the environments and substrates in which DNA is preserved differ considerably, eDNA research often requires bespoke approaches to generating eDNA data. Here, we explore how two experimental choices in eDNA study design—the number of PCR replicates and the depth of sequencing of PCR replicates—influence the composition and consistency of taxa recovered from eDNA extracts. We perform 24 PCR replicates from each of six soil samples using two of the most common metabarcodes for Fungi and Viridiplantae (ITS1 and ITS2), and sequence each replicate to an average depth of ~84,000 reads. We find that PCR replicates are broadly consistent in composition and relative abundance of dominant taxa, but that low abundance taxa are often unique to one or a few PCR replicates. Taxa observed in one out of 24 PCR replicates make up 21–29% of the total taxa detected. We also observe that sequencing depth or rarefaction influences alpha diversity and beta diversity estimates. Read sampling depth influences local contribution to beta diversity, placement in ordinations, and beta dispersion in ordinations. Our results suggest that, because common taxa drive some alpha diversity estimates, few PCR replicates and low read sampling depths may be sufficient for many biological applications of eDNA metabarcoding. However, because rare taxa are recovered stochastically, eDNA metabarcoding may never fully recover the true amplifiable alpha diversity in an eDNA extract. Rare taxa drive PCR replicate outliers of alpha and beta diversity and lead to dispersion differences at different read sampling depths. We conclude that researchers should consider the complexity and unevenness of a community when choosing analytical approaches, read sampling depths, and filtering thresholds to arrive at stable estimates.