基于环境DNA宏条形码技术的北京地区鱼类多样性调查和外来鱼种入侵风险评估

[目的]调查北京地区鱼类多样性和群落分布及评估外来鱼种的入侵风险.[方法]选取北京地区水库、湖泊和河流3种水体类型共33个采样点,于2020年6月10—17日开展水生态监测,利用环境DNA宏条形码技术对各样点的鱼类多样性和群落结构进行监测和分析,对目前北京地区水生态系统中本地鱼种和外来鱼种进行分类汇总,并评估典型外来入...     

Relationships between taxonomic and functional components of diversity: implications for conservation of tropical freshwater fishes

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Structure and diversity of fishes in a freshwater and coastal subtropical lagoon

This study examined the fish communities of Peri Lagoon in southern Brazil to aid in the development of an effective management plan because the area is under threat from human activities. Sampling of fish fauna, ichthyoplankton and limnological data were compared between sites, differing by habitat type and characteristics such as depth, substratum composition and vegetation type. Results were significantly related to site, with the highest diversity and abundance recorded at shallow vegetated sites. A total of 14 fish species were recorded throughout the lagoon, with the most abundant being Hyphessobrycon luetkenii. Of the 14 species, half were sampled at their larval stage, suggesting a healthy and protected system. Significantly more larvae and eggs were collected during colder months (autumn to winter) and at sites closer to stream flow, possibly owing to increased food sources and habitat protection. This study highlights the importance of Peri Lagoon as a nursery ground for a wide range of fish species, providing essential information for incorporation into the future protection of fish stocks throughout Brazil.     

Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

Current methods for monitoring marine fish (including bony fishes and elasmobranchs) diversity mostly rely on trawling surveys, which are invasive, costly, and time‐consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we used environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues, or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5 L‐water samples were collected onboard a wide‐scale oceanographic survey covering about 120,000 square kilometers in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality‐filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel, and blue whiting), but eDNA metabarcoding resulted in more detected bony fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fishes biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad‐scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.     

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.     

江西柘林水库鱼类群落结构及功能多样性分析

为了解江西柘林水库鱼类群落结构和多样性的时空变化特征,研究鱼类物种多样性和功能多样性的关系,于2020年9月至2021年4月在该水库调查分析了鱼类物种组成、优势度及群落物种多样性和功能多样性。结果表明,共采集鱼类53种,分属于5目12科36属。其中,鲤形目(38种)种类最多,占调查物种数的71.69%,柘林水库上、中、下游库区分别采集到鱼类36、40和32种,各库区均以鲤形目鱼类为主,分别占采集物种数的72.97%、85.00%和75.00%。优势物种主要是■(Hemiculter leucisculus)、鳙(Aristichthys nobilis)和黄尾鲴(Xenocypris davidi),重要种主要是草鱼(Ctenopharyngodon idella)、鲢(Hypophthalmichthys molitrix)、鳊(Parabramis pekinensis)、鲫(Carassius auratus)、蒙古红鲌(Erythroculter mongolicus)等。鱼类群落结构季节性差异大于空间格局差异,主要表现为秋季和冬季之间;生物多样性指数Margalef和功能丰富...     

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA‐based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high‐throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2 . Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3 ) and 41 (dada2 ) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA‐based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large‐scale capture‐based conventional methods. Our results suggest that eDNA‐based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.     

Responses of taxonomic distinctness and species diversity indices to anthropogenic impacts and natural environmental gradients in stream macroinvertebrates

1. Many studies have shown traditional species diversity indices to perform poorly in discriminating anthropogenic influences on biodiversity. By contrast, in marine systems, taxonomic distinctness indices that take into account the taxonomic relatedness of species have been shown to discriminate anthropogenic effects. However, few studies have examined the performance of taxonomic distinctness indices in freshwater systems. 2. We studied the performance of four species diversity indices and four taxonomic distinctness indices for detecting anthropogenic effects on stream macroinvertebrate assemblages. Further, we examined the effects of catchment type and area, as well as two variables (pH and total phosphorus) potentially describing anthropogenic perturbation on biodiversity. 3. We found no indications of degraded biodiversity at the putatively disturbed sites. However, species density, rarefied species richness, Shannon's diversity and taxonomic diversity showed higher index values in streams draining mineral as opposed to peatland catchments. 4. Of the major environmental gradients analysed, biodiversity indices showed the strongest relationships with catchment area, lending further support to the importance of stream size for macroinvertebrate biodiversity. Some of the indices also showed weak linear and quadratic relationships to pH and total phosphorus, and residuals from the biodiversity index‐catchment area regressions (i.e. area effect standardized) were more weakly related to pH and total phosphorus than the original index values. 5. There are a number of reasons why the biodiversity indices did not respond to anthropogenic perturbation. First, some natural environmental gradients may mask the effects of perturbation on biodiversity. Secondly, perturbations of riverine ecosystems in our study area may not be strong enough to cause drastic changes in biodiversity. Thirdly, multiple anthropogenic stressors may either increase or decrease biodiversity, and thus the coarse division of sites into reference and altered streams may be an oversimplification. 6. Although neither species diversity nor taxonomic distinctness indices revealed anthropogenic degradation of macroinvertebrate assemblages in this study, the traditional species diversity and taxonomic distinctness indices were very weakly correlated. Therefore, we urge that biodiversity assessment and conservation planning should utilize a number of different indices, as they may provide complementary information about biotic assemblages.     

连江鱼类群落多样性及其与环境因子的关系

目前连江梯级开发至12级,为了解梯级开发后连江鱼类群落状况,于2009年3月和2010年4月对连江上、中、下游7个代表江段的鱼类群落结构以及环境因子分别进行了调查,共采集鱼类98种,分属于9目20科75属。海南墨头鱼Garra pingi hainanensis、南方长须鳅鮀Gobiobtia longibarba meridionalis为连江新纪录种。银鮈Squalidus argentatus、黄颡鱼Pelteobagrus fulvidraco、小鳈Sarcocheilichthys parvus、马口鱼Opsariichthys bidens、餐Hemiculter lecuisculus等小型鱼类在鱼类群落结构中占优势地位。对鱼类群落进行聚类分析(CLUSTER)和非度量多维标度排序(NMDS)分析结果表明连江鱼类被划分为3个类群,即下游河口类群、中下游类群及中上游类群;S2、S3两个站位鱼类物种多样性(H’)、丰富度(D’)和均匀度(J’)均高于其他站位。通过对连江各站位鱼类群落与环境因子的典型对应分析发现:河宽、温度、海拔、pH值和水坝之间的距离5个因子与鱼类群落相关性较强(P<0.05)。与历史资料对比后发现,连江鱼类种类、分布、生态类型都发生了巨大变化。     

Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes

Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large‐scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.     

The effects of human disturbance on the species composition,species diversity and functional diversity of a Miombo woodland in northern Malawi

Anthropogenic disturbances have serious impacts on ecosystems across the world. Understanding the effects of disturbance on woodlands, especially in regions where local people depend on these natural resources, is essential for sustainable natural resource management and biodiversity conservation. In this study, we evaluated the effects of anthropogenic disturbance, specifically selective logging of Brachystegia floribunda, on woodlands by comparing species composition, species diversity and functional diversity of woody plants between disturbed and undisturbed woodlands. We combined species data and functional trait data for leaves, fruits and other traits related to resource and disturbance responses to calculate functional indices (functional richness, evenness and divergence) and community‐weighted means of each trait. Shifts in taxonomic species composition were analysed using nonmetric multi‐dimensional scaling. Species composition differed significantly between disturbed and undisturbed woodlands. Tree density was greater in disturbed woodlands, whereas evenness, functional evenness and functional divergence were greater in undisturbed woodlands. In terms of forest cover, selective logging of B. floribunda appeared to have little impact on Miombo woodlands, but some shifts in functional traits, such as the shift from a deciduous to evergreen phenology, may increase the vulnerability of these ecosystems to environmental change, especially drought.     

Geographic patterns and environmental correlates of phylogenetic relatedness and diversity for freshwater fish assemblages in North America

The tropical niche conservatism hypothesis suggests that most groups should be most phylogenetically clustered in cold, dry environments. This idea has been well-tested in plants and some animal groups, but not for fishes. We assess the geographic patterns of freshwater fish phylogenetic structure and investigate the relationships between these patterns and environmental variables across North America and within two biogeographic realms. Phylogenetic relatedness and diversity of 360 freshwater fish assemblages across North America were quantified with three metrics based on a well-dated phylogeny, and were related to 15 environmental variables using correlation and regression analyses. Geographically, the data were analyzed for North America as well as for separate biogeographic realms. We found that cold temperatures are the strongest determinant of phylogenetic clustering overall. However, in the arid west, clustering is most pronounced in the driest regions. In eastern North America, phylogenetic clustering increases at higher latitudes, while the reverse is true in western North America. The strongest phylogenetic clustering for freshwater fish assemblages on the continent is found in the most arid, rather than the coldest, climate in North America. Our results highlight that patterns of phylogenetic structure of freshwater fishes in North America are driven by both ecological and evolutionary processes that differ regionally.     

Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north‐eastern part of the Congo basin

This study evaluates the utility of DNA barcoding to traditional morphology‐based species identifications for the fish fauna of the north‐eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio ‘nearest‐neighbour distance/maximum intraspecific divergence’ was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.     

桂林岩溶石山青冈群落植物功能多样性和环境因子与坡向的关联研究

研究群落水平上的植物功能多样性和环境因子与不同坡向（阴坡、阳坡）的关联,有助于理解不同坡向上植物群落的形成过程及其构建机制。本研究以桂林岩溶石山不同坡向上的青冈群落为研究对象,分析阴坡、阳坡植物功能多样性指数和环境因子的变化规律及植物功能多样性指数与环境因子的相关性。研究结果表明：（1）不同坡向上的功能丰富度、功能均匀度、功能离散度和功能分离度指数均具有显著的差异,且均表现为阴坡大于阳坡。（2）不同坡向上的土壤全磷含量、岩石裸露率和土壤有效磷含量均具有显著的差异,土壤全磷含量表现为阴坡大于阳坡,而岩石裸露率和土壤有效磷含量表现为阳坡大于阴坡。（3）多元逐步回归分析结果表明,在阴坡上功能离散度和功能分离度分别与岩石裸露率呈显著的负相关,而在阳坡上其相关性不显著;在阳坡上功能均匀度与土壤全磷含量、功能分离度与土壤有效磷含量呈显著的正相关,而在阴坡上其相关性不显著。     

Ecological drivers of avian diversity in a subtropical landscape: Effects of habitat diversity,primary productivity and anthropogenic disturbance

Understanding the roles of ecological drivers in shaping biodiversity is fundamental for conservation practice. In this study, we explored the effects of elevation, conservation status, primary productivity, habitat diversity and anthropogenic disturbance (represented by human population density and birding history) on taxonomic, phylogenetic and functional avian diversity in a subtropical landscape in southeastern China. We conducted bird surveys using 1‐km transects across a total of 30 sites, of which 10 sites were located within a natural reserve. Metrics of functional diversity were calculated based on six functional traits (body mass, clutch size, dispersal ratio, sociality, diet and foraging stratum). We built simultaneous autoregression models to assess the association between the ecological factors and diversity of the local avian communities. Local avian diversity generally increased with increasing habitat diversity, human population density and primary productivity. We also detected phylogenetic and functional clustering in these communities, suggesting that the avian assemblages were structured mainly by environmental filtering, rather than interspecific competition. Compared with sites outside the natural reserve, sites within the natural reserve had relatively lower avian diversity but a higher level of phylogenetic heterogeneity.     

太子河流域鱼类功能群结构与多样性对土地利用类型的响应

研究河岸带土地利用方式对河流生物群落的影响对河岸带管理和河流生态系统修复至关重要。研究了太子河河岸带的土地利用类型(森林用地、森林耕作用地、耕地和城镇建设用地)和鱼类功能群的关系,结果表明:栖息地质量参数在不同土地利用类型内具有显著差异,森林用地区电导率、总溶解固体、淤泥和底质含沙量比例的平均值均较低,分别为(105.05μs/cm、80.38 mg/L、65.00 mL和0%),底质类型以石块为主;耕作区的水深、流量和淤泥的平均值均是最高(186.83 m、80.11 m~3和5333.33 mL),底质类型以沙质和淤泥为主。太子河流域鱼类功能群划分为5种类型(18个亚类),在不同土地利用类型内具有差异显著,森林用地内的鱼食性、石块栖功能群、昆虫食性和黏性卵功能群的比例最高;森林耕作用地内的植食性和底层栖功能群的比例最高;耕地内的沙栖功能群、中下层栖功能群和筑巢产卵功能群的比例最高;城镇建设用地内的淤泥栖功能群、耐污种、中下层栖功能群和杂食性功能群的比例最高。研究显示,栖息地评价得分高、栖境复杂的区域其个体数量较高,而栖息地得分低、底质类型以淤泥为主的区域其个体数量较低。     

Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next‐generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom‐designed group‐specific primer set and next‐generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture‐based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co‐occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture‐based methods, for improved mapping of species distribution patterns.