During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood
. Here we report a ...large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
West Island is the second largest island in the Hainan Province, China and its surrounding sea area has a well-preserved coral reef ecosystem and high species diversity of coral reef fishes. ...Undoubtedly, coral reef fishes and coral reefs have complex symbiotic relationships and fish species diversity should reflect the healthy status of coral reef ecosystems. Environmental DNA (eDNA) is a useful and sensitive tool to detect fish species and causes less environmental damage than traditional fish survey methods. This paper investigated coral reef fish species of West Island, Hainan Province, China, based on eDNA and provided scientific data for understanding and protection of the coral reef ecosystem of the South China Sea.
The sea area surrounding West Island is the most important component of the coral reef ecosystem in the northern part of the South China Sea, which is also an essential part of the largest National Coral Reef Reserve in China. However, complete data of fish species distributed in this region have been a long-term gap. This study provides information on 41 fish species belonging to 28 genera, 16 families and three orders in this sea area and is the first complete record of coral reef fishes surrounding the West Island. In addition, the information of Molecular Operational Taxonomic Units (MOTUs) for taxon identification were also provided and it could contribute to building specific eDNA taxonomy database of coral reef fishes of the South China Sea. The study includes three datasets, with aspects of fish taxon-occurrences, MOTUs sequences and information of environmental indicators surrounding West Island, Hainan Province, China. The "fish taxon occurrences" dataset presents records involving taxonomic, distribution, habitat condition, latitude and longitude of 41 coral reef fish species detected, based on eDNA, the "MOTUs sequences" dataset provides MOTUs sequences and their abundance of 31 species detected and the "information of environmental indicators" dataset presents records of transparency, temperature, water pressure, dissolved oxygen, electrical conductivity, hydrogen and redox potential measured from five sampling localities.
Environmental DNA (eDNA) has been used in research relevant to fish ecology such as species diversity and conservation studies, threatened and invasive species monitoring, and analyses of population ...structure and distribution. How to choose the optimal laboratory protocols on the basis of the research targets is the first question to be considered when conducting an eDNA study. In this review, we searched 554 published articles using the topic subject ((eDNA or environmental DNA) and (fish)) within the time span 2011–2021 via Thompson Reuters Web of Science (WoS) and China National Knowledge Infrastructure (CNKI) literature databases, and screened 371 articles related to eDNA research on fish ecology. These articles were categorized into “article (334)”, “review (36)”, and “letter (1)” based on the type, and “article” was divided into “article (method research)” and “article (eDNA application)” in line with the study objectives. The experimental methods adopted in each study were reviewed, and advantages and disadvantages of the main protocols were analyzed for each step. We recommend a set of optimal protocols for regular eDNA-based fish diversity detection and present the following suggestions for water sample collection and subsequent sample processing and experiments. Sample size is suggested to be 2 L regardless of the type of water bodies; three water replicates are recommended per sampling site, and water collection sites should be designed to cover various water layers and micro-habitats within research areas. Filtration is the best method for collecting eDNA from the larger water samples; 0.45 μm glass fiber/glass microfiber (GF) filters and mixed cellulose acetate and nitrate (MCE) filters are recommended for use, and MCE filters are suitable for use in turbid waters; pre-filtration (>10 μm filtering membranes) can be used to prevent clogging. Freezing temperature storage can slow eDNA degradation, and this is the optimal way to store DNA no matter what filtering method is applied. The Qiagen DNeasy Blood and Tissue DNA extraction kit was the most economical and efficient DNA extraction method compared to other commercial kits. The 12S rRNA gene is the first choice for detecting interspecies variation in fishes, and five 12s primer sets, Ac12S, MDB07, Mi-Fish, Vert-12SV5, and Teleo, are recommended. The TruSeq DNA PCR-free LT Sample Prep kit and NEBNext DNA Library Prep Master Mix Set for the 454 kit can be chosen. The Illumina HiSeq platform can obtain sufficient data depth for fish species detection. QIIME and OBITools are independent software packages used for eDNA sequences analysis of fishes, and bioinformatic analyses include several indispensable steps such as filtering raw reads, clustering filtered reads into molecular operational taxonomic units (MOTUs) or amplicon sequence variants (ASVs), and completing taxon annotation. Contamination, inhibition, lack of reference DNA data, and bioinformatic analysis are key challenges in future eDNA research, and we should develop effective experimental techniques and analysis software regarding these aspects. This review intends to help eDNA beginners to quickly understand laboratory protocols applied in fish ecological research; the information will be useful for the improvement and development of eDNA techniques in the future.
Wuzhizhou Island (WZZ) is located in Haitang Bay in the northern region of Sanya, Hainan Island. The sea area surrounding WZZ represents a typical tropical marine ecosystem, characterised by diverse ...and complex habitats. Therefore, there is a rich variety of marine fish species at WZZ. The marine ecosystem of WZZ was seriously destroyed initially in the 1970s-1980s and recovered in the 1990s, then constructed as the first national tropical marine ranch demonstration area of China in 2019. As fish is an important high trophic vertebrate in the marine ecosystem, understanding the composition and distribution of fish species could help us to recognise the status of the ecosystem of WZZ and supply scientific data for construction of the national marine ranch demonstration area. This study used eDNA technology to investigate the composition of fish community surrounding WZZ and provided a scientific basis for realising and protecting the marine ecosystem of the South China Sea. The WZZ is an offshore island in the South China Sea, harbouring abundant marine fish resources. Although previous research investigated fish species of WZZ, the data were, however, still incomplete due to limitation of sampling methods and survey seasons. In this study, we intended to take advantage of eDNA and supplement data of fish species at WZZ as much as possible. Based on eDNA, this study provided the data on 188 fish species (including nine undetermined species denoted by genus sp.) belonging to 17 orders, 63 families and 124 genera and they were the more comprehensive records of fish species surrounding WZZ. In addition, the information on Molecular Operational Taxonomic Units (MOTUs) for taxon identification was also provided, aiming to contribute to the establishment of a specific eDNA taxon database for fish of the South China Sea. This study included two datasets, which were occurrences of fish taxa at WZZ, as well as MOTUs sequences and geographical coordinate information of sampling sites. The “fish taxon occurrences” dataset presented records on taxonomic, distribution and habitat conditions of 188 fish species detected using eDNA, as well as the latitude and longitude information of the sampling sites, the "MOTUs information" dataset provided the MOTUs sequences, source of sequences, abundance of sequences for 188 fish species, also included the species matched in NCBI and the best NCBI BLAST sequence similarity.
Short‐term temporal variation of coastal marine eDNA Jensen, Mads Reinholdt; Sigsgaard, Eva Egelyng; Ávila, Marcelo de Paula ...
Environmental DNA (Hoboken, N.J.),
July 2022, Volume:
4, Issue:
4
Journal Article
Peer reviewed
Open access
Temporal variation in eDNA signals is increasingly explored for understanding community ecology in aquatic habitats. Seasonal changes have been addressed using eDNA sampling, but very little is known ...regarding short‐term temporal variation that spans hours to days. To address this, we filtered marine water samples from a single coastal site in Denmark every hour for 32 h. We used metabarcoding to target both fish and broader eukaryote diversity and evaluated temporal changes in this marine community. Results revealed variation in fish species richness (15–27) and eukaryote class richness (35–64) across the 32 h of sampling, and we further evaluated sampling efforts needed to reach different levels of diversity saturation. Relative read frequency data for both fish and eukaryotes indicated a clear diel change in community composition, with different communities detected during daylight versus dark hours. The abundance signals in our data reflected biological variation rather than stochastic variation, since replicates taken at the same hour were more similar to each other than those taken at different hours. Our compositional results indicated a dynamic community, rather than a static pool of eDNA—even across a few hours. The fish data showed a daily pattern of relative species abundances, and the uncoupling of fish and broader eukaryote data suggest that variation in eDNA profiles across a single day can provide valuable information reflecting diel changes, at least for highly mobile organism groups. However, our results also point to several pitfalls in current eDNA experimental design, in which samples are taken over large areas without relative time‐consistency or short‐term replication. Our findings shed new light on short‐term variation in coastal eDNA and have wide implications for experimental study design and for incorporating temporality into project conceptualization for future aquatic biodiversity monitoring.
Short‐term temporal variation in eDNA has been largely unexplored. We here show that fish and eukaryote communities at a coastal site change throughout the day, reflecting known biology of the species in question. These findings are important to consider regarding experimental design for future studies
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
AIM: To compile an inventory of freshwater fish species in China, and to investigate these data to determine spatial patterns in species richness, endemism and threatened species for the purpose of ...facilitating conservation. LOCATION: China METHODS: Literature, databases and fish collections were examined to create an inventory database of freshwater fishes of China. This list was analysed to determine species richness, endemism and threatened species. spss and origin software were used to determine relationships between these three parameters across the area and length of river basins. Coefficients of fish diversity for each major river were calculated using the Gleason Index. RESULTS: Chinese freshwater fish fauna is comprised of 1323 species; the majority of species belong to Cypriniformes and Cyprinidae. Of 877 species endemic to China, 161 of 199 threatened species are endemic, with most classified as ‘endangered’ (85 species) or ‘vulnerable’ (70). Species endemism and the number of threatened species correlate positively with species richness. River basin area and length have no direct bearing on either species richness or endemism. The Pearl River was identified as the most species‐rich system. It also has the most endemic and threatened fish species. MAIN CONCLUSIONS: China's vast size, variable geography and climate influence patterns in species diversity and endemism. Its freshwater fish fauna is rich and largely endemic and a significant number of these endemic species are threatened. Dam construction, water pollution, overfishing and invasive species pose threats to native biodiversity. National assessment of threatened species is urgently needed. The Yangtze, Yellow and Pearl rivers require prioritized national protection. Environmental effects of development require serious consideration and, potentially, proactive conservation efforts and mitigation. Development on international rivers needs to consider environmental policies of all countries owning spans of the systems, particularly the wishes and concerns of nations with lower spans of a system.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NMLJ, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UILJ, UKNU, UL, UM, UPUK
China is currently in a strategic opportunity period for green and high-quality development, and developing the digital economy is an important choice to achieve environmental pollution control, ...improve regional ecological efficiency, and enhance social welfare. In this context, the impact of the digital economy on ecological well-being performance and the role of environmental regulation need to be examined. In this study, the super-efficiency SBM-DEA model was used to measure the level of ecological well-being performance in 30 provinces of China from 2011 to 2019. On this basis, the mediating effect model and spatial Durbin model were adopted to explore the transmission mechanism and regional heterogeneity of the impact of the digital economy on ecological well-being performance. The empirical results show that the digital economy significantly contributes to regional ecological well-being performance in China, and there is significant spatial spillover as well. Moreover, the findings still hold under robustness tests. The results also show that environmental regulation is an important transmission path for the digital economy to enhance regional ecological well-being performance, and the impact of environmental regulation on ecological well-being performance varies by region; specifically, the impact in eastern China is positive but not significant. However, the digital economy plays a significant positive role in promoting ecological well-being performance in the central and western regions, and is more obvious in the central region. Finally, suggestions are put forward to enhance the role of the digital economy in regional ecological well-being performance, which is of great significance for promoting green economic growth and high-quality development.
Understanding the substitution effect and creation effect of digital transformation on the manufacturing industry is crucial to safeguarding employment stability and advancing manufacturing ...sophistication in China’s contemporary context. In this study, a bilateral stochastic frontier model is used to examine the aforementioned effects drawing on provincial panel data of China spanning 2011 to 2020. The study reveals that: Firstly, the substitution effect of digital economy development on manufacturing employment outweighs the creation effect, culminating in a 7.80% decrease below the frontier benchmark, contrasted by a 4.15% increase attributed to the creation effect. The two effects possess an inverse relationship, collectively inducing a 3.66% decline in manufacturing employment as compared to the frontier. Secondly, the prevailing influence of the digital economy upon manufacturing employment is predominantly characterized by the substitution effect. However, projected medium to long term trajectories intimate a diminishing potency of this substitution effect and the creation effect will become more pronounced. Thirdly, in terms of geographical areas, the weakening of the employment-substitution effect due to the digital economy is most evident in the central region, followed by the western, and then the eastern regions. Conclusively, the impact of the digital economy on manufacturing employment exhibits variances contingent upon distinct economic maturation and disparate human capital stratification.
•In this study, transcriptome analysis of mantle tissue of P. fucata with a black shell and red shell under different salinity stress.•GO functional annotation showed that the DEGs of P. fucata with ...two shell colors under different salinity stress were mainly annotated in cell part, cell, binding and cellular process.•The study showed that high salt stress had a greater influence on P. fucata with two shell colors, and P. fucata with a black shell made a positive immune defense response.•Our results will improve to further understand the salt tolerance mechanism of P. fucata with different shell colors.
To understand the molecular responses of Pinctada fucata with different shell colors to salinity stress, we used transcriptome sequencing on the mantle of P. fucata with a black shell and red shell color under the salinity of 20, 35, and 50. The 414 and 2371 differentially expressed genes (DEGs) in P. fucata with a black shell under low- or high-salt stress, while there were 588 and 3009 DEGs in P. fucata with a red shell. KEGG pathway enrichment analysis showed that, under low salt stress, the DEGs of P. fucata with the black shell were significantly enriched in pathways MAPK signaling pathway, protein processing in endoplasmic reticulum, vitamin B6 metabolism, longevity regulating pathway-multiple species, estrogen signaling pathway and antigen processing and presentation, the DEGs of P. fucata with a red shell were significantly enriched in pathways vitamin B6 metabolism. Under high salt stress, the DEGs of P. fucata with a red shell were significantly enriched in pathways arginine biosynthesis. 11 DEGs were randomly selected for quantitative real-time PCR, and the results were consistent with the RNA-seq. In addition, under high salt stress, DEGs were enriched into some pathways related to osmotic regulation and immune defense of P. fucata with black shell and red shell, such as Glycolysis / Gluconeogenesis, AMPK signaling pathway, Beta-Alanine metabolism, Glycine, serine and threonine metabolism, MAPK signaling pathway and Phagosome. The study showed that high salt stress had a greater influence on P. fucata with two shell colors, and P. fucata with a black shell made a positive immune defense response. Our results will improve to further understand the salt tolerance mechanism of P. fucata with different shell colors.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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