Can we manage fisheries with the inherent uncertainty from eDNA?

Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.     

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...     

分子标记技术在昆虫入侵研究中的应用

遗传变异与种群持续性及其进化潜力密切相关,而生物入侵导致种群遗传变异或遗传多样性的改变为研究自然界中各种生态和进化问题提供了理想模式。分子标记技术是调查种群遗传变异的重要工具,揭示了入侵种的入侵过程和结果,并预测未来的发生情况。本综述归纳了分子标记技术在昆虫入侵机制研究中的应用,以典型的研究个案为例,分别综述了分子标记技术在隐蔽入侵的监测应用,分子标记技术在重构入侵历史研究中的推算方式,分子标记技术在探索种群遗传变异与成功入侵机制方面取得的重要进展,并进一步介绍了高分辨率熔解曲线（high-resolution melting, HRM）分析在昆虫入侵研究中的应用前景。     

DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianus

Comparing introduced to ancestral populations within a phylogeographical context is crucial in any study aiming to understand the ecological genetics of an invasive species. Zaprionus indianus is a cosmopolitan drosophilid that has recently succeeded to expand its geographical range upon three continents (Africa, Asia and the Americas). We studied the distribution of mitochondrial DNA (mtDNA) haplotypes for two genes (CO‐I and CO‐II) among 23 geographical populations. mtDNA revealed the presence of two well‐supported phylogenetic lineages (phylads), with bootstrap value of 100%. Phylad I included three African populations, reinforcing the African‐origin hypothesis of the species. Within phylad II, a distinct phylogeographical pattern was discovered: Atlantic populations (from the Americas and Madeira) were closer to the ancestral African populations than to Eastern ones (from Madagascar, Middle East and India). This means that during its passage from endemism to cosmopolitanism, Z. indianus exhibited two independent radiations, the older (the Eastern) to the East, and the younger (the Atlantic) to the West. Discriminant function analysis using 13 morphometrical characters was also able to discriminate between the two molecular phylads (93.34 ± 1.67%), although detailed morphological analysis of male genitalia using scanning electron microscopy showed no significant differences. Finally, crossing experiments revealed the presence of reproductive barrier between populations from the two phylads, and further between populations within phylad I. Hence, a bona species status was assigned to two new, cryptic species: Zaprionus africanus and Zaprionus gabonicus, and both were encompassed along with Z. indianus and Zaprionus megalorchis into the indianus complex. The ecology of these two species reveals that they are forest dwellers, which explains their restricted endemic distribution, in contrast to their relative cosmopolitan Z. indianus, known to be a human‐commensal. Our results reconfirm the great utility of mtDNA at both inter‐ and intraspecific analyses within the frame of an integrated taxonomical project.     

中国外来入侵物种的分布与传入路径分析

外来物种入侵已成为全球性的环境问题,本文采用文献调研,实地考察与专家咨询相结合的方式,调查了全国陆生,淡水水生生态系统中外来入侵微生物,无脊椎动物,两栖爬行类,鱼类,鸟类,哺乳类,杂草,树木和海洋生态系统中外来入侵物种的种类及分类地位,起源,引入路径和环境影响等内容。查明我国共有283种外来入侵物种,其中外来入侵微生物,水生植物,陆生植物,水生无脊椎动物,陆生无脊椎动物,两栖爬行类,鱼类,哺乳类分别为19种,18种,170种,25种,33种,3种,10种和5种,来源于美洲,欧洲,亚洲,非洲,大洋洲的外来入侵物种分别占55.1%,21.7%,9.9%.8.1%和0.6%。我国对外来物种的引进存在一定程度的盲目性;50.%的外来入侵植物是作为牧草或饲料,观赏植物,纤维植物,药用植物,蔬菜,草坪模特而引进的;25%的外来入侵动物是用于养殖,观赏,生物防治的引种,对外来物种只重引进,疏于管理,也可能导致外来物种逃逸到自然环境中,造成潜在的环境意传入的;76.3%的外来入侵动物是由于检查不严,随贸易物品或运输工具传入我国的。因此,我国既要加强检疫工作,又要对外来物种的有意引进进行严格管理,实行外来物种引进的风险评估制度。     

外来种隐蔽入侵： 类型及影响

隐蔽入侵（cryptic invasion）是指在形态上与土著种（或早期建群种）不能或难以区分的外来种在人们未觉察的状态下成功入侵的过程。人们对这类入侵方式往往视而不觉。本文综述了外来种隐蔽入侵的类型以及生态影响。隐蔽入侵的类型主要包括外来姊妹种形式的隐蔽入侵、 不同遗传支系的隐蔽入侵、 不同地理种群的隐蔽入侵以及“返传入”。其中, “返传入”目前还是一种假说。由于这类入侵外来种更容易与土著种（或早期建群种）杂交或基因渗透, 因而可对入侵种自身或土著种产生深远的生态影响。鉴于隐蔽入侵现象的广泛性, 建议进一步加强该方面的研究。     

外来植物入侵对土壤生物多样性和生态系统过程的影响

随着科学家对生态系统地下部分的重视,评价外来植物入侵对土壤生态系统的影响成为当前入侵生态学领域的研究热点之一。本文综述了外来植物入侵对土壤微生物、土壤动物以及土壤碳、氮循环动态影响的研究,并探讨了其影响机制。已有的研究表明,植物入侵对土壤生物多样性及相关生态系统过程的影响均存在不一致的格局,影响机制也是复杂多样的。外来植物与土著植物凋落物的质与量、根系特征、物候等多种生理生态特性的差异可能是形成格局多样性和影响机制复杂性的最主要原因。今后,加强多尺度和多生态系统的比较研究、机制性研究、生物多样性和生态系统过程的整合性研究及土壤生态系统对植物入侵的反馈研究是评价外来植物入侵对土壤生态系统影响的发展趋势。     

基于分子生物学方法的外来入侵物种入侵历史重构

生物入侵是一个世界性的问题。全球每年因生物入侵造成的损失超过1万亿美元。探究入侵物种在入侵地的入侵历史对了解生物入侵的生物生态学机制、制定阻截及防除措施有重要意义。分子标记方法的兴起和大规模应用打开了入侵生物入侵历史研究的新天地。采用分子标记的方法可鉴定入侵物种的种类、追溯其来源地、回溯其扩散路径、分析扩散模式及探究物种入侵过程中对入侵种群本身的变化及其对生态系统所造成的各种影响。分子标记的应用使得多个入侵物种的入侵历史得以重现。由于分子标记方法重构的入侵历史受采样范围、采用的分子标记的种类及数量等因素的影响,该方法呈现入侵历史是否是真实发生的入侵过程还存在争议。     

The perils of plenty: what are we going to do with all these genes?

This new century's biology promises more of everything--more genes, more organisms, more species and, in short, more data. The flood of data challenges us to find better and quicker ways to summarize and analyse. Here, we present preliminary results and proofs of concept from three of our research projects that are motivated by our search for solutions to the perils of plenty. First, we discuss how models of evolution can accommodate change to better reflect the dynamics of sequence diversity, particularly when it is becoming a lot easier to obtain sequences at different times and across intervals where the probability of new mutations contributing to this diversity is high. Second, we describe our work on the use of a single locus for species delimitation; this research targets the new DNA-barcoding approach that aims to catalogue the entirety of life. We have developed a single-locus test based on the coalescent that tests the null hypothesis of panmixis. Finally, we discuss new sequencing technologies, the types of data available and the efficacy of alignment-free methods to estimate pairwise distances for phylogenetic analyses.     

Can filter‐feeding Asian carp invade the Laurentian Great Lakes? A bioenergetic modelling exercise

1. There is much concern that filter‐feeding Asian carp will invade the Laurentian Great Lakes and deplete crucial plankton resources. We developed bioenergetic models, using parameters from Asian carp and other fish species, to explore the possibility that planktonic food resources are insufficient to support the growth of silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) in the Great Lakes. 2. The models estimated basic metabolic requirements of silver and bighead carp under various body sizes, swimming speeds and reproductive stages. These requirements were then related to planktonic food resources and environmental temperature to predict when and where silver and bighead carp may survive in the Great Lakes, and how far they may travel. 3. Parameter values for respiration functions were derived experimentally in a coordinated study of silver and bighead carp, while consumption parameters were obtained from the literature on silver carp. Other model parameters lacking for Asian carp, such as those for egestion and excretion, were obtained from the literature on other fish species. 4. We found that full‐sized bighead carp required 61.0 kJ d^?1 just to maintain their body mass at 20 °C, approximately equivalent to feeding in a region with 255 μg L^?1 macrozooplankton (dry) or 10.43 μg L^?1 chlorophyll a. Silver carp energy requirements were slightly higher. 5. When applied to various habitats in the Great Lakes, our results suggest that silver and bighead carp will be unable to colonise most open‐water regions because of limited plankton availability. However, in some circumstances, carp metabolism at lower temperatures may be low enough to permit positive growth even at very low rations. Positive growth is even more likely in productive embayments and wetlands, and the modelled swimming costs in some of these habitats suggest that carp could travel >1 km d^?1 without losing biomass. 6. The simulation (and firmly hypothetical) results from this modelling study suggest when and where Asian carp could become established in the Great Lakes. Given the potential consequences to Great Lakes ecosystems if these filter feeders do prove capable of establishing reproducing populations, efforts to keep Asian carp out of the Great Lakes must not be lessened. However, we do encourage the use of bioenergetic modelling in a holistic approach to assessing the risk of Asian carp invasion in the Great Lakes region.     

Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)

DNA barcoding is a technique to identify species by using standardized DNA sequences. In this study, a total of 105 samples, representing 30 Parnassia species, were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As a single DNA marker, the ITS region provided the highest species resolution with 86.7%, followed by trnH-psbA with 73.3%. The combination of the core barcode regions, matK+rbcL, gave the lowest species identification success (63.3%) among any combination of multiple markers and was found unsuitable as DNA barcode for Parnassia. The combination of ITS+trnH-psbA achieved the highest species discrimination with 90.0% resolution (27 of 30 sampled species), equal to the four-marker combination and higher than any two or three marker combination including rbcL or matK. Therefore, matK and rbcL should not be used as DNA barcodes for the species identification of Parnassia. Based on the overall performance, the combination of ITS+trnH-psbA is proposed as the most suitable DNA barcode for identifying Parnassia species. DNA barcoding is a useful technique and provides a reliable and effective mean for the discrimination of Parnassia species, and in combination with morphology-based taxonomy, will be a robust approach for tackling taxonomically complex groups. In the light of our findings, we found among the three species not identified a possible cryptic speciation event in Parnassia.