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1.
Recent advances in DNA taxonomy 总被引：4，自引：0，他引：4
A. P. Vogler M. T. Monaghan 《Journal of Zoological Systematics and Evolutionary Research》2007,45(1):1-10
2.
Gergin A. Blagoev Jeremy R. deWaard Sujeevan Ratnasingham Stephanie L. deWaard Liuqiong Lu James Robertson Angela C. Telfer Paul D. N. Hebert 《Molecular ecology resources》2016,16(1):325-341
Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30 000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest‐neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11–22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30–50% higher than currently recognized. 相似文献
3.
不同海拔的三种杓兰属植物与菌根真菌群落组成相关性 总被引：1，自引：0，他引：1
本研究采集了四川黄龙沟沿海拔梯度3 170-3 400m上4个不同杓兰居群中3种杓兰植物根,利用克隆文库方法获得菌根真菌ITS序列,研究同一栖息地（黄龙沟）不同海拔梯度和不同杓兰对菌根真菌多样性和群落结构的影响。共得到18个可操作分类单元（OTU）,其中14个OTU隶属胶膜菌科Tulasnellaceae,为优势类群（99.6%）;2个OTU隶属腊壳菌科Sebacinaceae,2个OTU隶属亡革菌科Thelephoraceae。随着海拔升高,西藏杓兰菌根真菌多样性减少,而黄花杓兰和无苞杓兰没有明显变化;海拔对3种杓兰菌根真菌群落结构均无显著影响。3种杓兰之间菌根真菌群落结构差异显著且指示物种互不相同,说明在同一栖息地,杓兰对菌根真菌的偏好性显著影响其菌根真菌群落结构。这些研究结果利于了解环境变化对杓兰属植物菌根真菌区系组成的影响,为进一步探索菌根真菌与杓兰属植物的互作机制奠定基础。 相似文献
4.
Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest. 相似文献
5.
Trevor T. Bringloe Sarah J. Adamowicz Vivian F. I. Harvey John K. Jackson Karl Cottenie 《Freshwater Biology》2016,61(5):646-657
- Competitive interactions are assumed to play a role in governing species distributions but are difficult to infer using observational data. In addition, morphological identification may overlook species, obscuring patterns of competitive exclusion. To address these limitations, we showcase a molecular (DNA barcoding) approach to species‐unit delineation and sample stream insect communities at small spatial scales where environmental filtering and dispersal limitations are minimised.
- Rocks from riffles were sampled for stream insects, in particular caddisfly (Trichoptera), beetle (Coleoptera) and blackfly (Simuliidae) larvae from filterer and grazer guilds at White Clay Creek, Pennsylvania, U.S.A. (20 June, 2013). Additive partitioning of species diversity was used to establish at which spatial scale(s) variation in the distribution of species occurs; this informed us of the spatial scale at which to conduct checkerboard analyses, which tested for signatures of species segregations (e.g. competitive exclusion).
- Only a small portion of the total species diversity occurred at the smallest spatial level (mean = 30% on individual rocks). Distributional variation in species was greatest at the kilometre scale (where beta‐diversity was 37% and 41% for filterers and grazers respectively). At the scale of White Clay Creek sampled (c. 3 km extent), species of filterers showed a strong tendency to segregate on individual rocks, while grazers showed random structure approaching aggregation.
- This study demonstrates a potential approach to assessing the role of competition in structuring communities using observational data and highlights the importance of accurate species units for analysis (e.g. DNA barcoding). Using a combination of analyses, we were able to link patterns of segregation to competitive interactions among stream insect species in a filterer guild, while determining these interactions were not important in a grazer guild.
6.
Daniel L. Lindner Tor Carlsen R. Henrik Nilsson Marie Davey Trond Schumacher Håvard Kauserud 《Ecology and evolution》2013,3(6):1751-1764
The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single‐spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions. 相似文献
7.
Frank E. Zachos 《Mammal Review》2018,48(3):153-159
Mammalian taxonomy based on the diagnosability version of the Phylogenetic Species Concept has recently been declared the only sound approach to mammalian classification. In this article, based on the underlying evolutionary ontology of species taxa, I explain the fallacy of these arguments and hold that in a ‘grey area’ after lineage sundering, completely objective species delimitation is impossible, making both lumping and splitting equally correct or incorrect. As a consequence, we may have to get used to the idea that described species are often a poor guide to the delineation of meaningful taxonomic units for conservation. 相似文献
8.
北京地区手参内生真菌的区系组成分析 总被引：1，自引：0，他引：1
手参Gymnadenia conopsea是一种地生兰科植物,也是中国传统中药材之一。研究以ITS1为目标序列,应用 Illumina MiSeq高通量测序技术对北京地区松山和百花山的手参内生真菌区系组成进行测定分析。结果表明,从手参的根中获得有效序列50 420条,209个可操作分类单元（OTUs）,分属于3门9纲28目54科,包括盘菌纲Pezizomycetes（3个OTU）、伞菌纲Agaricomycetes（21个OTU）、锤舌菌纲Leotiomycetes（18个OTU）、粪壳菌纲Sordariomycetes（51个OTU）、接合菌纲Zygomycetes（18个OTU）、银耳纲Tremellomycetes（19个OTU）、散囊菌纲Eurotiomycetes（22个OTU）、酵母纲Saccharomycetes（8个OTU）、座囊菌纲Dothideomycetes（14个OTU）。其中,百花山手参根中内生真菌优势类群是鸡油菌目Cantharellales（38.62%）和柔膜菌目Helotiales（24.64%）真菌;松山手参的优势内生菌类群是盘菌目Pezizales（66.19%）和鸡油菌目Cantharellales（29.75%）真菌。这些结果利于系统了解手参根部内生真菌区系组成以及优势内生真菌类群,为今后开展相关内生真菌在手参人工繁育中的应用奠定了基础。 相似文献
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10.
Kathrin Theissinger Nina Rder Stefanie Allgeier Arne J. Beermann Carsten A. Brühl Anna Friedrich Susanne Michiels Klaus Schwenk 《Molecular ecology》2019,28(18):4300-4316
The Upper Rhine Valley, a “hotspot of biodiversity” in Germany, has been treated with the biocide Bacillus thuringiensis var. israelensis (Bti) for mosquito control for decades. Previous studies discovered Bti nontarget effects in terms of severe chironomid abundance reductions. In this study, we investigated the impact of Bti on species level and addressed the community composition of the nontarget family Chironomidae by use of community metabarcoding. Chironomid emergence data were collected in three mosquito‐control relevant wetland types in the Upper Rhine Valley. For all three sites the chironomid species composition, based on operational taxonomic units (OTUs), was different to varying degrees in the Bti‐treated samples versus control samples, ranging from a significant 63% OTU reduction to an OTU replacement. We assumed that predatory chironomids are less prone to Bti than filter feeders, as the latter feed on floating particles leading to direct ingestion of Bti. However, a comparable percentage of predators and filter feeders (63% and 65%, respectively) was reduced in the Bti samples, suggesting that the feeding strategy is not the main driver for Bti sensitivity in chironomids. Finally, our data was compared to a three‐year‐old data set, indicating possible chironomid community recovery due to species recolonization a few years after the last Bti application. Considering the currently discussed worldwide insect decline we recommend a rethinking of the usage of the biocide Bti, and to prevent its ongoing application especially in nature protection reserves to enhance ecological resilience and to prevent boosting the current biodiversity loss. 相似文献
11.
Petr Kohout Pavla Doubková Mohammad Bahram Jan Suda Leho Tedersoo Jana Voříšková Radka Sudová 《Molecular ecology》2015,24(8):1831-1843
Arbuscular mycorrhizal fungi (AMF) represent an important soil microbial group playing a fundamental role in many terrestrial ecosystems. We explored the effects of deterministic (soil characteristics, host plant life stage, neighbouring plant communities) and stochastic processes on AMF colonization, richness and community composition in roots of Knautia arvensis (Dipsacaceae) plants from three serpentine grasslands and adjacent nonserpentine sites. Methodically, the study was based on 454‐sequencing of the ITS region of rDNA. In total, we detected 81 molecular taxonomical operational units (MOTUs) belonging to the Glomeromycota. Serpentine character of the site negatively influenced AMF root colonization, similarly as higher Fe concentration. AMF MOTUs richness linearly increased along a pH gradient from 3.5 to 5.8. Contrary, K and Cr soil concentration had a negative influence on AMF MOTUs richness. We also detected a strong relation between neighbouring plant community composition and AMF MOTUs richness. Although spatial distance between the sampled sites (c. 0.3–3 km) contributed to structuring AMF communities in K. arvensis roots, environmental parameters were key factors in this respect. In particular, the composition of AMF communities was shaped by the complex of serpentine conditions, pH and available soil Ni concentration. The composition of AMF communities was also dependent on host plant life stage (vegetative vs. generative). Our study supports the dominance of deterministic factors in structuring AMF communities in heterogeneous environment composed of an edaphic mosaic of serpentine and nonserpentine soils. 相似文献
12.
Patrick F. Allison;Emily T. Pickich;Zanethia C. Barnett;Ryan C. Garrick; 《Ecology and evolution》2024,14(7):e70050
DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (NH) per species, and another that focused on total number of sequences (NS; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the NH and NS datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the NH dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding. 相似文献
13.
Christina Sagorny Carina Wesseler Daria Krmer Jrn von Dhren 《Journal of Zoological Systematics and Evolutionary Research》2019,57(3):497-519
Soft‐bodied marine taxa, like ribbon worms (Nemertea), often lack clear diagnostic morphological characters impeding traditional species delimitation. Therefore, recent studies concentrated on molecular genetic methods to solve taxonomic issues. Different delimitation methods were employed to explore species boundaries and the presence of cryptic species. However, the performance of the different delimitation methods needs to be tested. A particularly promising nemertean genus in this regard is the palaeonemertean genus Cephalothrix that is commonly found in European waters. In order to gain information on the number and distribution of European cephalotrichids and to test different tree‐based and non‐tree‐based delimitation methods, we analyzed a dataset comprising the barcoding region of the mitochondrial cytochrome c oxidase subunit I (COI) of 215 European Cephalothrix specimens, of which 78 were collected for this study. Our results show the presence of 12–13 European lineages of which several can be assigned to known European species. Analyzing a second dataset comprising 74 additional sequences from the Pacific and the Atlantic Oceans helped identify some of the unassigned European specimens. One resulting clade seems to represent a non‐native introduced Cephalothrix species, while another has never been recorded from Europe before. In our analysis, especially the tree‐based methods and the phylogenetic analysis proved to be a useful tool when delimiting species. It remains unclear whether the different identified clades result from cryptic speciation or from a high genetic variability of the COI gene. 相似文献
14.
Mycorrhizal fungi transfer nutrients to plants in exchange for photosynthates. Plants allocate up to 20% of their carbon to mycorrhizal structures, mycelium and fruit bodies of their fungal partners. Individuals of mycorrhizal fungi may encompass hundreds of square metres of soil and defragmented litter, linking multiple plant individuals of different species and size (Figure 1). Using a free‐air 13CO2 enrichment (web‐FACE) technique in a mature forest, interspecific transfer accounted for 40% of fine root carbon after 5 years of back and forth transfer between trees. In this issue of Molecular Ecology, Rog, Rosenstock, Körner, and Klein (2020) show that closely related trees shared relatively more mycorrhizal fungi than distantly related trees in the same experimental site, which correlated to increased carbon sharing. 相似文献
15.
Camila D. Ritter Alexander Zizka Christopher Barnes R. Henrik Nilsson Fabian Roger Alexandre Antonelli 《Ecography》2019,42(2):321-333
Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large‐scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro‐organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced. 相似文献
16.
Ramon Massana 《Molecular ecology》2015,24(12):2904-2906
Eukaryotic microbes comprise a diverse collection of phototrophic and heterotrophic creatures known to play fundamental roles in ecological processes. Some can be identified by light microscopy, generally the largest and with conspicuous shapes, while the smallest can be counted by epifluorescence microscopy or flow cytometry but remain largely unidentified. Microbial diversity studies greatly advanced with the analysis of phylogenetic markers sequenced from natural assemblages. Molecular surveys began in 1990 targeting marine bacterioplankton (Giovannoni et al. 1990 ) and first approached microbial eukaryotes in three studies published in 2001 (Díez et al. 2001 ; López‐García et al. 2001 ; Moon‐van der Staay et al. 2001 ). These seminal studies, based on cloning and Sanger sequencing the complete 18S rDNA, were critical for obtaining broad pictures of microbial diversity in contrasted habitats and for describing novel lineages by robust phylogenies, but were limited by the number of sequences obtained. So, inventories of species richness in a given sample and community comparisons through environmental gradients were very incomplete. These limitations have been overcome with the advent of high‐throughput sequencing (HTS) methods, initially 454‐pyrosequencing, today Illumina and soon others to come. In this issue of Molecular Ecology, Egge et al. ( 2015 ) show a nice example of the use of HTS to study the biodiversity and seasonal succession of a particularly important group of marine microbial eukaryotes, the haptophytes. Temporal changes were analysed first at the community level, then at the clade level, and finally at the lowest rank comparable to species. Interesting and useful ecological insights were obtained at each taxonomic scale. Haptophyte diversity differed along seasons in a systematic manner, with some species showing seasonal preferences and others being always present. Many of these species had no correspondence with known species, pointing out the high level of novelty in microbial assemblages, only accessible by molecular tools. Moreover, the number of species detected was limited, agreeing with a putative scenario of constrained evolutionary diversification in free‐living small eukaryotes. This study illustrates the potential of HTS to address ecological relevant questions in an accessible way by processing large data sets that, nonetheless, need to be treated with a fair understanding of their limitations. 相似文献
17.
Goldstein PZ DeSalle R 《BioEssays : news and reviews in molecular, cellular and developmental biology》2011,33(2):135-147
DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice. 相似文献
18.
DNA条形码技术在北京百花山地区夜蛾科物种鉴定中的应用 总被引：2，自引：0，他引：2
为了探讨DNA条形码技术在夜蛾物种鉴定中的可行性, 本研究利用条形码通用引物扩增了北京百花山地区43种夜蛾75个样本的线粒体细胞色素C氧化酶亚基I （mitochondrial cytochrome c oxidase subunit I, COI）基因序列, 以Kimura双参数模型进行种内种间遗传距离分析、 使用邻接法（neighbor-joining, NJ）和最大简约法（maximum parsimony, MP）分别构建系统发育树, 并利用分子序列差异阈值对样本进行分子可操作分类单元（molecular defined operational taxonomic units, MOTU）划分。结果表明： 所有夜蛾种类通过系统发育树可以成功区分; 种内平均遗传距离(0.03%)远远小于种间平均遗传距离(11.29%); 采用较为保守的1%的序列差异阈值将75个夜蛾样本分为42个MOTU, 正确率为95%, 除了MOTU04包含2个物种外, 剩余41个MOTU与形态种呈现一一对应的关系。结果显示, 基于COI基因的DNA条形码对于本研究中所涉及的夜蛾具有较好的区分, 可以作为一种有效的工具在夜蛾科昆虫物种鉴定中进行应用。 相似文献
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20.
Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored. 相似文献