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1.
Martin Ryberg 《Molecular ecology》2015,24(23):5770-5777
During the last couple of decades, an increasing number of studies use sequence clusters as units for taxonomic diversity. It is well known that such molecular operational taxonomic units (MOTUs) do not necessarily correspond to species, but they are treated as such when measuring diversity and testing theories. Here, I show that data from studies of molecular evolution and species diversification of fungi indicate that commonly used cut‐offs are likely to lump species in many cases. At the same time, empirical studies show that the mean within‐species variation is close to these cut‐offs. That the within‐species variation estimates are plausible is supported by coalescence modelling under a range of parameter settings. In addition, studies using crossing tests to delimit species show that there often is an overlap in within‐ and between‐species distances. The available data therefore indicate that sequence clusters are likely to misrepresent species. However, to keep a biological relevance, MOTUs should be kept in close agreement with species. Studies using them should therefore asses how sensitive the results are to differences between MOTUs and species – something that is rarely done. An even better solution is to directly include the uncertainty in species delimitation in the analyses, but in many cases, we need to increase our knowledge of taxonomy and evolution to do this accurately. Even if the empirical data referred to here pertain to the “barcoding” region of rDNA in fungi, there is nothing indicating that the situation is substantially better for other taxa or genes.  相似文献   

2.
山脉是生物多样性研究的热点地区,以往关于山脉的研究多集中于地上植物和脊椎动物,无脊椎动物相关的研究明显滞后。跳虫(Collembola)是土壤无脊椎动物的主要类群之一,在分解有机质、疏松和活化土壤过程中发挥着重要的作用。以跳虫为研究对象,采用梯度格局法,在长白山北坡自海拔800 m至1700 m,每隔150 m进行凋落物层和土壤层样品的采集,对比分析了土壤层和凋落物层的群落组成与群落结构,采用4个物种多样性指数(丰富度指数、Pielou均匀度指数、Shannon-Weiner多样性指数和Simpson多样性指数)和4个功能多样性指数(功能丰富度FRic指数、功能均匀度FEve指数、二次熵Rao''s Q指数和功能离散FEiv指数),探讨了多样性沿海拔梯度的分布格局。共获得跳虫5542头,隶属于12科42属83种,其中等节跳科为绝对优势类群(相对密度>50%)。非度量多维尺度分析结果表明,凋落物层和土壤层的跳虫群落结构差异显著,长角跳科、鳞跳科和疣跳科物种多分布于凋落物层,而棘跳科物种多分布于土壤层。线性或二次回归模型结果表明,在凋落物层跳虫的丰富度指数,Shannon-Weiner多样性指数和Simpson多样性指数沿海拔梯度的变化呈增加格局;但在土壤层跳虫物种多样性指数沿海拔梯度的变化无明显趋势。在凋落物层,跳虫的功能丰富度指数和功能离散度Rao''s Q指数随海拔梯度的变化呈现单峰分布格局;在土壤层,跳虫的功能丰富度指数随海拔梯度的变化也呈现单峰分布格局,但其他功能多样性指数沿海拔梯度的变化无明显趋势。研究表明凋落物层和土壤层跳虫的群落组成,群落结构及多样性存在显著差异,跳虫的物种多样性指数和功能多样性指数对海拔梯度变化的响应不同,未来在探讨土壤动物沿海拔梯度的分布格局及其物种共存机制时,应综合考量垂直分层(凋落物层和土壤层)和多个度量维度(物种多样性和功能多样性)。  相似文献   

3.
DNA条形码目前广泛用于昆虫多样性研究。本研究采用DNA条形码(即线粒体细胞色素c氧化酶亚基I基因COI 5′端),通过比较所获分子分类操作单元(Molecular operational taxonomic units,MOTU)的种内遗传距离,探究DNA条形码在亚热带森林(位于我国江西省新岗山)不同昆虫类群中的物种鉴定和界定效用。数据分析中结合数据库比对信息,采用jMOTU、ABGD、bPTP、GMYC 这4种物种界定方法获得MOTU,从而开展种内遗传距离分析。本研究共挑选出479个昆虫样本,获得475条COI序列,经NCBI、BOLD在线数据库比对属于6个目,与形态初步划分一致;物种界定分析获得288个MOTU,其中鳞翅目最多,达85个,膜翅目、双翅目、半翅目、鞘翅目次之,分别为80、74、21和20个,直翅目最少,仅8个。膜翅目和双翅目的种内遗传距离均值及标准偏差较大(膜翅目:0.89%±0.87%;双翅目:0.73%±0.58%),鳞翅目的最小(0.28%±0.20%)。研究表明:不同昆虫类群的种内遗传距离虽然整体在一定范围,但仍然存在一定的差异,因此不能笼统地依靠遗传距离的距离阈值进行物种划分;现有数据库需要补充足够的昆虫物种信息,才能提升物种鉴定效率。本研究丰富了亚热带森林昆虫分子数据库,同时也为进一步探索基于分子分类学开展昆虫多样性研究提供了基础数据和参考。  相似文献   

4.
Mites (Arachnida: Acariformes, Parasitiformes) are the most abundant and species‐rich group of arthropods in soil, but are also diverse in freshwater habitats, on plants, and as symbionts of larger animals. However, assessment of their diversity has been impeded by their small size and often cryptic morphology. As a consequence, published estimates of their species richness span more than two orders of magnitude (0.4–114 million). In this study we employ DNA barcoding and the Barcode Index Number (BIN) system to investigate mite diversity at over 1,800 sites across Canada, primarily from soil and litter habitats with smaller contributions from freshwater, plants, and animal hosts. Barcodes from 73,394 specimens revealed 7,077 BINs with representatives from all four orders (Ixodida, Mesostigmata, Sarcoptiformes, Trombidiformes) and 60% (186) of the known families. The BIN total is 2.4 times the number of species previously recorded from Canada (2,999), reflecting the unexpectedly high richness of several families. Richness projections suggest that more than 28,000 BINs occur at the sampled locations, indicating that the Canadian mite fauna almost certainly includes more than 30,000 species—a total similar to that for the most diverse insect order in Canada, Diptera. This unexpected diversity was partitioned into highly dissimilar, spatially‐structured assemblages that likely reflect dispersal limitation and environmental heterogeneity. Further sampling of a greater diversity of habitats will refine understanding of mite diversity in Canada, but similar analyses in other geographic regions will be essential to ascertain their diversity at a global scale.  相似文献   

5.
DNA barcodes are increasingly used to provide an estimate of biodiversity for small, cryptic organisms like nematodes. Nucleotide sequences generated by the barcoding process are often grouped, based on similarity, into molecular operational taxonomic units (MOTUs). In order to get a better understanding of the taxonomic resolution of a 3' 592-bp 18S rDNA barcode, we have analyzed 100 MOTUs generated from 214 specimens in the nematode suborder Criconematina. Previous research has demonstrated that the primer set for this barcode reliably amplifies all nematodes in the Phylum Nematoda. Included among the Criconematina specimens were 25 morphologically described species representing 12 genera. Using the most stringent definition of MOTU membership, where a single nucleotide difference is sufficient for the creation of a new MOTU, it was found that an MOTU can represent a subgroup of a species (e.g. Discocriconemella limitanea), a single species (Bakernema inaequale), or a species complex (MOTU 76). A maximum likelihood phylogenetic analysis of the MOTU dataset generated four major clades that were further analyzed by character-based barcode analysis. Fourteen of the 25 morphologically identified species had at least one putative diagnostic nucleotide identified by this character-based approach. These diagnostic nucleotides could be useful in biodiversity assessments when ambiguous results are encountered in database searches that use a distance-based metric for nucleotide sequence comparisons. Information and images regarding specimens examined during this study are available online.  相似文献   

6.
Biological invasions are increasingly recognized as a potent force altering native ecosystems worldwide. Many of the best documented cases involve the massive invasions of North America by plant and animal taxa native to Europe. In this study, we use DNA barcoding to survey the occurrence and genetic structure of two major groups of soil invertebrates in both their native and introduced ranges: Collembola and earthworms. Populations of ten species of earthworms and five species of Collembola were barcoded from both continents. Most of these species exhibited a similar genetic structure of large and stable populations in North America and Europe, a result supporting a scenario of multiple invasions. This was expected for earthworm species involved in human economic activities, but not foreseen for Collembola species de facto unintentionally introduced. This study also establishes that invasive species surveys employing DNA barcoding gain additional resolution over those based on morphology as they allow evaluation of cryptic lineages exhibiting different invasion histories.  相似文献   

7.
  1. Freshwater amphipods Gammarus fossarum and Gammarus pulex are widespread in Europe, with some evidence of cryptic diversity in the former. We used DNA barcoding to assess genetic diversity within and among amphipod populations and examined mate discrimination and pre‐copulatory pair formation between genetically divergent individuals.
  2. Eight distinct G. fossarum and four distinct G. pulex molecular operational taxonomic units (MOTUs) were detected. Among the 33 amphipod populations sampled, 11 contained a single MOTU, 11 had two and 11 were composed of three sympatric MOTUs. Genetic divergences between sympatric MOTUs (G. fossarum and G. pulex MOTUs combined) ranged up to 28% (Kimura two parameter estimates).
  3. In amphipod populations containing sympatric MOTUs, pre‐copulatory pair formation was random between MOTUs diverging by <4%. However, pre‐copulatory pairs involving amphipod individuals from MOTUs diverging by >4% were rare, suggesting mate discrimination between sympatric, highly divergent MOTUs.
  4. Although the likelihood decreased with genetic distance between partners, pre‐copulatory pair formation in the laboratory can occur between MOTUs diverging by c. 16% and led to successful mating: most female amphipod carried viable, fertilised eggs 48 h post‐mating.
  5. Data showed high cryptic diversity in the G. fossarum/G. pulex groups, even at a small spatial scale. Mate discrimination between genetically divergent amphipods in natural populations suggests that some of the MOTUs found in G. fossarum and G. pulex may be separated into (sub)species. However, amphipods from different MOTUs can still form pre‐copulatory pairs and females produce viable eggs. Overall, data suggest that cryptic diversity is common in the G. fossarum/G. pulex groups and that pre‐zygotic isolation through mate discrimination, rather than post‐zygotic incompatibility, is likely to drive cryptic speciation.
  相似文献   

8.
Studies on the biogeography of host-parasitoid interactions are scarce, mainly because of technical difficulties associated with rearing and species identification. DNA barcoding is increasingly recognized as a valuable tool for taxon identification, allowing to link different life history stages of a species. We evaluate the usefulness of a protocol based on cytochrome oxidase I (COI) sequencing for the study of geographical variation of host-parasitoid interactions. Larvae of Acroclita subsequana (Lepidoptera: Tortricidae) were collected in Macaronesia and dissected to search for parasitoid larvae. Both hosts and parasitoids were sequenced and assigned to molecular operational taxonomic units (MOTUs) based on pairwise genetic distances, tree-based and similarity-based methods. Hosts were grouped into six MOTUs, usually with an allopatric distribution, while parasitoids clustered into 12 MOTUs, each of which was mostly found attacking a single host MOTU. Available COI sequence databases failed to provide identification to species level for these MOTUs. Three challenges related to the applicability of DNA barcoding in this type of studies are identified and discussed: (i) more suitable primers need to be developed for both parasitoids and hosts; (ii) the most commonly used approaches for inferring MOTUs have different limitations (e.g. arbitrary nature of defining a threshold to separate MOTUs) and need to be improved or replaced by other techniques; and (iii) for the identification of MOTUs, it is imperative to increase the range of sequenced taxa in the currently available reference databases. Finally, in spite of these difficulties, we discuss how DNA barcoding will help ecological and biogeographical studies of host-parasitoid interactions.  相似文献   

9.

Background

Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested.

Methodology/Principal Findings

Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI) gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada''s three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%). Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas.

Conclusions/Significance

Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor role in Arctic recolonization following deglaciation. This study highlights the value of DNA barcoding for providing rapid insights into species distributions and biogeographic patterns in understudied groups.  相似文献   

10.
Climate change will have profound and unanticipated effects on species distributions. The pace and nature of this change is largely unstudied, especially for the most diverse elements of terrestrial communities--the arthropods--here we have only limited knowledge concerning the taxonomy and the ecology of these groups. Because Arctic ecosystems have already experienced significant increases in temperature over the past half century, shifts in community structure may already be in progress. Here we utilise collections of a particularly hyperdiverse insect group--parasitoid wasps (Hymenoptera; Braconidae; Microgastrinae)--at Churchill, Manitoba, Canada in the early and mid-twentieth century to compare the composition of the contemporary community to that present 50-70 years ago. Morphological and DNA barcoding results revealed the presence of 79 species of microgastrine wasps in collections from Churchill, but we estimate that 20% of the local fauna awaits detection. Species composition and diversity between the two time periods differ significantly; species that were most common in historic collections were not found in contemporary collections and vice versa. Using barcodes we compared these collections to others from across North America; contemporary Churchill species are most affiliated with more south-western collections, while historic collections were more affiliated with eastern collections. The past five decades has clearly seen a dramatic change of species composition within the area studied coincident with rising temperature.  相似文献   

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