植物DNA条形码、物种形成和分类学

<正>DNA条形码最大的特点是用一段标准DNA序列就可以鉴定生物材料(特别是不具有分类特征的残缺或来自幼小个体的材料)和生物产品的物种来源(Hebert et al.,2003)。已有研究发现,动物中线粒体基因组的COI基因序列能鉴定多个动物类群的物种,被认为是理想的DNA条形码片段(Ward et al.,2005;TavaresBaker,2008)。而植物DNA条形码序列的确定还存在争议,例如应选择一个片段还是多     

Mitochondrial DNA phylogenetics of the Galaxias vulgaris complex from South Island, New Zealand: rapid radiation of a species flock

Mitochondrial control region sequence variation was examined in the Galaxias vulgaris complex, a group of freshwater-limited galaxiid fishes endemic to South Island, New Zealand. Phylogenetic analyses were used to test the monophyly of seven non-migratory ( G. vulgaris complex) and one migratory ( G. brevipinnis ) species. Newly-described taxa, some diagnosed on the basis of subtle differences in morphology, are associated with strongly monophyletic mtDNA lineages. Although the current taxonomy is supported generally, sequence data suggest that Southland G. anomalus should be attributed to G. gollumoides , whereas Southland and Stewart Island G. depressiceps represent a new southern lineage. Molecular clock calibrations suggest that migratory and non-migratory forms, separated by a maximum of 6·4% sequence divergence, diverged no earlier than the mid-late Pliocene. Biogeographical implications of high diversity (eight lineages) in the south (Otago-Southland) and low diversity (one lineage) in central South Island (Canterbury) are discussed. The unresolved relationships among species may reflect a rapid evolutionary radiation, essentially a star phylogeny.     

How DNA barcodes complement taxonomy and explore species diversity: the case study of a poorly understood marine fauna

Background

The species boundaries of some venerids are difficult to define based solely on morphological features due to their indistinct intra- and interspecific phenotypic variability. An unprecedented biodiversity crisis caused by human activities has emerged. Thus, to access the biological diversity and further the conservation of this taxonomically muddling bivalve group, a fast and simple approach that can efficiently examine species boundaries and highlight areas of unrecognized diversity is urgently needed. DNA barcoding has proved its effectiveness in high-volume species identification and discovery. In the present study, Chinese fauna was chosen to examine whether this molecular biomarker is sensitive enough for species delimitation, and how it complements taxonomy and explores species diversity.

Methodology/Principal Findings

A total of 315 specimens from around 60 venerid species were included, qualifying the present study as the first major analysis of DNA barcoding for marine bivalves. Nearly all individuals identified to species level based on morphological traits possessed distinct barcode clusters, except for the specimens of one species pair. Among the 26 individuals that were not assigned binomial names a priori, twelve respectively nested within a species genealogy. The remaining individuals formed five monophyletic clusters that potentially represent species new to science or at least unreported in China. Five putative hidden species were also uncovered in traditional morphospecies.

Conclusions/Significance

The present study shows that DNA barcoding is effective in species delimitation and can aid taxonomists by indicating useful diagnostic morphological traits, informing needful revision, and flagging unseen species. Moreover, the BOLD system, which deposits barcodes, morphological, geographical and other data, has the potential as a convenient taxonomic platform.     

Ecological rebound on Phillip Island, South Pacific

Summary  Pigs released on Phillip Island (half-way between Sydney, Australia and Fiji) in 1793 were followed by goats and rabbits by 1830, quickly destroying the sub-tropical vegetation and the soil. By 1856, the island was described as mostly bare red ground with little remnant vegetation. The pigs and goats had gone by about 1900 but rabbits prevented most plant establishment. An experimental programme begun in 1979 to investigate the effect of the rabbits and the island's potential for regeneration quickly provided spectacular evidence. An eradication programme followed, initially using a highly virulent strain of myxoma virus which was very effective but resupply failed. Poisoning with 1080 supplemented by shooting, trapping and gassing finally achieved effective eradication in March 1986, with the removal of the last single rabbit in 1988. Regeneration by native and weed species has been spectacular with consequent faunal changes. Some changes present policy challenges.     

DNA barcodes provide new evidence of a recent radiation in the genus Sporophila (Aves: Passeriformes)

The capuchinos are a group of birds in the genus Sporophila that has apparently radiated recently, as evidenced by their lack of mitochondrial genetic diversity. We obtained cytochrome c oxidase I (COI) sequences (or DNA barcodes) for the 11 species of the group and various outgroups. We compared the patterns of COI variability of the capuchinos with those of the largest barcode data set from neotropical birds currently available (500 species representing 51% of avian richness in Argentina), and subjected COI sequences to neighbour-joining, maximum parsimony and Bayesian phylogenetic analyses as well as statistical parsimony network analysis. A clade within the capuchinos, the southern capuchinos, showed higher intraspecific and lower interspecific divergence than the remaining Argentine species. As most of the southern capuchinos shared COI haplotypes and pairwise distances within species were in many cases higher than distances between them, the phylogenetic affinities within the group remained unresolved. The observed genetic pattern is consistent with both incomplete lineage sorting and gene flow between species. The southern capuchinos constitute the only large group of species among the neotropical birds barcoded so far that are inseparable when using DNA barcodes, and one of few multispecies avian groups known to lack reciprocal monophyly. Extending the analysis to rapidly evolving nuclear and mitochondrial markers will be crucial to understanding this radiation. Apart from giving insights into the evolution of the capuchinos, this study shows how DNA barcoding can rapidly flag species or groups of species worthy of deeper study.     

植物DNA条形码在系统发育研究中的应用

<正>1常用植物DNA条形码物种的准确鉴定是开展科学研究和生物多样性保护的先决条件,但根据形态学特征进行物种鉴定对非专业人员而言比较困难。即使是专业人员,面对纷繁复杂的物种,要想逐一鉴定也难以实现。DNA条形码技术(DNA barcoding)为物种的快速、准确鉴定提供了可能(Hebert et al.,2003)。线粒体COI基因作为动物的DNA条形码已得到广泛应用。但对     

DNA barcodes of Philippine accipitrids

DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster (white-bellied sea eagle), Ichthyophaga ichthyaetus (grey-headed fish eagle), Spilornis holospilus (crested serpent-eagle), Spizaetus philippensis (Philippine hawk-eagle), and Pithecophaga jefferyi (Philippine eagle), are reported for the first time. All individuals sampled are kept at the Philippine Eagle Center in Davao City, Philippines. Basic local alignment search tool results demonstrated that the COI sequences for these species were unique. The COI gene trees constructed using the maximum-likelihood and neighbour-joining (NJ) methods supported the monophyly of the booted eagles of the Aquilinae and the sea eagles of the Haliaeetinae but not the kites of the Milvinae.     

Beyond Clientelism: Neighbourhood Leaders on a Philippine Island

In coastal neighbourhoods just north of Dumaguete City on Negros Island, the pressures of ‘modernity’ have encouraged low-income groups—many of them fishing families—to establish and maintain larger kin-based residential clusters. While clientelism has a strong presence in the wider Philippine polity and is easily observed at the local level during elections, this article questions the view that neighbourhood leaders establish power and authority largely by attaching themselves to patrons, bosses, and governing elites. To elaborate on the nature of these leaders' independence from clientelism, the article engages studies of everyday politics and related literature which demonstrates that ordinary people in Southeast Asia—peasants, landless workers, the urban poor—are not captives of the discourses and practices of elites. In addition to the wealth and class dimensions highlighted in the everyday politics literature, it shows how kinship factors and settler status are relevant for understanding how low-income groups mobilise power on their own and establish neighbourhood leadership in the lowland Philippines.     

DNA barcodes for biosecurity: invasive species identification

Biosecurity encompasses protecting against any risk through 'biological harm', not least being the economic impact from the spread of pest insects. Molecular diagnostic tools provide valuable support for the rapid and accurate identification of morphologically indistinct alien species. However, these tools currently lack standardization. They are not conducive to adaptation by multiple sectors or countries, or to coping with changing pest priorities. The data presented here identifies DNA barcodes as a very promising opportunity to address this. DNA of tussock moth and fruit fly specimens intercepted at the New Zealand border over the last decade were reanalysed using the cox1 sequence barcode approach. Species identifications were compared with the historical dataset obtained by PCR-RFLP of nuclear rDNA. There was 90 and 96% agreement between the methods for these species, respectively. Improvements included previous tussock moth 'unknowns' being placed to family, genera or species and further resolution within fruit fly species complexes. The analyses highlight several advantages of DNA barcodes, especially their adaptability and predictive value. This approach is a realistic platform on which to build a much more flexible system, with the potential to be adopted globally for the rapid and accurate identification of invasive alien species.     

Larvae of Crystallodytes pauciradiatus(Perciformes: Creediidae) from Easter Island, South Pacific

Larvae of Crystallodytes pauciradiatus (Creediidae) are described from 47 individuals (2·9–21·3 mm). They are elongate, slender, lightly pigmented, have prominent preopercular spines and unique small spines on the lower jaw. Early stages are restricted to the nearshore water around Easter Island, South Pacific.     

The promise of a DNA taxonomy

Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional 'species'. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re-analysis and meta-analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possible.     

Identifying the ichthyoplankton of a coral reef using DNA barcodes

Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large‐scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.     

Neotropical bats: estimating species diversity with DNA barcodes

DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.     

Critical factors for assembling a high volume of DNA barcodes

Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.