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Book ChapterDOI

DNA Barcoding: A Tool to Assess and Conserve Marine Biodiversity

TL;DR: More collaborative efforts are needed to explore the potentialities of DNA barcoding in proper species identification across all taxa, and a threshold of the genetic variation in species delimitation is set to find out the cryptic species.
Abstract: Accurate Species diagnosis is the key element for biodiversity studies and conservation planning. Conventionally, morphological characters are used to identify a species. But, this approach needs a thorough expertise in identifying the external features which often leads to narrowing down of specialization with regard to ascertaining a species within a limited group of taxa. The approach may be particularly valuable for species identification of organisms that are rare, fragile, and/or small, especially when morphological identification is problematic and errors are likely due to simple or evolutionarily conserved body plans. However, each time a new technique has been introduced in science it was accompanied by some debate and distress, and DNA barcoding was no exception. Therefore, more collaborative efforts are needed to explore the potentialities of DNA barcoding in proper species identification across all taxa. At the same time, we need to set a threshold of the genetic variation in species delimitation to find out the cryptic species. It is also an important point to know that the benefits of DNA barcoding are not restricted to taxonomic or systematic research only. The discovery of high-throughput sequencing technologies are going to change the dimension of these techniques in the years to come.
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Journal ArticleDOI
TL;DR: In this paper, the results indicated that single ITS and concatenated ITS/matK/rbcL both conducted better species resolution than single matK and rbcL. Nevertheless, single ITS was more convenient.
Abstract: Seagrasses constitute a significant part of coral reef ecosystems, representing high primary productivity and one of the most important coastal habitats in marine ecosystems. Though seagrasses possess irreplaceable ecological services to the marine environment, taxonomical ambiguity still exists due to similar morphological characters and phenotypic plasticity. As an emerging technology, DNA barcoding can effectively identify cryptic species using a short orthologous DNA region. In this study, we collected samples from five different locations (Daya Bay, Xincun Bay, Sanya Bay, Xisha Islands, and Nansha Islands), and three seagrass species Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis was evaluated. Moreover, ITS, matK and rbcL genes were used as DNA barcodes. The results indicated that single ITS and concatenated ITS/matK/rbcL both conducted better species resolution than single matK and rbcL. Nevertheless, single ITS was more convenient. Furthermore, in all the four topology trees, three species resolved as 3 clusters as well H. ovalis and T. hemprichii grouped as sister clade. In the meantime, differentiation lay in intra-species based on the result of single ITS and three-locus analysis. Within H. ovalis and T. hemprichii separately, individuals from Xisha Islands first group together, then grouped with individuals from Nansha Islands and/or Xincun Bay and/or Sanya Bay and/or Daya Bay, which indicated that geographical distribution influenced population evolution. However, intra-species differentiation did not emerge in the tree of matK or rbcL.

1 citations

References
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Journal ArticleDOI
15 May 1997-Nature
TL;DR: In this paper, the authors have estimated the current economic value of 17 ecosystem services for 16 biomes, based on published studies and a few original calculations, for the entire biosphere, the value (most of which is outside the market) is estimated to be in the range of US$16-54 trillion (10^(12)) per year, with an average of US $33 trillion per year.
Abstract: The services of ecological systems and the natural capital stocks that produce them are critical to the functioning of the Earth's life-support system. They contribute to human welfare, both directly and indirectly, and therefore represent part of the total economic value of the planet. We have estimated the current economic value of 17 ecosystem services for 16 biomes, based on published studies and a few original calculations. For the entire biosphere, the value (most of which is outside the market) is estimated to be in the range of US$16-54 trillion (10^(12)) per year, with an average of US$33 trillion per year. Because of the nature of the uncertainties, this must be considered a minimum estimate. Global gross national product total is around US$18 trillion per year.

18,139 citations

Journal ArticleDOI
TL;DR: It is concluded that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.
Abstract: GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbourjoining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus—were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.

3,212 citations

Journal ArticleDOI
TL;DR: The results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness, and illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.
Abstract: Astraptes fulgerator, first described in 1775, is a common and widely distributed neotropical skipper butterfly (Lepidoptera: Hesperiidae). We combine 25 years of natural history observations in northwestern Costa Rica with morphological study and DNA barcoding of museum specimens to show that A. fulgerator is a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic divergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.

3,112 citations

Journal ArticleDOI
TL;DR: This comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 km2 yr−1 since 1980 and that 29% of the known areal extent has disappeared since seagRass areas were initially recorded in 1879.
Abstract: Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 km(2) yr(-1) since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% yr(-1) before 1940 to 7% yr(-1) since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

3,088 citations

Journal ArticleDOI
TL;DR: The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species, and implies that a standard screening threshold of sequence difference could speed the discovery of new animal species.
Abstract: Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10× average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.

2,115 citations