DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, marK, trnH- ...psbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection. Forensic investigators have also applied these plant DNA barcodes in the regulatory areas of traffic in endangered species and monitoring commercial products, such as foods and herbal supplements. Major challenges ahead will focus on building the global plant DNA barcode library and adopting genomic sequencing technologies for a more efficient and cost- effective workflow in applying these genetic identification markers to additional fields of biological and commercial endeavors.
A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been ...limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level.
Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species.
A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.
Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important ...component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (rbcL, trnH-psbA and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (rbcL and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The rbcL locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt's sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Theory predicts shifts in the magnitude and direction of biodiversity effects on ecosystem function (BEF) over succession, but this theory remains largely untested. We studied the relationship ...between aboveground tree biomass dynamics (Δbiomass) and multiple dimensions of biodiversity over 8–16 years in eight successional rainforests. We tested whether successional changes in diversity–Δbiomass correlations reflect predictions of niche theories. Diversity–Δbiomass correlations were positive early but weak later in succession, suggesting saturation of niche space with increasing diversity. Early in succession, phylogenetic diversity and functional diversity in two leaf traits exhibited the strongest positive correlations with Δbiomass, indicating complementarity or positive selection effects. In mid‐successional stands, high biodiversity was associated with greater mortality‐driven biomass loss, i.e. negative selection effects, suggesting successional niche trade‐offs and loss of fast‐growing pioneer species. Our results demonstrate that BEF relationships are dynamic across succession, thus successional context is essential to understanding BEF in a given system.
BACKGROUND: Most tropical and subtropical plants are biotically pollinated, and insects are the major pollinators. A small but ecologically and economically important group of plants classified in 28 ...orders, 67 families and about 528 species of angiosperms are pollinated by nectar-feeding bats. From a phylogenetic perspective this is a derived pollination mode involving a relatively large and energetically expensive pollinator. Here its ecological and evolutionary consequences are explored. SCOPE AND CONCLUSIONS: This review summarizes adaptations in bats and plants that facilitate this interaction and discusses the evolution of bat pollination from a plant phylogenetic perspective. Two families of bats contain specialized flower visitors, one in the Old World and one in the New World. Adaptation to pollination by bats has evolved independently many times from a variety of ancestral conditions, including insect-, bird- and non-volant mammal-pollination. Bat pollination predominates in very few families but is relatively common in certain angiosperm subfamilies and tribes. We propose that flower-visiting bats provide two important benefits to plants: they deposit large amounts of pollen and a variety of pollen genotypes on plant stigmas and, compared with many other pollinators, they are long-distance pollen dispersers. Bat pollination tends to occur in plants that occur in low densities and in lineages producing large flowers. In highly fragmented tropical habitats, nectar bats play an important role in maintaining the genetic continuity of plant populations and thus have considerable conservation value.
Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been ...particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.
Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.
As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
DNA barcoding is an emerging molecular identification and classification technology that has been applied to medicinal plants since 2008. The application of this technique has greatly ensured the ...safety and effectiveness of medicinal materials. In this paper, we review the application of DNA barcoding and some related technologies over the past 10 years with respect to improving our knowledge of medicinal plant identification and authentication. From single locus-based DNA barcodes to combined markers to genome-scale levels, DNA barcodes contribute more and more genetic information. At the same time, other technologies, such as high-resolution melting (HRM), have been combined with DNA barcoding. With the development of next-generation sequencing (NGS), metabarcoding technology has also been shown to identify species in mixed samples successfully. As a widely used and effective tool, DNA barcoding will become more useful over time in the field of medicinal plants.
•Our manuscript is the first comprehensive review of the application of DNA barcodes in ethnobotany and herbal medicines.•The applications of genome and HRM technology in DNA barcoding are reviewed.•The future development direction and trend of DNA barcoding are pointed out.
Use of DNA barcodes to identify flowering plants Kress, W.J; Wurdack, K.J; Zimmer, E.A ...
Proceedings of the National Academy of Sciences - PNAS,
06/2005, Letnik:
102, Številka:
23
Journal Article
Recenzirano
Odprti dostop
Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate ...sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (≈450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.
DNA barcodes for ecology, evolution, and conservation Kress, W. John; García-Robledo, Carlos; Uriarte, Maria ...
Trends in ecology & evolution (Amsterdam),
January 2015, 2015-Jan, 2015-01-00, 20150101, Letnik:
30, Številka:
1
Journal Article
Recenzirano
•DNA barcodes are becoming an integral tool for the identification of species and the understanding of the evolution and ecology of biodiversity.•Although the specification of a single short DNA ...region as a universal identifier for all of biodiversity has not materialized, a few genetic markers have now been identified to assist in the DNA barcode endeavor.•DNA barcodes are providing resolved local phylogenies of plant taxa to aid understanding of the principles of how species are assembled into communities and the evolution of functional traits in these assemblages.•Previous attempts to resolve multispecies interactions have been enhanced through use of DNA barcodes in investigations of trophic interactions and ecological forensics.
The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed.
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