W. John Kress

A DNA barcode for land plants

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

Background 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. Methodology/Principal Findings 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. Conclusions/Significance 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.

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama.

The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.

Leafsnap: a computer vision system for automatic plant species identification

We describe the first mobile app for identifying plant species using automatic visual recognition. The system --- called Leafsnap --- identifies tree species from photographs of their leaves. Key to this system are computer vision components for discarding non-leaf images, segmenting the leaf from an untextured background, extracting features representing the curvature of the leafs contour over multiple scales, and identifying the species from a dataset of the 184 trees in the Northeastern United States. Our system obtains state-of-the-art performance on the real-world images from the new Leafsnap Dataset --- the largest of its kind. Throughout the paper, we document many of the practical steps needed to produce a computer vision system such as ours, which currently has nearly a million users.

DNA barcodes: Genes, genomics, and bioinformatics

It is not a coincidence that DNA barcoding has developed in concert with genomics-based investigations. DNA barcoding (a tool for rapid species identification based on DNA sequences) and genomics (which compares entire genome structure and expression) share an emphasis on large-scale genetic data acquisition that offers new answers to questions previously beyond the reach of traditional disciplines. DNA barcodes consist of a standardized short sequence of DNA (400–800 bp) that in principle should be easily generated and characterized for all species on the planet (1). A massive on-line digital library of barcodes will serve as a standard to which the DNA barcode sequence of an unidentified sample from the forest, garden, or market can be matched. Similar to genomics, which has accelerated the process of recognizing novel genes and comparing gene function, DNA barcoding will allow users to efficiently recognize known species and speed the discovery of species yet to be found in nature. DNA barcoding aims to use the information of one or a few gene regions to identify all species of life, whereas genomics, the inverse of barcoding, describes in one (e.g., humans) or a few selected species the function and interactions across all genes (Fig. 1). The work of Lahaye et al. (2) reported in a recent issue of PNAS brings the application of DNA barcoding one step closer to implementation in plants.

The evolution of bat pollination: a phylogenetic perspective.

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.

Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly.

Ecology Letters (2010) 13: 1503-1514 ABSTRACT: The phylogenetic structure and distribution of functional traits in a community can provide insights into community assembly processes. However, these insights are sensitive to the spatial scale of analysis. Here, we use spatially explicit, neighbourhood models of tree growth and survival for 19 tree species, a highly resolved molecular phylogeny and information on eight functional traits to quantify the relative efficacy of functional similarity and shared ancestry in describing the effects of spatial interactions between tree species on demographic rates. We also assess the congruence of these results with observed phylogenetic and functional structure in the neighbourhoods of live and dead trees. We found strong support for models in which the effects of spatial neighbourhood interactions on tree growth and survival were scaled to species-specific mean functional trait values (e.g., wood specific gravity, leaf succulence and maximum height) but not to phylogenetic distance. The weak phylogenetic signal in functional trait data allowed us to independently interpret the static neighbourhood functional and phylogenetic patterns. We observed greater functional trait similarity in the neighbourhoods of live trees relative to those of dead trees suggesting that environmental filtering is the major force structuring this tree community at this scale while competitive interactions play a lesser role.

DNA barcodes for ecology, evolution, and conservation.

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.

300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants

DNA barcodes have been successfully applied to a limited number of animal groups with the application of the mitochondrial gene, cytochrome c oxidase subunit 1. Recently two DNA regions, the plastid trnH-psbA spacer and nuclear ribosomal ITS region, have been shown to have potential as an identification barcode for land plants, although with some significant drawbacks. The ideal barcode should be relatively short in length (∼700 bp), more variable between than within species, and easily amplifiable with universal primers. Building on current success, ongoing investigations are searching for the best barcode to apply to all land plants. Once established, a plant barcode may be effectively used in biodiversity inventories, conservation assessments, and applied forensic investigations. Advances in sequencing technology and the completion of the DNA barcode library have the potential to provide the public with increased access to information about the natural world.

Searching the World’s Herbaria: A System for Visual Identification of Plant Species

We describe a working computer vision system that aids in the identification of plant species. A user photographs an isolated leaf on a blank background, and the system extracts the leaf shape and matches it to the shape of leaves of known species. In a few seconds, the sys- tem displays the top matching species, along with textual descriptions and additional images. This system is currently in use by botanists at the Smithsonian Institution National Museum of Natural History. The primary contributions of this paper are: a description of a working com- puter vision system and its user interface for an important new applica- tion area; the introduction of three new datasets containing thousands of single leaf images, each labeled by species and verified by botanists at the US National Herbarium; recognition results for two of the three leaf datasets; and descriptions throughout of practical lessons learned in constructing this system.