Gradients in the diversity of plants and large herbivores revealed with DNA barcoding in a semi arid African savanna
DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
more »
« less
- Award ID(s):
- 1930820
- PAR ID:
- 10318334
- Publisher / Repository:
- Barcode of Life Data Systems
- Date Published:
- Edition / Version:
- 1.0
- Subject(s) / Keyword(s):
- Life sciences biology
- Format(s):
- Medium: X Other: txt/xml/html/tsv/image
- Sponsoring Org:
- National Science Foundation
More Like this
-
Abstract Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.more » « less
-
Abstract Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA‐based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS,rbcL,matK, andtrnH‐psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR‐and‐sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared withrbcLandmatK, ITS andtrnH‐psbAhave better species discrimination rates (80.6% and 63.2%, respectively). When ITS andtrnH‐psbAare simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual‐barcode approaches (e.g., ITS + trnH‐psbA) might be the efficient and cost‐effective method in DNA‐based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.more » « less
-
We study topological entropy of compactly supported Hamiltonian diffeomorphisms from a perspective of persistent homology and Floer theory. We introduce barcode entropy, a Floer-theoretic invariant of a Hamiltonian diffeomorphism, measuring exponential growth under iterations of the number of not-too-short bars in the barcode of the Floer complex. We prove that the barcode entropy is bounded from above by the topological entropy and, conversely, that the barcode entropy is bounded from below by the topological entropy of any hyperbolic invariant set, e.g., a hyperbolic horseshoe. As a consequence, we conclude that for Hamiltonian diffeomorphisms of surfaces the barcode entropy is equal to the topological entropy.more » « less
An official website of the United States government
