31 research outputs found
msat_sequences
This file contains the nucleotide sequence information for the described microsatellite markers. Primer sites are indicated in the sequences
High-Throughput Sequencing—The Key to Rapid Biodiversity Assessment of Marine Metazoa?
<div><p>The applications of traditional morphological and molecular methods for species identification are greatly restricted by processing speed and on a regional or greater scale are generally considered unfeasible. In this context, high-throughput sequencing, or metagenetics, has been proposed as an efficient tool to document biodiversity. Here we evaluated the effectiveness of 454 pyrosequencing in marine metazoan community analysis using the 18S rDNA: V1-V2 region. Multiplex pyrosequencing of the V1-V2 region was used to analyze two pooled samples of DNA, one comprising 118 and the other 37 morphologically identified species, and one natural sample taken directly from a North Sea zooplankton community. A DNA reference library comprising all species represented in the pooled samples was created by Sanger sequencing, and this was then used to determine the optimal similarity threshold for species delineation. The optimal threshold was found at 99% species similarity, with 85% identification success. Pyrosequencing was able to identify between fewer species: 67% and 78% of the species in the two pooled samples. Also, a large number of sequences for three species that were not included in the pooled samples were amplified by pyrosequencing, suggesting preferential amplification of some genotypes and the sensitivity of this approach to even low levels of contamination. Conversely, metagenetic analysis of the natural zooplankton sample identified many more species (particularly gelatinous zooplankton and meroplankton) than morphological analysis of a formalin-fixed sample from the same sampling site, suggesting an increased level of taxonomic resolution with pyrosequencing. The study demonstrated that, based on the V1-V2 region, 454 sequencing does not provide accurate species differentiation and reliable taxonomic classification, as it is required in most biodiversity monitoring. The analysis of artificially prepared samples indicated that species detection in pyrosequencing datasets is complicated by potential PCR-based biases and that the V1-V2 marker is poorly resolved for some taxa.</p></div
Present and paleo potential distribution maps.
<p>The potential distribution of the Antarctic decapod shrimps <i>N. lanceopes</i>, <i>N. antarcticus</i> and <i>C. antarcticus</i> computed with Maxent 3.3.3e derived from current conditions (A–C) and projected onto a Last Glacial Maximum scenario (D–F). Habitat suitability ranges from low (blue) to high (red). Also shown are the summer and winter sea-ice extent and the Polar Front. Shaded areas (MESS) indicate climate conditions out of the species range.</p
Present potential distribution maps.
<p>The potential distribution of <i>N. lanceopes</i>, <i>N. antarcticus</i> and <i>C. antarcticus</i> (A–C) computed with Maxent 3.3.3e derived from current conditions. Display window for the area Weddell Sea and Antarctic Peninsula. Indicated the early summer near-surface currents <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046283#pone.0046283-Lumpkin1" target="_blank">[78]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046283#pone.0046283-Lumpkin2" target="_blank">[79]</a>, which are likely to affect the drift of larval stages. Shaded areas (MESS) indicate climate conditions out of the species range.</p
Cluster analysis conducted on modified reference libraries (characterized by 5-mer, 4-mer, 3-mer and 2-mer homopolymers, respectively) using different similarity thresholds (97–100%, at 1% intervals).
<p>Cluster analysis conducted on modified reference libraries (characterized by 5-mer, 4-mer, 3-mer and 2-mer homopolymers, respectively) using different similarity thresholds (97–100%, at 1% intervals).</p
Comparison of taxonomic composition of a morphologically analyzed (individuals/m<sup>3</sup>) and a pyrosequenced zooplankton sample, as aliquots ZPHTS1 and ZPHTS2 (no. of reads per species).
<p>Identifications of the pyrosequenced sample determined by searching against a V1-V2 reference library (99% similarity) and the GenBank database (MEGABLAST search > 90% identity).</p
Species delineation results for the Sanger-generated reference library at a 98% similarity threshold.
<p>For each cluster comprising more than one sequence a representative sequence* is presented.</p
Read coverage distribution of sample aliquots inferred from pyrosequencing after clustering against the reference library at 99% similarity.
<p><b>(A)</b> Dataset showing strong positive correlation between aliquot 1 (<i>x</i>-axis) and aliquot 2 (<i>y</i>-axis) of pooled ALLDNA sample (Spearman r = 0.98, P < 0.001). (<b>B)</b> Dataset showing strong positive correlation between aliquot 1 (<i>x</i>-axis) and aliquot 2 (<i>y</i>-axis) of pooled ZPDNA sample (Spearman r = 0.94, P < 0.001).</p
Environmental profiles.
<p>Environmental conditions at sample localities for <i>C. antarcticus</i>, <i>N. lanceopes</i> and <i>N. antarcticus</i>.</p
Higher taxa composition and number of different species per taxa analyzed for the Sanger-sequence reference library used in the pooled DNA samples.
<p>Higher taxa composition and number of different species per taxa analyzed for the Sanger-sequence reference library used in the pooled DNA samples.</p