Tiny insects, big troubles: a review of BOLD's COI database for Thysanoptera (Insecta)

DNA Barcoding is an important tool for disciplines such as taxonomy, phylogenetics and phylogeography, with Barcode of Life Data System (BOLD) being the largest database of partial cytochrome c oxidase subunit I (COI) sequences. We provide the first extensive revision of the information available in this database for the insect order Thysanoptera, to assess: how many COI sequences are available; how representative these sequences are for the order; and the current potential of BOLD as a reference library for specimen identification and species delimitation. The COI database at BOLD currently represents only about 5% of the over 6400 valid thrips species, with a heavy bias towards a few species of economic importance. Clear Barcode gaps were observed for 24 out of 33 genera evaluated, but many outliers were also observed. We suggest that the COI sequences available in BOLD as a reference would not allow for accurate identifications in about 30% of Thysanoptera species in this database, which rises to 40% of taxa within Thripidae, the most sampled family within the order. Thus, we call for caution and a critical evaluation in using BOLD as a reference library for thrips Barcodes, and future efforts should focus on improving the data quality of this database.

Integrative taxonomy peeps a new torrent catfish species of genus Amblyceps (Siluriformes: Amblycipitidae) in Kaladan River of Mizoram, India

BACKGROUND

Explorations of the Kaladan River of Mizoram, India during the last decade have given a large number of new species. Integrative taxonomy, when used at the time of discovery of new species, can correlate the morphological characters with the species-specific DNA signatures and ameliorate the process of species identification. Based on this approach, Amblyceps hmolaii sp. nov., a new torrent catfish species is described from the Kaladan River drainage.

METHODS AND RESULTS

The new species is distinguished from all twenty-two congeners by morphometric measurements and meristic counts. Sequence analysis of mitochondrial gene cytochrome c oxidase subunit I (COI), generated in this study and those available in NCBI, separated A. hmolaii sp. nov. from seven species of Amblyceps. Analysis of COI sequences, with ABGD software to delimit the species, also provided eight stable groups corresponding to the eight species of Amblyceps. The new species was separated from its congeners with an average genetic distance of 11.77%. Maximum-likelihood (ML) phylogenetic tree was constructed using the best fit nucleotide substitution model HKY + G + I.

CONCLUSION

This study used all the twenty-two congeners in morphomeristic analysis and seven congeners in molecular analysis, for comparison with the new species. This approach unambiguously resolved the new species from other species of Amblyceps and created its species-specific DNA signatures. The discovery of new species even marked the first record of genus Amblyceps from the Kaladan drainage.

Plant DNA Barcoding Principles and Limits: A Case Study in the Genus Vanilla

Powerful DNA barcodes have been much more difficult to define in plants than in animals. In 2009, the international Consortium for the Barcoding Of Life (CBOL) chose the combination of the chloroplast genes (rbcL + matK) as the proposed official barcode for plants. However, this system has got important limits. First, any barcode system will only be useful if there is a clear barcode gap and if species are monophyletic. Second, chloroplast and mitochondrial (COI gene used for animals) barcodes will not be usable for discriminating hybrid species. Moreover, it was also shown that, using chloroplast regions, maximum species discrimination would be around 70% and very variable among plant groups. This is why many authors have more recently advocated for the addition of the nuclear ITS region to this barcode because it reveals more variations and allows the resolution of hybrid or closely related species. We tested different chloroplast genes (rbcL, matK, psaB, psbC) and the nuclear ITS region in the genus Vanilla, a taxonomically complex group and therefore a good model to test for the efficiency of different barcode systems. We found that the CBOL official barcode system performed relatively poorly in Vanilla (76% species discrimination), and we demonstrate that adding ITS to this barcode system allows to increase resolution (for closely related species and to the subspecies level) and to identify hybrid species. The best species discrimination attained was 96.2% because of one paraphyletic species that could not be resolved.

Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider

Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analysed for success species identification using DNA barcodes, specifically inter- and intra-specific variations together with the success rates of PCR amplification and sequencing. Although the gap between inter- and intra-specific variations was narrow, ITS met the qualification standards for a target DNA barcode. Overlapping inter- and intra-specific pairwise distances were observed in nLSU, tef-1α, mtSSU, and rpb2. The success rates of PCR amplification and sequencing in mtSSU and rpb1 were lower than those of others. Gene combinations were also investigated for resolution of species recognition. ITS-rpb2 was suggested as the likely target DNA barcode for Russula, owing to the two viatal standards above. Since nLSU has the lowest minimum of inter-specific variation, and tef-1α has the highest overlap between intra- and inter-species variations among the candidate genes, they are disqualified from the selection for DNA barcode of Russula.

Molecular data reveal cryptic speciation and host specificity in Toxascaris leonina (Nematoda: Ascarididae)

Toxascaris leonina (Ascarididae) is a cosmopolitan and polyxenical parasite whose host are canids and felids. To date, molecular phylogenetic studies included toxascarid representatives collected only from dogs or felids, therefore the intra-species differences between T. leonina collected from different host species has not been noticed. In this paper, we test the hypothesis of cryptic speciation in the T. leonina complex based on extended sequence data (ITS1, nad1, cox1) and individuals collected from dogs, felids and foxes. Phylogenetic analysis clustered T. leonina representatives into three well-supported clades depending on their host species, i.e. dogs and wolves, wild felids and foxes. Both genetic distances and the barcoding-gap analysis strongly support the species status of populations inhabiting different hosts. The results suggest additional genetic separation in felids. However, to determine the actual size of the Toxascaris complex, it would be necessary to analyse individuals collected from other canid and felid Toxascaris leonina host species.

Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi)

BACKGROUND

Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species. The nrITS region is considered the universal barcode of Fungi, and the ITS1 and ITS2 sub-regions have been applied as metabarcoding markers. In this study, we performed a large-scale analysis of all the available Basidiomycota sequences from GenBank. We carried out a rigorous trimming of the initial dataset based in methodological principals of DNA Barcoding. Two different approaches (PCI and barcode gap) were used to determine the performance of the complete ITS region and sub-regions.

RESULTS

For most of the Basidiomycota genera, the three genomic markers performed similarly, i.e., when one was considered a good marker for the identification of a genus, the others were also; the same results were observed when the performance was insufficient. However, based on barcode gap analyses, we identified genomic markers that had a superior identification performance than the others and genomic markers that were not indicated for the identification of some genera. Notably, neither the complete ITS nor the sub-regions were useful in identifying 11 of the 113 Basidiomycota genera. The complex phylogenetic relationships and the presence of cryptic species in some genera are possible explanations of this limitation and are discussed.

CONCLUSIONS

Knowledge regarding the efficiency and limitations of the barcode markers that are currently used for the identification of organisms is crucial because it benefits research in many areas. Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species.

DNA barcoding of Jamaican bats: implications to Neotropical biodiversity

We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study.

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC

Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.