Response to the critique of Sameer Padhye and Neelesh Dahanukar (2019) (original) (raw)
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DNA barcoding is the technique of sequencing a short fragment of cytochrome c oxidase subunit I (COI) mtDNA -a 'DNA barcode' -from a taxonomically unknown organism. This DNA barcode is then matched against a reference library of barcodes of known species origin to make a species identification. Since 2004 an international consortium has been promoting DNA barcoding as a global standard for taxonomic identifications ). While we applaud for bringing DNA barcoding to the attention of researchers in Malaysia, we have concerns about their understanding of the theory and methods of DNA barcoding which we discuss below.
One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire
Molecular Ecology Resources, 2015
Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance-based, tree-based and character-based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree-, distance-and character-based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.
Molecular Ecology Resources, 2012
1 Abstract 1 Spider: SPecies IDentity and Evolution in R, is a new R package implement-2 ing a number of useful analyses for DNA barcoding studies and associated 3 research into species delimitation and speciation. Included are functions es-4 sential for generating important summary statistics from DNA barcode data, 5 assessing specimen identification efficacy, and for testing and optimising diver-6 gence threshold limits. In terms of investigating evolutionary and taxonomic 7 questions, techniques for assessing diagnostic nucleotides and probability of re-8 ciprocal monophyly are also provided. Additionally, a sliding window function 9 offers opportunities to to analyse information across a gene, essential for marker 10 design in degraded DNA studies. Spider capitalises on R's extensible ethos, 11 and offers an integrated platform ideal for the analysis of both nucleotide and 12 morphological data. The program can be obtained from the comprehensive 13 R archive network (CRAN, http://cran.r-project.org), and from the R-Forge 14 package development site (http://spider.r-forge.r-project.org/).
Insect Science, 2015
Genotyping of two well-known weevil species from the genus Ceutorhynchus (Coleoptera, Curculionidae) distributed in west Palearctic, C. erysimi and C. contractus, revealed phenotype vs. genotype inconsistencies in a set of 56 specimens (25 C. erysimi and 31 C. contractus) collected from 25 locations in Serbia and Montenegro. An analysis of the mitochondrial cytochrome oxidase subunit I gene (COI), widely used as a barcoding region, and a nuclear gene, elongation factor-1α (EF-1α), revealed stable genetic divergence among these species. The average uncorrected pairwise distances for the COI and EF-1α genes were 3.8%, and 1.3%, respectively, indicating two genetically well-segregated species. However, the genetic data were not congruent with the phenotypic characteristics of the studied specimens. In the first place, C. erysimi genotypes were attached to specimens with phenotypic characteristics of C. contractus. Species-specific PCR-RFLP assays for the barcoding gene COI were applied for the molecular identification of 101 additional specimens of both morphospecies (33 C. erysimi and 68 C. contractus) and were found to confirm this incongruity. The discrepancy between the genetic and morphological data raises the question of the accuracy of using a barcoding approach, as it may result in misleading conclusions about the taxonomic position of the studied organism. Additionally, the typological species concept shows considerable weakness when genetic data are not supported with phenotypic characteristics as in case of asymmetric introgression, which may cause certain problems, especially in applied studies such as biological control programs in which the biological properties of the studied organisms are the main focus.
Valid identification of species of freshwater zooplankton is the first step to understand population structures, abundance, and diversity in the pelagic environment. While some Australian taxa can be easily identified morphologically, e.g., Calamoecia ampulla (Searle, 1911), most other species of freshwater micrometazoans are difficult to identify without specialised training, resulting in limited and even incorrect identification of the various taxa. The use of DNA barcodes, for species identification and discrimination, has added a new dimension to the traditional phenotypic approach and allows researchers to understand the patterns of genetic variability and to overcome taxonomic difficulties in the identification of the species from different life history stages. We used mitochondrial gene cytochrome c oxidase I (COI) to examine the species status of common planktonic microcrustaceans in two South Australian reservoirs. COI analyses indicated that the zooplankton specimens examined from the order Diplostraca and the class Maxillopoda, which were assigned binomial names a priori from the genera Bosmina, Boeckella, Chydorus, Calamoecia and Daphnia, possessed distinct COI sequences and nested cohesively within the genealogy, except for individuals of Ceriodaphnia cf. cornuta and a Ceriodaphnia species complex that formed 4 clusters. These clusters were not explicitly identified morphologically. The present study does improve and contribute to the understanding of the status of taxonomy and biogeography of micro-crustaceans in South Australia. This information is crucial for the application of these species in studies of local and regional environmental change over varying time scales. We recommend the integration of traditional morphology with DNA barcoding-based examination, to facilitate species identification, especially for applied research.
DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics
2007
DNA barcoding aims to provide an efficient method for species-level identifications and, as such, will contribute powerfully to taxonomic and biodiversity research. As the number of DNA barcode sequences accumulates, however, these data will also provide a unique 'horizontal' genomics perspective with broad implications. For example, here we compare the goals and methods of DNA barcoding with those of molecular phylogenetics and population genetics, and suggest that DNA barcoding can complement current research in these areas by providing background information that will be helpful in the selection of taxa for further analyses.
DNA barcoding gap: reliable species identification over morphological and geographical scales
Molecular ecology resources, 2015
The philosophical basis and utility of DNA barcoding have been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a 'barcoding gap' by comparing intra- and interspecific means, medians and overlap in more than 75,000 computed Kimura 2-parameter (K2P) genetic distances in three families. Our second test compared K2P distances of congeneric species with high vs. low morphological distinctness in 20 genera of 11 families. Our third test explored the effect of enlarging geographical sampling area at a continental scale on genetic variability in DNA barcodes within 20 species of nine families. Our results generally point towards a high utility of DNA barcodes in identifying spider ...
As currently recognized, Ecsenius pulcher includes Salarias pulcher (type material has a banded color pattern), S. anom-alus (non-banded), and S. phantasticus (banded). The color patterns are not sex linked, and no other morphological features apparently distinguish the three nominal species. The recent collection of banded and non-banded specimens of Ecsenius pulcher from Iran has provided the first tissue samples for genetic analyses. Here we review the taxonomic history of E. pulcher and its included synonyms and genetically analyze tissue samples of both color patterns. Salarias anom-alus is retained as a synonym of E. pulcher because DNA barcode data suggest that they represent banded and non-banded color morphs of a single species. Furthermore, the large size of the largest type specimen of S. anomalus (herein designated as the lectotype) suggests that it belongs to E. pulcher. A single non-banded specimen from Iran is genetically distinct from E. pulcher and appears to represent an undescribed species. Salarias phantasticus is retained as a synonym of E. pulcher because the primary morphological difference between the two nominal species—presence of spots on the dorsal fin in E. pulcher and absence of those spots in S. phantasticus—is not a valid taxonomic character; rather, the spots represent galls that contain the larval stages of a parasitic crustacean. As males and females of Ecsenius species have been confused in the literature, we describe and illustrate the genital regions of both and comment on possible new blenniid synapomorphies that our investigation revealed.
Evaluating the Accuracy of Morphological Identification of Larval Fishes by Applying DNA Barcoding
PLoS ONE, 2013
Due to insufficient morphological diagnostic characters in larval fishes, it is easy to misidentify them and difficult to key to the genus or species level. The identification results from different laboratories are often inconsistent. This experiment aims to find out, by applying DNA barcoding, how inconsistent the identifications can be among larval fish taxonomists. One hundred morphotypes of larval fishes were chosen as test specimens. The fishes were collected with either larval fish nets or light traps in the northern, southern and northwestern waters of Taiwan. After their body lengths (SL) were measured and specimen photos were taken, all specimens were delivered, in turn, to five laboratories (A-E) in Taiwan to be identified independently. When all the results were collected, these specimens were then identified using COI barcoding. Out of a total of 100 specimens, 87 were identified to the family level, 79 to the genus level and 69 to the species level, based on the COI database currently available. The average accuracy rates of the five laboratories were quite low: 80.1% for the family level, 41.1% for the genus level, and 13.5% for the species level. If the results marked as ''unidentified'' were excluded from calculations, the rates went up to 75.4% and 43.7% for the genus and species levels, respectively. Thus, we suggest that larval fish identification should be more conservative; i.e., when in doubt, it is better to key only to the family and not to the genus or species level. As to the most misidentified families in our experiment, they were Sparidae, Scorpaenidae, Scombridae, Serranidae and Malacanthidae. On the other hand, Mene maculata and Microcanthus strigatus were all correctly identified to the species level because their larvae have distinct morphology. Nevertheless, barcoding remains one of the best methods to confirm species identification.