The taxonomy’s new clothes: a little more about the DNA-based taxonomy

The use of DNA sequences, including DNA barcoding, as a taxonomical tool has been happening for some time (Tautz et al., 2003; Hajibabaei et al., 2007; Packer et al., 2009). However, the description of new species based solely on DNA sequences is a new idea (Cook et al., 2010) and a new practice (Brower, 2010). Our aim is not to further polarize the war between advocates of strictly molecular or strictly morphological systematics (following, e.g., Pires & Marinoni 2010). The objectives here are (i) to present some arguments regarding the perils of the proposition of a model (theory) for solely DNA-based descriptions (Cook et al. 2010) and the actual publication (practice) of such descriptions (Brower 2010), (ii) to discuss some reasons why we believe that adopting strictly DNA taxonomy for species description, setting aside everything we have learned from classic taxonomy, may not be the best alternative and (iii) to present the point of view about these matters of a PhD candidate and a recently graduated PhD working with taxonomy in a developing country.

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Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽

10.1139/g06-025 ◽

2006 ◽

Vol 49 (7) ◽

pp. 851-854 ◽

Cited By ~ 48

Author(s):

Mehrdad Hajibabaei ◽

Gregory AC Singer ◽

Donal A Hickey

Keyword(s):

New Species ◽

Cryptic Species ◽

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Primate Species ◽

Dna Barcodes ◽

Global Biodiversity ◽

Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

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Nine new species of the subgenus Stegana (Steganina) from China, with DNA barcoding information (Diptera: Drosophilidae)

Zootaxa ◽

10.11646/zootaxa.4576.1.4 ◽

2019 ◽

Vol 4576 (1) ◽

pp. 81

Author(s):

BINGXUE LI ◽

YUAN ZHANG ◽

HONGWEI CHEN

Keyword(s):

New Species ◽

Cytochrome C ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Molecular Analysis ◽

Dna Sequences ◽

Mitochondrial Cytochrome ◽

Neighbor Joining ◽

Species Groups ◽

Mtcoi Gene

Eleven (two known and nine new) species of the subgenus Stegana (Steganina) from China are described or redescribed: S. (S.) longifibula Takada, 1968, S. (S.) toyaensis Okada & Sidorenko, 1992, S. (S.) biflava sp. nov., S. (S.) flavivittata sp. nov., S. (S.) hirtifoliacea sp. nov., S. (S.) latitabula sp. nov., S. (S.) panda sp. nov., S. (S.) pinguifoliacea sp. nov., S. (S.) spatulata sp. nov., S. (S.) stachydifolia sp. nov. and S. (S.) unguiculata sp. nov.; they are assigned into the coleoptrata, ornatipes and undulata species groups, respectively. A total of 130 DNA sequences of partial mitochondrial cytochrome c oxidase subunit I (mtCOI) gene of 38 species (including the 11 species) of above-mentioned three groups are newly obtained in this study. These sequences and other available barcoding sequences of the three groups are involved in a molecular analysis using neighbor-joining (NJ) method, in order to assess the availability of DNA barcoding for delimiting the Steganina species. The result indicates that all the sampled Steganina morphospecies within the three groups are monophyletic.

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DNA barcoding unravels three new species and a subspecies of Olepa Watson, 1980 (Lepidoptera, Erebidae, Arctiinae) from India, with morphotypes

Journal of Insect Biodiversity ◽

10.12976/jib/2020.19.2.2 ◽

2020 ◽

Vol 19 (2) ◽

pp. 44-60

Author(s):

APARNA SURESHCHANDRA KALAWATE ◽

K. P. DINESH ◽

A. SHABNAM

Keyword(s):

New Species ◽

Dna Barcoding ◽

Dna Sequences ◽

Dna Barcode ◽

Coi Gene ◽

Male And Female ◽

Morphological Variations ◽

Three New Species ◽

First Time ◽

Respective Species

The genus Olepa is distributed in Palearctic and Oriental regions with more species in India and Sri Lanka. In the recent studies, morphological variations within the group were well established, with couple of first set of mt COI DNA barcodes for at least three species. In the present account, three new species and a new subspecies are described from the northern Western Ghats region of Maharashtra based on mt COI DNA barcode studies. Due to high morphological divergence and complete genetic homogeneity on the mt COI DNA, four morphotypes under two species are reported. Morphological and genital characters of male and female are provided along with their respective species morphotypes for the first time under this genus from India. The genitalia and the habitus of male and female are illustrated. Preliminary phylogenetic tree based on the mt COI DNA sequences available in the GenBank for the genus with the sequences for the new species also provided and discussed. Key words: new taxa, morphotype, Maharashtra, DNA barcoding, mt COI gene

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Accelerating the knowledge of Peruvian Chalcididae (Insecta, Hymenoptera, Chalcidoidea) with integrative taxonomy

Biodiversity Data Journal ◽

10.3897/bdj.7.e35907 ◽

2019 ◽

Vol 7 ◽

Author(s):

Bruno Cancian de Araujo ◽

Marcelo Tavares ◽

Thales Renan Brotto ◽

Juliana Silva-Freitas ◽

Max Estefani Santos ◽

...

Keyword(s):

New Species ◽

Dna Barcoding ◽

Dna Sequences ◽

Fold Increase ◽

Integrative Taxonomy ◽

Morphological Data ◽

Peruvian Amazon ◽

Insect Biodiversity ◽

Canopy Fogging ◽

Molecular Dataset

We present the first regional inventory of the fauna of Chalcididae in the Peruvian Amazon, with a nearly 6-fold increase in the number of species recorded for the country. A total of 418 specimens of Chalcididae were collected between 2000 and 2017 at the Panguana Reserve, Peruvian Amazon, 400 of which were obtained using Malaise traps and the remaining 18 specimens by canopy fogging. The morphological analyses indicated that these specimens represent 183 species of Chalcididae in 10 different genera, with 173 new to Peru and 134 potentially new species. We submitted 268 specimens, representing 167 species, to DNA barcoding. Of these, 141 specimens yielded sequences, 136 of them with a minimum of 300 bp. Sixty specimens were assigned a BIN by the Barcode of Life Database System (BOLD), resulting in 50 BINs. A cluster analysis of 138 individuals that yielded DNA sequences longer than 100 bp revealed 118 MOTUs (molecular operative taxonomic units), all of them highly congruent with the morphological data. Prior to the present study, 37 species in 9 genera of Chalcididae were known from Peru. With our results, this number was increased to 210 species in 13 genera. The present study is the result of a joint effort between the SNSB - Zoologische Staatssammlung München, Germany (ZSM) and the Insect Biodiversity Laboratory of the Universidade Federal do Espírito Santo, Vitória, Brazil (LaBI-UFES), intending to apply an accelerated taxonomic treatment of the Chalcididae of the Panguana reserve using traditional morphological approaches in combination with DNA barcoding. The complete molecular dataset and associated voucher information is publicly available through BOLD. The new species that were discovered as part of the study are being formally described elsewhere as part of taxonomic treatments of Neotropical and world generic revisions at LaBI-UFES.

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Description, DNA barcoding and phylogenetic placement of a remarkable new species of Eopelma (Hymenoptera: Eupelmidae) from Borneo

Zootaxa ◽

10.11646/zootaxa.4263.3.7 ◽

2017 ◽

Vol 4263 (3) ◽

Author(s):

LUCIAN FUSU ◽

ANDREW POLASZEK

Keyword(s):

New Species ◽

Dna Barcoding ◽

Citizen Science ◽

Dna Sequences ◽

Compound Eye ◽

Dna Barcode ◽

Phylogenetic Position ◽

Phylogenetic Placement ◽

Chalcid Wasp

Eopelma gibsoni sp. nov. is described based on a male recently collected in Borneo. It is the second species of the genus to be described, and the first species of chalcid wasp in which a pattern of dark stripes on the compound eye is described. The presence of similar dark stripes on the eyes of other chalcid wasps is discussed, highlighting the importance of citizen science. The description is accompanied by a DNA barcode sequence to assist future identification and association of the sexes. The phylogenetic position of E. gibsoni based on 28S DNA sequences is discussed.

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New Species of Soldier Fly—Sargus bipunctatus (Scopoli, 1763) (Diptera: Stratiomyidae), Recorded from a Human Corpse in Europe—A Case Report

Insects ◽

10.3390/insects12040302 ◽

2021 ◽

Vol 12 (4) ◽

pp. 302

Author(s):

Marek Michalski ◽

Piotr Gadawski ◽

Joanna Klemm ◽

Krzysztof Szpila

Keyword(s):

Case Report ◽

New Species ◽

Dna Barcoding ◽

Forensic Entomology ◽

Morphological Characters ◽

Lower Limbs ◽

Black Soldier Fly ◽

Hermetia Illucens ◽

Practical Applications ◽

Human Corpse

The only European Stratiomyidae species known for feeding on human corpses was the black soldier fly Hermetia illucens (Linnaeus, 1758). Analysis of fauna found on a human corpse, discovered in central Poland, revealed the presence of feeding larvae of another species from this family: the twin-spot centurion fly Sargus bipunctatus (Scopoli, 1763). The investigated corpse was in a stage of advanced decomposition. The larvae were mainly observed in the adipocere formed on the back and lower limbs of the corpse, and in the mixture of litter and lumps of adipocere located under the corpse. Adult specimens and larvae were identified based on morphological characters, and final identification was confirmed using DNA barcoding. Implementing a combination of morphological and molecular methods provided a reliable way for distinguishing the larvae of S. bipunctatus and H. illucens. The potential of S. bipunctatus for practical applications in forensic entomology is currently difficult to assess. Wide and reliable use of S. bipunctatus in the practice of forensic entomology requires further studies of the bionomy of this fly.

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DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽

10.1515/mammalia-2020-0138 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Álvaro J. Benítez ◽

Dina Ricardo-Caldera ◽

María Atencia-Pineda ◽

Jesús Ballesteros-Correa ◽

Julio Chacón-Pacheco ◽

...

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Genetic Distances ◽

Northern Region ◽

Coi Gene ◽

Individual Species ◽

Species Variation ◽

Molossus Molossus ◽

Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

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Nothing in (sponge) biology makes sense – except when based on holotypes

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415000521 ◽

2015 ◽

Vol 96 (2) ◽

pp. 305-311 ◽

Cited By ~ 10

Author(s):

Dirk Erpenbeck ◽

Merrick Ekins ◽

Nicole Enghuber ◽

John N.A. Hooper ◽

Helmut Lehnert ◽

...

Keyword(s):

New Species ◽

Reference Material ◽

Species Identification ◽

Dna Sequences ◽

Morphological Plasticity ◽

Morphological Characters ◽

Molecular Techniques ◽

Reference Sequences ◽

Species Descriptions ◽

Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

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