An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens

Zootaxa ◽  
2011 ◽  
Vol 3104 (1) ◽  
pp. 42 ◽  
Author(s):  
MICHELE CESARI ◽  
ILARIA GIOVANNINI ◽  
ROBERTO BERTOLANI ◽  
LORENA REBECCHI
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Original Description ◽  
Morphological Characters ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Type Locality ◽  
Moss Sample ◽  
Voucher Specimens

We have in recent papers revealed that an integrative taxonomy approach helps to solve taxonomic problems in tardigrades. However, whole tardigrades are required for DNA work, which leaves no hologenophore voucher specimens with adult morphology. Using a novel methodology for the Tardigrada, we introduce the practice of collecting high quality maximum magnification light microscopy images of recently thawed animals to act as hologenophore voucher specimens of animals later used for DNA barcode sequencing. Within the framework of a DNA barcoding project on tardigrades, we collected a moss sample from the type locality of Macrobiotus terminalis Bertolani & Rebecchi, 1993 (Castelsantangelo, Central Apennines, Italy), a species of the “Macrobiotus hufelandi group”. Within the moss sample we found several animals and eggs with a morphology that corresponded to the original description of M. terminalis, while others were attributable to Macrobiotus macrocalix Bertolani & Rebecchi, 1993. In this study, molecular (cox1 mtDNA) analyses demonstrated no intraspecific variability in M. terminalis from the type locality but very large interspecific differences when compared with M. macrocalix and GenBank data for other species within the M. “hufelandi group”. There was also a large difference between our M. terminalis sequences and the GenBank data of a specimen attributed to the same species. The GenBank sequence originated from a population in the Northern Apennines, whose morphology appeared to be like that of the specimens of the locus typicus. This confirmed the importance in utilising material from the type locality for linking molecular data to the species’ morphological characters. Our paper underlines the importance of an integrative taxonomy in species diagnoses and demonstrates a scenario where morphological observations alone are not always sufficient. Lastly, this work adds reliable information to the sequence reference library that provides a useful building block for further studies on similar and related tardigrade taxa.

Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae)

Nematology ◽  
2016 ◽  
Vol 18 (4) ◽  
pp. 455-473 ◽  
Author(s):  
Dmitry M. Miljutin ◽  
Maria A. Miljutina
Keyword(s):  
Deep Sea ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Discrimination ◽  
Species Differentiation ◽  
Lateral Field ◽  
Operational Taxonomic Units ◽  
General Arrangement ◽  
Taxonomic Approach

Acantholaimusis a species-rich genus of deep-sea nematodes, often with dozens of species found at the same locality but each represented by single or few individuals. Species discrimination by morphological characters in this genus is therefore often difficult due to transitional forms that may be referred to several species because of lack of data on intraspecific variability. The aim of this study was to evaluate the intraspecific variability of morphological characters that are most often used inAcantholaimustaxonomy, in order to distinguish those which are most informative for species differentiation. A reverse taxonomic approach was applied for initial species discrimination. Two loci, one each from small and large subunits of rRNA, were sequenced for 59Acantholaimusspecimens from two deep-sea locations. Twenty-seven Molecular Operational Taxonomic Units (MOTU) were identified, of which 12 were represented by more than one individual. These were then analysed for intraspecific variability in morphological characters. Some of the examined characters showed high intraspecific variability; specifically: length of cephalic setae; distance from anterior end to amphid; shape of anterior setae; position and arrangement of cervical setae. In the absence of genetic data, these characters should be used with caution for differential diagnoses or species discrimination. Other characters were more conservative within the same MOTU: body proportions; length of outer labial setae; amphidial diam.; appearance of lateral field; general arrangement of cervical setae; and shape of tail. These characters may be successfully used for species discrimination in the absence of molecular data.

scholarly journals A DNA barcode reference library of the French Polynesian shore fishes

2019 ◽  
Author(s):  
Erwan Delrieu-Trottin ◽  
Jeffrey T. Williams ◽  
Diane Pitassy ◽  
Amy Driskell ◽  
Nicolas Hubert ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Biological Diversity ◽  
Dna Barcode ◽  
Reef Fishes ◽  
French Polynesia ◽  
Morphological Characters ◽  
Reference Library ◽  
Society Islands ◽  
Extensive Collection ◽  
I Gene

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data

Zootaxa ◽  
2021 ◽  
Vol 4995 (1) ◽  
pp. 111-128
Author(s):  
LUCIANO DIOTTI ◽  
ROBERTO CALDARA ◽  
IVO TOŠEVSKI
Keyword(s):  
New Species ◽  
Morphological Study ◽  
Host Plants ◽  
Molecular Study ◽  
Morphological Characters ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
The Other ◽  
Distribution Data ◽  
Two New Species

Two new species of the weevil genus Rhamphus from Italy are herein described: R. bavierai n. sp. (Sicily) and R. hampsicora n. sp. (Sardinia). Both are morphologically and from a molecular perspective close to R. oxyacanthae (Marsham, 1802) and R. monzinii Pesarini & Diotti, 2012. Aside from a diagnostic description and a synoptic key, distribution data and notes on the host plants of the four species are reported. Whereas R. monzinii can be distinguished by several morphological characters, the other three species are morphologically very similar to each other and separable only by the combination of a few subtle characters. On the contrary, a preliminary molecular study revealed substantial divergences of mtCOI from 6.2 to 14.9% between the species, confirming the importance of an integrative taxonomy.  

A proposal for a new generic structure of the killifish family Aphaniidae, with the description of Aphaniops teimorii (Teleostei: Cyprinodontiformes)

Zootaxa ◽  
2020 ◽  
Vol 4810 (3) ◽  
pp. 421-451 ◽  
Author(s):  
JÖRG FREYHOF ◽  
BARAN YOĞURTÇUOĞLU
Keyword(s):  
Original Description ◽  
Morphological Characters ◽  
Molecular Data ◽  
Zoological Nomenclature ◽  
Meristic Characters ◽  
Generic Structure ◽  
Incertae Sedis ◽  
Species Groups ◽  
Colour Patterns ◽  
Fossil Genus

Following an exhaustive review of published molecular data and morphological characters, we propose a new generic classification for the Cyprinodontiform family Aphaniidae. The generic concept applied is based on monophyly, reasonable compactness, and morphological diagnoses. The proposed genera are monophyletic and compact groups that can be diagnosed by a combination of morphological characters. All species in Aphaniidae are morphologically homogeneous and have similar scale patterns, fin positions, and meristic characters. However, only a handful of morphological characters, including colour patterns, permit identification. We propose separation of Aphaniidae into eight monophyletic genera: Anatolichthys, Aphaniops, Aphanius, Kosswigichthys, Paraphanius, and Tellia, in addition to the new genera Esmaeilius and Apricaphanius, which are described for the species of the A. sophiae and A. iberus species groups, respectively. The original description of Aphanius hormuzensis does not fulfil the criteria of the International Commission on Zoological Nomenclature, therefore this taxon is re-described as A. teimorii. Esmaeilius arakensis, E. kavirensis, E. mesopotamicus, and E. pluristriatus are treated as synonyms of E. sophiae. Esmaeilius farsicus is a junior synonym of E. persicus (Jenkins, 1910). The fossil genus Brachylebias is considered as incertae sedis since it lacks diagnostic characters which would permit it to be assigned to any of the extant genera recognised in this study. 

scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

Description of a new species of Plutomurus Yosii (Collembola: Tomoceridae) from Georgia, Caucasus and notes on the morphology of Plutomurus birsteini Djanashvili & Barjadze

Zootaxa ◽  
2020 ◽  
Vol 4790 (2) ◽  
pp. 375-386
Author(s):  
SHALVA BARJADZE ◽  
ROSANNA GIORDANO ◽  
FELIPE SOTO-ADAMES
Keyword(s):  
New Species ◽  
Original Description ◽  
Morphological Characters ◽  
Identification Key ◽  
Type Locality ◽  
Similar Species ◽  
The Caucasus ◽  
Invertebrate Communities ◽  
A New Species

Plutomurus jordanai sp. nov. from Zeda Kvilishori Cave (Tskaltubo Municipality, Imereti region, Western Georgia) is described, illustrated and differentiated from other morphologically similar species‒‒P. kelasuricus Martynova, 1969 and P. eristoi Barjadze, Baquero, Soto-Adames, Giordano & Jordana, 2016. In addition, morphological characters omitted or erroneously provided in the original description of Plutomurus birsteini Djanashvili & Barjadze, 2011 are described and illustrated from the specimen sampled in the type locality‒‒Sakishore Cave (Racha region, Western Georgia). An identification key to the species of the genus Plutomurus reported from the Caucasus is presented. A list of the invertebrate communities for Zeda Kvilishori and Sakishore caves is provided. 

scholarly journals Integrative taxonomists should use and produce DNA barcodes

Zootaxa ◽  
2007 ◽  
Vol 1586 (1) ◽  
pp. 67-68 ◽  
Author(s):  
JOSÉ M. PADIAL ◽  
IGNACIO DE LA RIVA
Keyword(s):  
Dna Barcoding ◽  
Media Coverage ◽  
General Public ◽  
Sequence Divergence ◽  
Integrative Taxonomy ◽  
Dna Fragments ◽  
Dna Barcodes ◽  
Identification Method ◽  
Voucher Specimens ◽  
Scientific Citation

Put simply, DNA barcoding (DNAB) is an identification method that aims to relate short, specific DNA fragments from unidentified specimens to sequences of previously identified voucher specimens through comparison of sequence divergence (Hebert et al. 2003). DNAB has produced noticeable success in terms of scientific citation and media coverage because it is technically feasible, commercially attractive, and philosophically acceptable to many scientists (Smith 2005). Irrespective of the utility to the general public (Cameron et al. 2006), and contrary to other DNA-based methods with taxonomic purposes (Vogler & Monaghan 2006), identification through DNAB is becoming widely available (www.barcodinglife.org). While DNAB is rejected by some taxonomists who view it as a competitor for funds, or a danger to taxonomy (Will & Rubinoff 2004; Ebach & Holdrege 2005), we argue for the complete incorporation of DNAB into integrative taxonomy (sensu Will et al. 2005).

Integrative approach reveals underestimated Peyssonneliales diversity in Brazil: registering the first occurrence of Ramicrusta and Incendia, with the description of three new species

Phytotaxa ◽  
2020 ◽  
Vol 439 (1) ◽  
pp. 39-55
Author(s):  
EDILENE MARIA DOS SANTOS PESTANA ◽  
GOIA DE MATTOS LYRA ◽  
GABRIEL DO NASCIMENTO SANTOS ◽  
CIBELE CONCEIÇÃO DOS SANTOS ◽  
VALÉRIA CASSANO ◽  
...  
Keyword(s):  
New Species ◽  
Original Description ◽  
Morphological Characters ◽  
Type Locality ◽  
Integrative Approach ◽  
Brazilian Coast ◽  
Monophyletic Clade ◽  
Sister Relationship ◽  
First Occurrence ◽  
Three New Species

Peyssonneliaceae represents a monophyletic clade of red encrusting algae classified Peyssonneliales. Molecular analyses have been important for revealing unknown diversity in this family, which includes small, cryptic organisms, frequently distinguished solely by discrete anatomical characters. Brazil however, remains virtually unknown. To assess this diversity, phylogenetic and barcoding analyses using rbcL, COI-5P and SSU data, as well as morpho-anatomical analyses were performed. Here we report the first occurrence of two genera on the Brazilian coast: Ramicrusta and Incendia, and describe three new species: Ramicrusta fujiiana sp. nov., Ramicrusta paradoxa sp. nov. and Incendia yoneshigueana sp. nov. Ramicrusta was resolved as a monophyletic clade in the three reconstructed phylogenies, and had congruent topologies. In the rbcL phylogeny, Ramicrusta fujiiana formed a well-supported clade sister to a well-supported clade including R. aranea (Vanuatu, type locality) and R. textilis (Jamaica, type locality). Morphological characters of R. paradoxa are not in agreement with the original description of the genus. Therefore, we present an updated and broader concept of Ramicrusta. Incendia was resolved as a monophyletic clade with full support for rbcL. Incendia yoneshigueana is in a sister relationship with I. glabra (Vanuatu, type locality). This study extends the distributions of Ramicrusta and Incendia, proposes three new species, and confirms the effectiveness of rbcL, COI-5P and SSU in inferring phylogenetic relationships and delimiting species in the Peyssonneliales. The integrative approach established clear taxonomic concepts for the studied genera and species, and identified useful characters for genera delimitation in Peyssonneliaceae.

DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species

Zootaxa ◽  
2011 ◽  
Vol 2997 (1) ◽  
pp. 19 ◽  
Author(s):  
ROBERTO BERTOLANI ◽  
LORENA REBECCHI ◽  
ILARIA GIOVANNINI ◽  
MICHELE CESARI
Keyword(s):  
Dna Barcoding ◽  
Integrative Taxonomy ◽  
Genetic Distances ◽  
Type Locality ◽  
Morphological Data ◽  
New Taxon ◽  
Black Forest ◽  
Mt Dna ◽  
Additional Material ◽  
Starting Point

Within the framework of a DNA barcoding project on tardigrade species, a study was carried out on Macrobiotus hufelandi C.A.S. Schultze 1834, the first formally described tardigrade species. We used samples collected from the type locality and additional material from other European sites containing species of the “M. hufelandi group”. The study was performed by integrating morphological, karyological and molecular (mt-DNA cox1) information and comparing these data with morphological data from the type material. Several species from this group were found in the type locality of M. hufelandi (near Freiburg, Black Forest, Germany) and these were all barcoded. One was M. hufelandi, the other two were: Macrobiotus sandrae Bertolani & Rebecchi 1993 (originally described from the same locality), and Macrobiotus vladimiri Bertolani, Biserov, Rebecchi & Cesari in press (type locality Andalo, Italy), all with interspecific genetic distances of more than 19%. A fourth cryptic species, which had the same morphology as M. hufelandi but a genetic distance of 6.7%, was not described as a new taxon but named M. cf. hufelandi sp.1 for this study. Macrobiotus sandrae and M. vladimiri were also present (and barcoded) in Italy (Alps). Additional individuals (animals and eggs) were also found, and barcoded, in Italy (Apennines) and Switzerland that belonged to the haplogroup Macrobiotus cf. hufelandi sp. 1. These data together with other recent studies on tardigrade DNA barcoding represent a starting point for further studies on tardigrade biogeography, phylogeography and diversity.

scholarly journals New species of the genus Inversidens Haas, 1911 (Unionoida, Unionidae, Gonideinae) from Jiangxi Province, China

ZooKeys ◽  
2021 ◽  
Vol 1054 ◽  
pp. 85-93
Author(s):  
Ruiwen Wu ◽  
Xiongjun Liu ◽  
Takaki Kondo ◽  
Shan Ouyang ◽  
Xiaoping Wu
Keyword(s):  
New Species ◽  
Dna Barcode ◽  
Freshwater Mussel ◽  
Morphological Characters ◽  
Molecular Data ◽  
Jiangxi Province ◽  
Morphological Description ◽  
Mitochondrial Coi ◽  
Mussel Species

We diagnose and describe a new freshwater mussel species of the genus Inversidens, I. rentianensissp. nov. from Jiangxi Province, China based on morphological characters and molecular data. This paper includes a morphological description and photograph of the holotype, and partial sequences of mitochondrial COI as DNA barcode data.

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