scholarly journals New insight into the taxonomic resolution of the genus Bythotrephes Leydig (Crustacea: Cladocera) based on molecular data from Central Europe

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maciej Karpowicz ◽  
Magdalena Świsłocka ◽  
Joanna Moroz ◽  
Łukasz Sługocki
Keyword(s):  
Genetic Analysis ◽  
Central Europe ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Monotypic Genus ◽  
Mtdna Coi ◽  
Xix Century ◽  
Insight Into

AbstractThe taxonomic status of the genus Bythotrephes Leydig (Crustacea: Cladocera) has been debated since the second half of the XIX century. The most widespread view of recent decades has been that Bythotrephes is a monotypic genus, which was support by preliminary molecular data. However, the recent detailed morphological revision of this genus clearly distinguishes at least seven species. Therefore, we performed a multi-lake survey in Central Europe to give new insight into the taxonomic status of Bythotrephes by combining genetic analysis with traditional morphology-based taxonomy. Based on the morphology we identified two species in Central Europe, B. brevimanus and B. lilljeborgi, as well as hybrid forms. For the genetic analysis, we used newly obtained 113 sequences of mtDNA COI gene of the 535-bp length Bythotrephes from Central Europe and sequences downloaded from GenBank. There were no significant differences between all analyzed sequences, which supports the hypothesis that Bythotrephes is a monotypic genus, with only one highly polymorphic species. On the other hand, the results of our work could point out that the COI gene is insufficient to evaluate the taxonomic status of Bythotrephes. Nonetheless, we have identified 29 new haplotypes of mtDNA COI, and one which was the same as the haplotype found in North America and Finland. Furthermore, this haplotype was the source variant from which most other haplotypes were derived.

Notes on the molecular taxonomy of the Proclossiana eunomia complex (Lepidoptera, Nymphalidae: Argynnini): analysis of DNA barcodes

2018 ◽  
Vol 8 (1) ◽  
pp. 222-232 ◽  
Author(s):  
R. V. Yakovlev ◽  
N. A. Shapoval ◽  
G. N. Kuftina ◽  
A. V. Kulak ◽  
S. V. Kovalev
Keyword(s):  
Body Size ◽  
Molecular Taxonomy ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Coi Gene ◽  
Wing Pattern ◽  
Molecular Approach ◽  
Dna Barcodes ◽  
Morphological Differences ◽  
Proclossiana Eunomia

The Proclossiana eunomia (Esper, 1799) complex is currently composed of the several subspecies distributed throughout Palaearсtic region and North America. Despite the fact that some of the taxa have differences in wing pattern and body size, previous assumptions on taxonomy not supported by molecular data. Therefore, the identity of certain populations of this complex has remained unclear and the taxonomic status of several recently described taxa is debated. Here, we provide insights into systematics of some Palaearctic members of this group using molecular approach, based on the analysis of the barcoding fragment of the COI gene taking into account known morphological differences.

Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

Zootaxa ◽  
2017 ◽  
Vol 4286 (1) ◽  
pp. 93 ◽  
Author(s):  
OLGA KLISHKO ◽  
MANUEL LOPES-LIMA ◽  
ELSA FROUFE ◽  
ARTHUR BOGAN ◽  
LYUDMILA VASILIEV ◽  
...  
Keyword(s):  
Freshwater Mussel ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Data Set ◽  
Widespread Species ◽  
Molecular Analyses ◽  
Morphological Variations ◽  
Mtdna Coi ◽  
Morphological And Molecular Data

The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio, in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus. Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al. (2004) and Bogatov & Kijashko (2016). 

scholarly journals Integrative Taxonomy of Two Peruvian Strains of Brachionus plicatilis Complex with Potential in Aquaculture

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 671
Author(s):  
Pedro Pablo Alonso Sánchez-Dávila ◽  
Giovanna Sotil ◽  
Araceli Adabache-Ortiz ◽  
Deivis Cueva ◽  
Marcelo Silva-Briano
Keyword(s):  
Egg Production ◽  
Brachionus Plicatilis ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Reproductive Age ◽  
Coi Gene ◽  
Phylogenetic Position ◽  
Mtdna Coi ◽  
The Relationship

Two Peruvian strains of the genus Brachionus were isolated from impacted coastal wetlands. With an integrative taxonomic view, we described their taxonomic status, morphological characters, productive parameters, and phylogenetic position. In the case of both strains, the relationship between biometrics and productive parameters obtained with Principal Components Analysis indicated that the lorica length was associated with longevity, progeny, egg production, and reproductive age, while the lorica width and aperture were associated with the maximum number of eggs carried. Maximum Likelihood and Bayesian Inference analysis carried out with mtDNA COI gene and rDNA ITS1 region showed that both strains were clustered in two clades with distinct phylogenetic positioning from what is currently known for Brachionus plicatilis s.l. One of the strains, Z010-VL, is proposed to be a subspecies of L4 (B. paranguensis), and the other strain, Z018-SD, is proposed as a sub species of SM2 (B. koreanus). In addition, 33 and 31 aquaculture production lineages are proposed, delimited by COI and concatenated COI+ITS1 sequences, respectively. Finally, this study provides new tools that enhance the traceability of the origin of each sub-species throughout the world.

scholarly journals Taxonomic resolution of Stylonychia notophora (Alveolata, Ciliophora, Hypotricha) sensu Sapra and Dass 1970 using an integrative approach

2020 ◽  
Vol 70 (6) ◽  
pp. 3939-3952
Author(s):  
Harpreet Kaur ◽  
Shashi ◽  
Alan Warren ◽  
Ram Krishan Negi ◽  
Komal Kamra
Keyword(s):  
18S Rdna ◽  
Species Delimitation ◽  
Indian Population ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Taxonomic Resolution ◽  
Integrative Approach ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
River Yamuna

The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only minor differences in morphometry, morphogenesis and in 18S rDNA sequences. The 18S rDNA sequences of all six populations had 99% similarity to both T. pustulata and S. notophora. These findings support the contention that S. notophora sensu Sapra and Dass, 1970 was misidentified and is a population of T. pustulata. This study supports the need for adopting an integrative approach based on morphological, morphogenetic and molecular data in order to understand species delimitation in ciliated protists.

scholarly journals Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene

2021 ◽  
Vol 22 (3) ◽  
Author(s):  
Sri Riani ◽  
ROMANUS EDY PRABOWO ◽  
Agus Nuryanto
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Field Trips ◽  
Coi Gene ◽  
Molecular Characteristics ◽  
Severe Problem ◽  
Molecular Barcoding ◽  
Level Identification

Abstract. Riani S, Prabowo RE, Nuryanto A. 2021. Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene. Biodiversitas 22: 1456-1466. Amphibalanus variegatus and A. reticulatus have similar external morphology. Morphological similarities can be a severe problem for direct species-level identification. The problem can be overcome through anatomy-based identification and validated through molecular barcoding. Molecular characterization using the cytochrome c oxidase 1 (COI) gene provides a useful tool for precise species identification. This study attempted to assess the molecular characteristics of morphologically similar barnacle (Amphibalanus) specimens collected at five localities in Indonesia to validate their taxonomic status. Forty-five barnacle specimens were collected during the field trips in Lampung, Jakarta, Semarang, Bali, and Lombok. The COI gene was amplified using LCO1490 and HCO2198 primers. The gene was sequenced using bidirectional sequencing at 1st base Asia. The specimens' taxonomic status was determined based on sequence identity, genetic distance, monophyly, nucleotide compositions, and nucleotides in a particular position. Shell shapes-based identification placed barnacle specimens into A. reticulatus. However, anatomical-based identification placed barnacle samples into two different anatomic groups, which was further validated by molecular data that two anatomic groups of Amphibalanus samples have significant differences in their COI gene. Based on the molecular characteristics, 43 samples were identified as A. reticulatus, while the two remaining samples were identified as A. variegatus.

scholarly journals New acoustic and molecular data shed light on the poorly known Amazonian frog Adenomera simonstuarti (Leptodactylidae): implications for distribution and conservation

2020 ◽  
Author(s):  
Thiago R. Carvalho ◽  
Leandro J.C.L. Moraes ◽  
Ariadne Angulo ◽  
Fernanda P. Werneck ◽  
Javier Icochea ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Taxonomic Resolution ◽  
Future Research ◽  
Nominal Species ◽  
Phenotypic Data ◽  
Voucher Specimen ◽  
Genetic Lineages ◽  
Conservation Concern

Adenomera simonstuarti is a poorly known species complex inhabiting western Amazonia. Here we reevaluate the species diversity within this complex based on previously documented and newly acquired molecular and phenotypic data. We also redescribe the calling pattern of the nominal species based on the original recording (Peru) and a new recording (Brazil). Our results indicate eight geographically structured genetic lineages and the nominal species with a multi-note call pattern. This is the first association of calls and DNA sequence from a voucher specimen, thereby enabling the assignment of A. simonstuarti to one specific lineage within the complex. The multi-note call was not previously reported and represents an important additional diagnostic character within Adenomera. The geographic distribution of A. simonstuarti is substantially narrowed down to the southwestern portion of the entire geographic range recognized for the complex. The lack of taxonomic resolution in the complex is a major conservation concern by preventing us from evaluating the potential threats and extinction risks of each of the lineages. Future research should follow the protocol of combining calls and DNA sequences associated with voucher specimens as a means to address the taxonomic status of genetic lineages within the A. simonstuarti complex.

scholarly journals Assessment of the macroinvertebrate community of the Vjosa river through non-destructive DNA metabarcoding of preservative ethanol

2021 ◽  
Vol 4 ◽  
Author(s):  
Marie Brasseur ◽  
Simon Vitecek ◽  
Vera Zizka ◽  
Jan Martini ◽  
Remo Wüthrich ◽  
...  
Keyword(s):  
Habitat Diversity ◽  
Molecular Data ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Natural State ◽  
Dna Metabarcoding ◽  
Balkan Region ◽  
Stream Biodiversity ◽  
Dna Template ◽  
Non Destructive

Streams and rivers represent hotspots of biodiversity in their natural state. This biodiversity is declining worldwide due to pollution, exploitation and hydromorphological degradation of these systems. One of the last big, natural rivers in Europe is the Vjosa in the Balkan region. The catchment is characterized by natural flow dynamics, resulting in high habitat diversity and turnover, and hosts several sensitive and endemic species (e.g. Isoperla vjosae). DNA metabarcoding represents a promising approach to characterize this biodiversity but methodological drawbacks such as primer bias or incomplete reference databases limit the application, particularly in taxonomically underexplored regions. Here, we assessed stream biodiversity with a focus on macrozoobenthic (MZB) taxa via a non-destructive, voucher-preserving DNA metabarcoding protocol. In this approach, ethanol used for preservation of multi-habitat samples in the field was used as DNA template, allowing to retain the integrity of the original sample and further comparison of molecular and morphological taxa lists. Samples were taken in spring and autumn 2018 at 48 sites allocated over the Vjosa catchment. The preservative ethanol was filtered through 0.43 um nitrocellulose membranes from which DNA was extracted. Subsequently, a 421 bp fragment of the COI gene was amplified with the primer pair BF2/BR2 and Illumina sequenced. After filtering for sequences with similarity to reference entries >85%, 4,123 OTUs were obtained, of which 921 were identified as MZB taxa. Dipterans and ephemeropterans were most abundant, followed by plecopterans. Some taxa (e.g. molluscs) were not identified due to a known primer bias and >7,000 OTUs could not be assigned above 85 % similarity. Using the here presented voucher-preserving approach allowed us to identify the pitfalls of DNA metabarcoding as tool for biodiversity assessment in taxonomically unexplored regions such as the Vjosa catchment. However, the comparison of specimen abundance data and molecular data showed the power of non-destructive fixative metabarcoding for detecting MZB communities with highly increased taxonomic resolution.

Serpinema cayennensis n. sp. (Nematoda: Camallanidae), a parasite of the freshwater turtle Rhinoclemmys punctularia Daudin (Reptilia: Testudines: Geoemydidae) from French Guiana: morphology and phylogenetic relationships with other turtle-parasitising camallanids

Zootaxa ◽  
2019 ◽  
Vol 4679 (1) ◽  
pp. 181-193
Author(s):  
FLORENCE HARNOSTER ◽  
ROMAN SVITIN ◽  
LOUIS DU PREEZ
Keyword(s):  
French Guiana ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Molecular Data ◽  
Coi Gene ◽  
Freshwater Turtle ◽  
Freshwater Turtles ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit 1 ◽  
A New Species

The genus Serpinema was erected from the genus Camallanus to include species parasitising freshwater turtles. Following this, the taxonomic status of Serpinema was challenged by different authors considering it as a subgenus or junior synonym of Camallanus. Several specimens of these nematodes were retrieved from the spot-legged wood turtle Rhinoclemmys punctularia from Cayenne, French Guiana. These specimens clearly differed from previously reported Serpinema and Camallanus species parasitising turtles by the number of caudal papillae, shape of spicules and development of vulvar lips. Based on morphological characters the nematodes were assigned to the genus Serpinema and described as a new species S. cayennensis n. sp. The description followed by the molecular data analyses based on 28S, 18S rDNA and cytochrome oxidase subunit 1 (COI) gene sequences. 

Species composition and molecular phylogeny of the Indo-Pacific teatfish (Echinodermata:Holothuroidea) bêche-de-mer fishery

2004 ◽  
Vol 55 (8) ◽  
pp. 837 ◽  
Author(s):  
Sven Uthicke ◽  
Tim D. O'Hara ◽  
Maria Byrne
Keyword(s):  
Conservation Management ◽  
Sequence Divergence ◽  
Taxonomic Status ◽  
Wide Distribution ◽  
Coi Gene ◽  
Mtdna Sequences ◽  
The Indian Ocean ◽  
Commercially Important ◽  
Colour Morphs ◽  
Insight Into

Using mtDNA sequences we found that the Indo-Pacific teatfish fishery comprises at least three species, clarifying confusion on the taxonomic status of these commercially important holothurians. Traditional taxonomic characters, including the morphology of skeletal structures, could not be used to differentiate the species. Sequences of the COI gene (529 bp) distinguished three haplotype clusters, corresponding to distinct colour forms and, to some extent, previously described species. The white teatfish, Holothuria fuscogilva, comprises a range of colour morphs and has a wide distribution over the tropical Indo-Pacific region. The large sequence divergence indicates potential for the presence of several cryptic species in the white teatfish complex. In contrast to current taxonomy, we identified two species of black teatfish that appear to be allopatric: H. whitmaei is entirely black and has a Pacific distribution; whereas H. nobilis has white ventro-lateral dots and only occurs in the Indian Ocean. There is evidence for allopatric speciation between the black teatfish species, possibly driven by separation of the oceans and altered current patterns during the Pliocene, resulting in relatively young species with low intraspecific sequence divergence. These results provide insight into speciation in these tropical holothurians and are crucial for their conservation management.

scholarly journals DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 107 ◽  
Author(s):  
Arely Martínez-Arce ◽  
Alberto De Jesús-Navarrete ◽  
Francesca Leasi
Keyword(s):  
Dna Barcoding ◽  
Low Cost ◽  
Nematode Species ◽  
Molecular Data ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Species List ◽  
Nematode Diversity ◽  
Coi Sequences ◽  
Morphological And Molecular Data

Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

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