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

Mammalia ◽  
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.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta) based on COI and ITS2 genes in China

2021 ◽  
Author(s):  
Tingting Zhou ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Morphological Identification ◽  
Lumbriculus Variegatus ◽  
Mitochondrial Coi ◽  
Aquatic Oligochaete ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaete could serve as an excellent indicator in aquatic monitoring programs. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial COI gene and nuclear ITS2 gene of 83 specimens belonging to 36 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae, and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree based on ITS2 gene, which was coincident with morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even aquatic oligochaete.

scholarly journals Variasi Sekuens Gen COI untuk DNA Barcoding Ikan Tuna

2020 ◽  
Vol 8 (2) ◽  
pp. 70
Author(s):  
Beivy J Kolondam
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Marker Gene ◽  
Bluefin Tuna ◽  
Yellowfin Tuna ◽  
Coi Gene ◽  
Species Variation ◽  
Thunnus Orientalis ◽  
Fish Food ◽  
Tuna Fish

DNA barcoding has been used for species identification of fishes, especially for fish product authentication. In tuna fish food products authentication, DNA barcoding is needed due to its requirement of small amount of samples for species identification. The COI gene, located in mitochondria of animal cells, is established as standard marker for animal DNA barcoding. This research aimed to study the variation in COI gene of tuna fish species in three groups, such as Bluefin tuna (five species), Yellowfin tuna (three species), and other tuna species (five species). The variation comparison showed that this gene can differentiate 11 out of 13 tuna species. The Thunnus orientalis and T. thynnus has 100% similarity over COI gene (identical). Therefore, another marker gene is required to differentiate this two species. Variation in COI gene has the ability to differentiate all species in the genus Thunnus with other genus (Auxis, Euthynnus, and Katsuwonus) by 29 nucleotide sites. Bluefin tuna group has one site unique to two other groups. Yellowfin tuna group did not have site for differentiation. Other tuna species has 33 nucleotide sites for differentiation with two other groups.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

2021 ◽  
Vol 9 ◽  
Author(s):  
Tingting Zhou ◽  
Wei Jiang ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Its2 Region ◽  
Aquatic Oligochaetes ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
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.

scholarly journals The Utility of DNA Barcoding for the Species Identification of Larval Fish in the Lower Ing River, Thailand

2020 ◽  
Vol 20 (9) ◽  
pp. 671-679
Author(s):  
Dutrudi Panprommin ◽  
Kanyanat Soontornprasit ◽  
Siriluck Tuncharoen ◽  
Niti Iamchuen
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Larval Fish ◽  
Average Length ◽  
Conservation Status ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Coi Gene ◽  
Fishery Resource ◽  
Sustainable Fishery

The species identification of larval fish is very important for sustainable fishery resource management. However, identification based on morphological characters is very difficult, complex and error-prone. DNA barcoding with the sequence of cytochrome c oxidase I (COI) gene was used to identify larval fish species from 10 stations in the tributaries of the lower Ing River. One hundred and six samples were collected between May 2016 and April 2017. The average length of the COI nucleotide sequences was approximately 640 bp. A total of 99 nucleotide sequences were identified in 35 species, 31 genera, 19 families and 9 orders, with 97-100% identity with entries in both the GenBank and BOLD databases. The genetic distance within species ranged from 0.000 to 0.004. However, seven samples were identified at only the genus level because their sequences had not been reported in any databases. Based on IUCN conservation status, most species were classified as least concern (77.14%). Approximately 69.23% of all species were related to human uses in fisheries, aquaculture or aquariums, whereas 30.77% of species were not assessed. Trichopsis vittata (family Osphronemidae) (90%) had the most frequency of occurrence, followed by Oryzias minutillus (family Adrianichthyidae) (70%) and Trichopodus trichopterus (family Osphronemidae) (70%).

scholarly journals Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding

2016 ◽  
Author(s):  
Ziheng Yang ◽  
Bruce Rannala
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Model Comparison ◽  
Sequence Data ◽  
Single Species ◽  
Species Variation ◽  
Distance Threshold ◽  
Coalescent Model ◽  
Multispecies Coalescent ◽  
Bayesian Model Comparison

A number of methods have been developed to use genetic sequence data to identify and delineate species. Some methods are based on heuristics, such as DNA barcoding which is based on a sequence-distance threshold, while others use Bayesian model comparison under the multispecies coalescent model. Here we use mathematical analysis and computer simulation to demonstrate large differences in statistical performance of species identification between DNA barcoding and Bayesian inference under the multispecies coalescent model as implemented in the bpp program. We show that a fixed genetic-distance threshold as used in DNA barcoding is problematic for delimiting species, even if the threshold is "optimized", because different species have different population sizes and different divergence times, and therefore display different amounts of intra-species versus inter-species variation. In contrast, bpp can reliably delimit species in such situations with only one locus and rarely supports a wrong assignment with high posterior probability. While under-sampling or rare specimens may pose problems for heuristic methods, bpp can delimit species with high power when multi-locus data are used, even if the species is represented by a single specimen. Finally we demonstrate that bpp may be powerful for delimiting cryptic species using specimens that are misidentified as a single species in the barcoding library.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

scholarly journals DNA Barcoding: A Study of Guppy Fish (Poecilia reticulata) in East Java, Indonesia

2019 ◽  
Vol 11 (2) ◽  
pp. 272-278
Author(s):  
Sucipto Hariyanto ◽  
Hasan Adro’i ◽  
Mahrus Ali ◽  
Bambang Irawan
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Sequences ◽  
Poecilia Reticulata ◽  
Phylogenetic Reconstruction ◽  
Coi Gene ◽  
West Java ◽  
Advance Research ◽  
Phylogeny And Evolution ◽  
Guppy Fish

Poecilia reticulata is a freshwater fish from the northeastern part of South America and spread widely to various countries in Asia and other continents. However, research about P. reticulate is limited even though it is a well-known fish species in Indonesia. The purpose of study was to identify the fish species of P. reticulata through DNA barcoding using the COI gene to determine the phylogenetic relationships among fish populations in East Java, Indonesia. In a present study, there were eight samples of P. reticulata from four different freshwater locations in East Java. Extraction, amplification, and sequencing of DNA samples were conducted to obtain the genetic data and construct a phylogenetic tree based on DNA sequences. The COI gene is the most popular markers to study genetic populations and phylogeography among the animal kingdom. Our phylogenetic reconstruction showed a clear that there were two groups of P. reticulata. The first group was obtain through species from East Java, Sukabumi, West Java (KU692776.1), Dominican Republic, Pandeglang, Banten and Myanmar. The second group was P. reticulata from southern Africa, Brazil, and Sukabumi, West Java (KU692775.1). The result of this study indicate that the guppy fish in East Java identic with P. reticulata from West Java (KU692776.1), which a widely used in classification based on evolutionary relationships. The findings of this study have important implication for the development of advance research about adaptation, phylogeny, and evolution of fish, especially of guppy fish.

Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)

Zootaxa ◽  
2007 ◽  
Vol 1522 (1) ◽  
pp. 1-68 ◽  
Author(s):  
THOMAS KNEBELSBERGER ◽  
MICHAEL A. MILLER
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Coi Gene ◽  
Parthenogenetic Species ◽  
Mediterranean Countries ◽  
Coi Sequences

Until recently the subaptera-group of Phyllodromica contained only one species. The revision of the subaptera-group  herein consists of the two newly described bisexual species, P. iberica and P. quadracantha, endemic to the Iberian Peninsula and a parthenogenetic species, P. subaptera (Rambur, 1838), which is widely distributed over most of the Mediterranean countries and islands. Within P. iberica three conspecific morphotypes are distinguished. The morphological characteristics of the subaptera-group are described. The species and their distributions are described and depicted. A key for the morphological determination of P. quadracantha and the morphotypes of P. iberica is given. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene are included in the species descriptions. The sequence data are suitable for species identification (DNA barcodes). A cladistic analysis of the morphological data and a phylogenetic analysis of the DNA sequences were performed to infer the phylogenetic relationships between the species of the subaptera-group.

scholarly journals Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

2021 ◽  
Author(s):  
Chuanjiang Zhou ◽  
Mengxia Feng ◽  
Yongtao Tang ◽  
Changxing Yang ◽  
Xiaolin Meng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Morphological Characteristics ◽  
Henan Province ◽  
Coi Gene ◽  
Morphological Identification ◽  
Freshwater Shrimp

Freshwater shrimp is an extremely rich species group with a long and problematic taxonomic history, attributed to its wide distribution, numerous species and similar morphology. Shrimp diversity and species identification is utmost important for fisheries management. However, identification based on morphological characteristics is difficult and complex for a non-specialist to perform. The water system of Henan Province is relatively abundant, but there are few investigations of freshwater shrimps and no description of molecular features. The aim of this study was to uncover the species diversity and phylogenetic of freshwater shrimp in Henan province by combining morphological identification and molecular species delimitation (barcoding gene: COI gene). About 1,200 freshwater shrimp samples from 46 sampling sites were collected for preliminary traditional morphological identification, 222 samples of these were been further microscopic examination and molecular delimitation. Here we used tree based method (NJ, ML) and distance based method (ABGD, bPTP) mainly to define species, detect the cryptic species and assess the validity of the barcoding in molecular. Comprehensive morphological identification and molecular delimitation results, there were 9 effective species and more than one cryptic species of freshwater shrimp in the province and moreover all of them can be identified by DNA barcoding. The results of morphological identification and molecular identification show high consistency, which proves the high efficiency in freshwater shrimp species identification of the DNA barcoding and the presence of cryptic species.

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