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.

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 on Bacteria: A Review

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
D. E. Lebonah ◽  
A. Dileep ◽  
K. Chandrasekhar ◽  
S. Sreevani ◽  
B. Sreedevi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Agricultural Production ◽  
Sequence Data ◽  
Bacterial Pathogens ◽  
Review Article ◽  
Food Spoilage ◽  
Identification Technique

Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.

scholarly journals The BPP program for species tree estimation and species delimitation

2015 ◽  
Vol 61 (5) ◽  
pp. 854-865 ◽  
Author(s):  
Ziheng Yang
Keyword(s):  
Species Delimitation ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Species Tree ◽  
Joint Analysis ◽  
Coalescent Model ◽  
Species Phylogeny ◽  
Multispecies Coalescent ◽  
Tree Estimation ◽  
Nuclear Loci

Abstract This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.

scholarly journals A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

2019 ◽  
Vol 37 (4) ◽  
pp. 1211-1223 ◽  
Author(s):  
Tomáš Flouri ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals MtDNA Barcode Identification of Finfish Larvae from Vellar Estuary, Tamilnadu, India

2015 ◽  
Vol 7 (1) ◽  
pp. 16-19 ◽  
Author(s):  
Ramakrishnan THIRUMARAISELVI ◽  
Sourin DAS ◽  
Vellaichamy RAMANADEVI ◽  
Muthusamy THANGARAJ
Keyword(s):  
Genetic Distance ◽  
Data Base ◽  
Species Identification ◽  
Sequence Variation ◽  
Sequence Data ◽  
Species Level ◽  
Gene Marker ◽  
Species Variation ◽  
Mtdna Sequence ◽  
Vellar Estuary

Planktonic larvae were captured in the shallow Vellar estuary, Tamilnadu, India, during January to June 2013 using zooplankton net. Larvae were identified to the species level by comparison with Genbank data base using MtDNA sequence data. Further analysis showed that there is no sequence variation within-species, whereas between-species variation was more than 25%, supporting the suitability for species identification. The highest genetic distance was observed between A. nigropunctatus and M. cephalus (0.434) and the lowest genetic distance was observed between T. jarbua and S. commersoni (0.256). Given the current worldwide interest in DNA barcoding and species identification using MtDNA gene marker (CO1), it was confirmed the efficacy of the Fish-F1 and -R1 primer set, which gave the possibility for identification of finfish larvae at species level.

scholarly journals Identifiability of speciation times under the multispecies coalescent

2020 ◽  
Author(s):  
Laura Kubatko ◽  
Julia Chifman
Keyword(s):  
Sequence Data ◽  
Hypothesis Test ◽  
Gene Trees ◽  
Species Trees ◽  
Computationally Efficient ◽  
Coalescent Model ◽  
Sequencing Technologies ◽  
Multispecies Coalescent ◽  
Branch Lengths ◽  
And Performance

AbstractThe advent of rapid and inexpensive sequencing technologies has necessitated the development of computationally efficient methods for analyzing sequence data for many genes simultaneously in a phylogenetic framework. The coalescent process is the most commonly used model for linking the underlying genealogies of individual genes with the global species-level phylogeny, but inference under the coalescent model is computationally daunting in the typical inference frameworks (e.g., the likelihood and Bayesian frameworks) due to the dimensionality of the space of both gene trees and species trees. Here we consider estimation of the branch lengths in a fixed species tree, and show that these branch lengths are identifiable. We also show that in the case of four taxa simple estimators for the branch lengths can be derived based on observed site pattern frequencies. Properties of these estimators, such as their asymptotic variances and large-sample distributions, are examined, and performance of the estimators is assessed using simulation. Finally, we use these estimators to develop a hypothesis test that can be limit species under the coalescent model.

scholarly journals DNA Barcoding for Identification and Detection of Species

2021 ◽  
Vol 11 (2) ◽  
pp. 3542-3548
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequence ◽  
Sequence Data ◽  
Basic Unit ◽  
Phylogenetic Position ◽  
Comprehensive List ◽  
Dna Sequence Data ◽  
Biological Classification

Identification is a very important part of the taxonomy. Since a species represents the basic unit of biological classification, identifying species is important to understand the systematics and the precise phylogenetic position of particular species. In recent years, species identification and delimitation have seen major improvements because of the incorporation of DNA sequence data. This review provides a comprehensive list of commonly employed nuclear and chloroplast regions used for the barcoding of plants.

scholarly journals High-Level Diversity of Dinoflagellates in the Natural Environment, Revealed by Assessment of Mitochondrial cox1 and cob Genes for Dinoflagellate DNA Barcoding

2008 ◽  
Vol 75 (5) ◽  
pp. 1279-1290 ◽  
Author(s):  
Senjie Lin ◽  
Huan Zhang ◽  
Yubo Hou ◽  
Yunyun Zhuang ◽  
Lilibeth Miranda
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Natural Environment ◽  
Diagnostic Technique ◽  
Long Island Sound ◽  
Distance Threshold ◽  
Mirror Lake ◽  
Primer Sets ◽  
The One ◽  
High Level

ABSTRACT DNA barcoding is a diagnostic technique for species identification using a short, standardized DNA. An effective DNA barcoding marker would be very helpful for unraveling the poorly understood species diversity of dinoflagellates in the natural environment. In this study, the potential utility for DNA barcoding of mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob) was assessed. Among several primer sets examined, the one amplifying a 385-bp cob fragment was most effective for dinoflagellates. This short cob fragment is easy to sequence and yet possess reasonable taxon resolution. While the lack of a uniform gap between interspecific and intraspecific distances poses difficulties in establishing a phylum-wide species-discriminating distance threshold, the variability of cob allows recognition of species within particular lineages. The potential of this cob fragment as a dinoflagellate species marker was further tested by applying it to an analysis of the dinoflagellate assemblages in Long Island Sound (LIS) and Mirror Lake in Connecticut. In LIS, a highly diverse assemblage of dinoflagellates was detected. Some taxa can be identified to the species and some to the genus level, including a taxon distinctly related to the bipolar species Polarella glacialis, and the large number of others cannot be clearly identified, due to the inadequate database. In Mirror Lake, a Ceratium species and an unresolved taxon were detected, exhibiting a temporal transition from one to the other. We demonstrate that this 385-bp cob fragment is promising for lineage-wise dinoflagellate species identification, given an adequate database.

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.

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