The multiple applications of DNA barcodes in avian evolutionary studies

Genome ◽  
2016 ◽  
Vol 59 (11) ◽  
pp. 899-911 ◽  
Author(s):  
Ana S. Barreira ◽  
Darío A. Lijtmaer ◽  
Pablo L. Tubaro
Keyword(s):  
Dna Barcode ◽  
Quality Data ◽  
Dna Barcodes ◽  
Reciprocal Monophyly ◽  
High Quality Data ◽  
Continental Scale ◽  
Interspecific Divergence ◽  
Data Source ◽  
Coi Sequences ◽  
Rich Data

DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit. In addition, we review studies that employed large DNA barcode datasets to study the molecular evolution of mitochondrial genes and the biogeography of islands, continents, and even at a multi-continental scale. These studies showed that DNA barcodes offer high-quality data well beyond their main purpose of serving as a molecular tool for species identification.

scholarly journals DNA barcodes and morphology of P. krempfi, P. mekongensis, and P. elongatus

2016 ◽  
Vol 14 (1) ◽  
pp. 29-37 ◽  
Author(s):  
Dương Thúy Yên ◽  
Nguyễn Kiệt ◽  
Bùi Sơn Nên ◽  
Nguyễn Văn Thường ◽  
Nguyễn Bạch Loan ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Mekong Delta ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Gill Rakers ◽  
Coi Sequences ◽  
Relationship Of ◽  
Metric Traits ◽  
I Gene

Three Pangasius species including P. krempfi, P. elongatus and P. mekongensis, are economically important. They can be mis-identified due to similar external appreance at small sizes. This study aimed to distinguish these species based on their differences in DNA barcode, COI (cytochrome c oxidase subunit I) gene, and morphological characteristics. Fish with various sizes (>90 samples/species) were sampled at the lower Mekong delta region. Kimura-2 parameter genetic distances based on COI sequences of three species (15 samples, in which, 4 unique sequences were assigned Genbank accession numbers from KT289877 to KT289880) are relatively high, ranging 9.33 – 12.10 %. Morphological measurements show that coutanble traits including numbers of fin rays and the first gill rakers vary in similar ranges but ratios of metric traits are significantly different among three species (P<0.01). Principle component analysis using metric traits sets three species apart. P. elongatus is characterized by elongated body, long caudal preduncle, large eyes, and retangle palatine tooth plates. P. krempfi differs from P. mekongesis in characteristics on their head. The number of sections, shape and length of barbel are different among three species. Phylogenetic relationship of three species based on morphology and COI sequences indicate that P. krempfi is closer to P. mekongenis rather than P. elongatus, and that the distance between P. mekongenis and P. elongatus is the largest.

scholarly journals A new species of Litarachna Walter, 1925 (Acari: Hydrachnidia: Pontarachnidae) from Corozal Bay (Belize), described based upon morphology and DNA barcodes

Acarologia ◽  
2021 ◽  
Vol 61 (3) ◽  
pp. 602-613
Author(s):  
Lucia Montes-Ortiz ◽  
Tom Goldschmidt ◽  
Lourdes Vásquez-Yeomans ◽  
Manuel Elías-Gutiérrez
Keyword(s):  
Dna Barcode ◽  
Morphological Description ◽  
Estuarine System ◽  
Dna Barcodes ◽  
Sem Images ◽  
The Family ◽  
Coi Sequences ◽  
First Time ◽  
A New Species ◽  
Electronic Microscope

A new planktonic species of the marine water mites of the family Pontarachnidae Koenike, 1910 is described from Corozal Bay, an estuarine system in Belize. The morphological description includes Scanning Electronic Microscope (SEM) images and is augmented by an analysis of DNA cytochrome c oxidase I (COI) sequences, the DNA barcode, used for the first time for a species description in this group.

scholarly journals DNA barcodes identify medically important tick species in Canada

Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 74-84 ◽  
Author(s):  
Danielle A. Ondrejicka ◽  
Kevin C. Morey ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcode ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Genetic Cluster ◽  
Potential Health ◽  
Intraspecific Divergence ◽  
Coi Sequences ◽  
I Gene ◽  
Barcode Gap

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

scholarly journals Data Fusion for Correcting Measurement Errors

2018 ◽  
Vol 7 (2) ◽  
pp. 175-200
Author(s):  
Tracy Schifeling ◽  
Jerome P Reiter ◽  
Maria Deyoreo
Keyword(s):  
Data Fusion ◽  
National Survey ◽  
Measurement Errors ◽  
College Graduates ◽  
Quality Data ◽  
High Quality ◽  
High Quality Data ◽  
Unrealistic Assumption ◽  
Data Source ◽  
Fusion Framework

AbstractOften in surveys, key items are subject to measurement errors. Given just the data, it can be difficult to determine the extent and distribution of this error process and, hence, to obtain accurate inferences that involve the error-prone variables. In some settings, however, analysts have access to a data source on different individuals with high-quality measurements of the error-prone survey items. We present a data fusion framework for leveraging this information to improve inferences in the error-prone survey. The basic idea is to posit models about the rates at which individuals make errors, coupled with models for the values reported when errors are made. This can avoid the unrealistic assumption of conditional independence typically used in data fusion. We apply the approach on the reported values of educational attainments in the American Community Survey, using the National Survey of College Graduates as the high-quality data source. In doing so, we account for the sampling design used to select the National Survey of College Graduates. We also present a process for assessing the sensitivity of various analyses to different choices for the measurement error models. Supplemental material is available online.

Simulation-driven machine learning for robotics and automation

2019 ◽  
Vol 86 (11) ◽  
pp. 673-684 ◽  
Author(s):  
Mohamed El-Shamouty ◽  
Kilian Kleeberger ◽  
Arik Lämmle ◽  
Marco Huber
Keyword(s):  
Machine Learning ◽  
Quality Data ◽  
High Quality Data ◽  
Industrial Manufacturing ◽  
Physics Simulation ◽  
Individualized Production ◽  
Data Source ◽  
Lot Sizes ◽  
Industrial Use ◽  
Mass Personalization

AbstractMass personalization—a megatrend in industrial manufacturing and production—requires fast adaptations of robotics and automation solutions to continually decreasing lot sizes. In this paper, the challenges of applying robot-based automation in a highly individualized production are highlighted. To face these challenges, a framework is proposed that combines latest machine learning (ML) techniques, like deep learning, with high-end physics simulation environments. ML is used for programming and parameterizing machines for a given production task with minimal human intervention. If the simulation environment realistically captures physical properties like forces or elasticity of the real world, it provides a high-quality data source for ML. In doing so, new tasks are mastered in simulation faster than in real-time, while at the same time existing tasks are executed. The functionality of the simulation-driven ML framework is demonstrated on an industrial use case.

scholarly journals The Taxa of the Hyponephele lycaon – H. lupina Species Complex (Lepidoptera, Nymphalidae, Satyrinae): Deep DNA Barcode Divergence despite Morphological Similarity

2021 ◽  
Vol 69 (1) ◽  
pp. 11-21
Author(s):  
Vladimir A. Lukhtanov ◽  
Elena A. Pazhenkova
Keyword(s):  
Male Genitalia ◽  
Species Complex ◽  
Dna Barcode ◽  
Type Material ◽  
Wing Pattern ◽  
Dna Barcodes ◽  
Morphological Similarity ◽  
Phenotypic Similarity ◽  
Interspecific Divergence ◽  
Accepted Standard

The genus Hyponephele includes about 40 species distributed throughout the southern part of the Palaearctic area. Within this genus, the taxa of the H. lycaon – H. lupina species complex are similar with respect to the wing pattern and genitalia structure. Here we revise this group using analysis of butterfly morphology, DNA barcodes, and study of the type material. We show that, with a few exceptions, the species in this group are allopatric in distribution. Allopatry in combination with phenotypic similarity may be theoretically interpreted as evidence for the conspecifity of these taxa. Here we falsify this hypothesis by using DNA barcode analysis. We show that the species of this complex are genetically very distant and cannot be combined together as a polytypic species. We also demonstrate that H. lupina consists of two deeply diverged allopatric clades, H. lupina s. s. and H. mauritanica comb. & stat. nov. The barcode p-distance between these taxa (3.4-4.9%) is significantly higher than the generally accepted 'standard' minimum interspecific divergence (2.0-3.0% ) threshold. These two clades can also be distinguished by the color of the upperside of the wing in males (brown with conspicuous golden reflection in H. lupina ; dark brown without golden reflection in H. mauritanica) and by details in male genitalia and male androconia structures. Syntypes of Hyponephele sifanica, H. cheena cheena, H. cheena iskander, and H. cheena kashmirica are studied and figured.

scholarly journals Splitting the leafmining shield-bearer moth genus Antispila Hübner (Lepidoptera, Heliozelidae): North American species with reduced venation placed in Aspilanta new genus, with a review of heliozelid morphology

ZooKeys ◽  
2020 ◽  
Vol 957 ◽  
pp. 105-161
Author(s):  
Erik J. van Nieukerken ◽  
Charles S. Eiseman
Keyword(s):  
Central America ◽  
New Genus ◽  
Dna Barcode ◽  
Single Species ◽  
Dna Barcodes ◽  
Host Family ◽  
Main Host ◽  
Candidate Species ◽  
Coi Sequences ◽  
Rich Fauna

The new genus Aspilantagen. n. is described to harbour Nearctic heliozelid moths with reduced venation, previously placed in Antispila Hübner, 1825, with type species Antispila oinophylla van Nieukerken &amp; Wagner, 2012. The erection of this genus has become possible now that monophyly has been supported by a recent phylotranscriptomics analysis. Six species are combined in this genus: Aspilanta oinophylla (van Nieukerken &amp; Wagner, 2012), comb. n., A. hydrangaeella (Chambers, 1874), comb. n., A. ampelopsifoliella (Chambers, 1874), comb. n., A. voraginella (Braun, 1927), comb. n., A. argentifera (Braun, 1927), comb. n., A. viticordifoliella (Clemens, 1860), comb. n. and two candidate species are recognised. DNA barcode COI sequences of Malaise trapped specimens suggest a rich fauna of Aspilanta in Central America. All are leafminers, with Vitaceae as main host family, and single species feeding respectively on Hydrangeaceae and Myricaceae. The species are briefly diagnosed, and data on biology, DNA barcodes and distribution are provided. To place the genus in context, a review of heliozelid morphology and phylogeny is presented and a key to Nearctic genera is given. The genus is confined to North and Central America, possibly also occurring in South America. Aspilanta oinophylla is also an invasive species on grapevine in Italy. The genus is sister to Coptodisca Walsingham, 1895. Another species is removed from Antispila: Heliozela eugeniella (Busck, 1900), comb. n., feeding on Eugenia (Myrtaceae), from Florida.

scholarly journals DNA barcodes of birds from northern Colombia

2021 ◽  
Vol 9 ◽  
Author(s):  
Paulo Pulgarín-R ◽  
Martha Olivera-Angel ◽  
Luisa Ortíz ◽  
Duván Nanclares ◽  
Sara Velásquez-Restrepo ◽  
...  
Keyword(s):  
South America ◽  
Tropical Forest ◽  
Dna Barcode ◽  
Bird Species ◽  
Taxonomic Identification ◽  
Dna Barcodes ◽  
Laboratory Methods ◽  
Blood Samples ◽  
Lowland Tropical Forest ◽  
Coi Sequences

DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood-sampled birds in a lowland tropical forest with various degrees of intervention using standard 3 × 12 m mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 26 COI sequences from 18 species, 10 families and three orders and found that barcodes largely matched (but not always) phenotypic identification (&gt; 90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.

scholarly journals Validity of Pampus liuorum Liu & Li, 2013, Revealed by the DNA Barcoding of Pampus Fishes (Perciformes, Stromateidae)

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 618
Author(s):  
Jiehong Wei ◽  
Renxie Wu ◽  
Yongshuang Xiao ◽  
Haoran Zhang ◽  
Laith A. Jawad ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Valid Species ◽  
Dna Barcodes ◽  
Operational Taxonomic Units ◽  
Barcoding Gap ◽  
Coi Barcoding ◽  
Commercially Important ◽  
Coi Sequences ◽  
Morphological Species ◽  
Fishery Species

The genus Pampus contains seven valid species, which are commercially important fishery species in the Indo-Pacific area. Due to their highly similar external morphologies, Pampus liuorum has been proposed as a synonym of Pampus cinereus. In this study, partial sequences of COI (582 bp) and Cytb (1077 bp) were presented as potential DNA barcodes of six valid Pampus species and the controversial species P. liuorum. A species delimitation of the seven Pampus species was performed to verify their validities. Explicit COI barcoding gaps were found in all assessed species, except for P. liuorum and P. cinereus, which resulted from their smaller interspecific K2P distance (0.0034–0.0069). A Cytb barcoding gap (0.0200) of the two species was revealed, with a K2P distance ranging from 0.0237 to 0.0277. The longer Cytb fragment is thus a more suitable DNA barcode for the genus Pampus. In the genetic tree, using concatenated Cytb and COI sequences, the seven species reciprocally formed well-supported clades. Species delimitations with ABGD, GMYC, and bPTP models identified seven operational taxonomic units, which were congruent with the seven morphological species. Therefore, all of the seven analyzed species, including P. liuorum, should be kept as valid species.

scholarly journals DNA barcodes from northern birds of Colombia

2021 ◽  
Author(s):  
Paulo Pulgarín-R ◽  
Martha Olivera-Angel ◽  
Luisa Ortíz ◽  
Duván Nanclares ◽  
Sara Velásquez-Restrepo ◽  
...  
Keyword(s):  
South America ◽  
Tropical Forest ◽  
Dna Barcode ◽  
Bird Species ◽  
Taxonomic Identification ◽  
Dna Barcodes ◽  
Laboratory Methods ◽  
Blood Samples ◽  
Lowland Tropical Forest ◽  
Coi Sequences

DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood sampled birds in a lowland tropical forest with various degrees of intervention using standard 10 × 12 mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 28 COI sequences from 19 species, 10 families and 3 orders and found that barcodes largely matched (but not always) phenotypic identification (>90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.

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