DNA barcodes reveal cryptic genetic diversity within the blackfly subgenus Trichodagmia Enderlein (Diptera: Simuliidae: Simulium) and related taxa in the New World

Zootaxa ◽  
2012 ◽  
Vol 3514 (1) ◽  
pp. 43 ◽  
Author(s):  
LUIS MIGUEL HERNÁNDEZ-TRIANA ◽  
JAMES LEE CRAINEY ◽  
ANDY HALL ◽  
FARRAH FATIH ◽  
JACQUELINE MACKENZIE-DODDS ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Divergence ◽  
New World ◽  
Distinct Species ◽  
Good Resolution ◽  
Dna Barcodes ◽  
Species Complexes ◽  
Taxonomic Concept ◽  
Species Groups

In this paper we investigate the utility of the COI DNA barcoding region for species identification and for revealing hidden diversity within the subgenus Trichodagmia and related taxa in the New World. In total, 24 morphospecies within the current expanded taxonomic concept of Trichodagmia were analyzed. Three species in the subgenus Aspathia and 10 species in the subgenus Simulium s.str. were also included in the analysis because of their putative phylogenetic relationship with Trichodagmia. In the Neighbour Joining analysis tree (NJ) derived from the DNA barcodes most of the specimens grouped together according to species or species groups as recognized by other morphotaxonomic studies. The interspecific genetic divergence averaged 11.2% (range 2.8–19.5%), whereas intraspecific genetic divergence within morphologically distinct species averaged 0.5% (range 0–1.2%). Higher values of genetic divergence (3.2–3.7%) in species complexes suggest the presence of cryptic diversity. The existence of well defined groups within S. piperi, S. duodenicornium, S. canadense and S. rostratum indicate the possible presence of cryptic species within these taxa. Also, the suspected presence of a sibling species in S. tarsatum and S. paynei is supported. DNA barcodes also showed that specimens from species that were taxonomically difficult to delimit such as S. hippovorum, S. rubrithorax, S. paynei, and other related taxa (S. solarii), grouped together in the NJ analysis, confirming the validity of their species status. The recovery of partial barcodes from specimens in collections was time consuming and PCR success was low from specimens more than 10 years old. However, when a sequence was obtained, it provided good resolution for species identification. Larvae preserved in ‘weak’ Carnoy’s solution (9:1 ethanol:acetic acid) provided full DNA barcodes. Adding legs directly to the PCR mix from recently collected and preserved adults was an inexpensive, fast methodology to obtain full barcodes. In summary, DNA barcoding combined with a sound morphotaxonomic framework provides an effective approach for the delineation of species and for the discovery of hidden diversity in the subgenus Trichodagmia.

DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 348-357 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Fernanda Montes De Oca ◽  
Sean W.J. Prosser ◽  
Paul D.N. Hebert ◽  
T. Ryan Gregory ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Black Flies ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
Species Groups

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

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.

New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation

Zootaxa ◽  
2008 ◽  
Vol 1737 (1) ◽  
pp. 1 ◽  
Author(s):  
S. BLAIR HEDGES ◽  
WILLIAM E. DUELLMAN ◽  
MATTHEW P. HEINICKE
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
New World ◽  
Distinct Species ◽  
Species Level ◽  
Southeastern Brazil ◽  
Caribbean Region ◽  
New Taxon ◽  
Distribution Maps ◽  
Species Groups

New World frogs recently placed in a single, enormous family (Brachycephalidae) have direct development and reproduce on land, often far away from water. DNA sequences from mitochondrial and nuclear genes of 344 species were analyzed to estimate their relationships. The molecular phylogeny in turn was used as the basis for a revised classification of the group. The 882 described species are placed in a new taxon, Terrarana, and allocated to four families, four subfamilies, 24 genera, 11 subgenera, 33 species series, 56 species groups, and 11 species subgroups. Systematic accounts are provided for all taxa above the species level. Two families (Craugastoridae and Strabomantidae), three subfamilies (Holoadeninae, Phyzelaphryninae, and Strabomantinae), six genera (Bryophryne, Diasporus, Haddadus, Isodactylus, Lynchius, and Psychrophrynella), and two subgenera (Campbellius and Schwartzius) are proposed and named as new taxa, 13 subspecies are considered to be distinct species, and 613 new combinations are formed. Most of the 100 informal groups (species series, species groups, and species subgroups) are new or newly defined. Brachycephalus and Ischnocnema are placed in Brachycephalidae, a relatively small clade restricted primarily to southeastern Brazil. Eleutherodactylidae includes two subfamilies, four genera, and five subgenera and is centered in the Caribbean region. Craugastoridae contains two genera and three subgenera and is distributed mainly in Middle America. Strabomantidae is distributed primarily in the Andes of northwestern South America and includes two subfamilies, 16 genera, and three subgenera. Images and distribution maps are presented for taxa above the species level and a complete list of species is provided. Aspects of the evolution, biogeography, and conservation of Terrarana are discussed.

scholarly journals Newly Emerging Pest in China, Rhynchaenus maculosus (Coleoptera: Curculionidae): Morphology and Molecular Identification with DNA Barcoding

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 568
Author(s):  
Rui-Sheng Yang ◽  
Ming-Yang Ni ◽  
Yu-Jian Gu ◽  
Jia-Sheng Xu ◽  
Ying Jin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Molecular Identification ◽  
Morphological Characters ◽  
Information Storage ◽  
Morphological Description ◽  
Quick Response ◽  
Dna Barcodes ◽  
Pairwise Divergence ◽  
Coding Capacity

The oak flea weevil, Rhynchaenus maculosus Yang et Zhang 1991, is a newly emerging pest that severely damages oak (genus Quercus) in China. The first R. maculosus outbreak occurred in 2020 and caused spectacular damage to all oak forests in Jilin province, northeast China. The lack of key morphological characters complicates the identification of this native pest, especially in larva and pupa stages. This is problematic because quick and accurate species identification is crucial for early monitoring and intervention during outbreaks. Here, we provided the first detailed morphological description of R. maculosus at four life stages. Additionally, we used DNA barcodes from larva and pupa specimens collected from three remote locations for molecular identification. The average pairwise divergence of all sequences in this study was 0.51%, well below the 2% to 3% (K-2-parameter) threshold set for one species. All sample sequences matched the R. maculosus morphospecies (KX657706.1 and KX657707.1), with 99.23% to 100% (sequence identity, E value: 0.00) matching success. The tree based on barcodes placed the specimens into the Rhynchaenus group, and the phylogenetic relationship between 62 sequences (30 samples and 32 from GeneBank) had high congruence with the morphospecies taxa. The traditional DNA barcodes were successfully transformed into quick response codes with larger coding capacity for information storage. The results showed that DNA barcoding is reliable for R. maculosus identification. The integration of molecular and morphology-based methods contributes to accurate species identification of this newly emerging oak pest.

DNA barcodes fail to accurately differentiate species in Hawaiian plant lineages

2019 ◽  
Vol 190 (4) ◽  
pp. 374-388 ◽  
Author(s):  
Jeffery K Stallman ◽  
Vicki A Funk ◽  
Jonathan P Price ◽  
Matthew L Knope
Keyword(s):  
Genetic Distance ◽  
Dna Barcoding ◽  
Animal Species ◽  
Oceanic Islands ◽  
Dna Barcodes ◽  
Geographical Data ◽  
Rapid Speciation ◽  
High Incidence ◽  
Nuclear Its ◽  
Species Groups

AbstractDNA barcoding has been largely successful in differentiating animal species, but the most effective loci and evaluative methods for plants are still debated. Floras of young, oceanic islands are a challenging test of DNA barcodes, because of rapid speciation, high incidence of hybridization and polyploidy. We used character-based, tree-based and genetic distance-based methods to test DNA barcoding of 385 species of native Hawaiian plants constituting 20 lineages at the nuclear ITS(2) locus, nine lineages at each of the plastid loci trnH-psbA and rbcL, eight lineages at the plastid locus matK and four lineages with concatenated data. We also incorporated geographical range information and tested if varying sample sizes within a lineage influenced identification success. Average discrimination success was low (22% maximum) with all methods of analysis across all loci. The character-based method generally provided the highest identification success, there were limited benefits from incorporating geographical data and no relationship between number of species sampled in a lineage and identification success was found. Percentages of identification success are the lowest reported in a DNA barcoding study of comparable scale, and multi-species groups that radiated in the Hawaiian archipelago probably cannot be identified based on current DNA barcoding loci and methodologies.

Reply to the comment by L. Prendini on "Identifying spiders through DNA barcodes"

2005 ◽  
Vol 83 (3) ◽  
pp. 505-506 ◽  
Author(s):  
Paul D.N Hebert ◽  
Rowan D.H Barrett
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcodes ◽  
Automated Systems ◽  
Life Movement

Our paper on spiders provides an early demonstration of the power of DNA barcoding; we believe that its conclusions will prove scalable to all eukaryotes. We further anticipate that the "Barcode of Life" movement will soon lead to automated systems for species identification and discovery. However, we emphasize that these systems will operate within a Linnaean framework and that collaborations between molecular and morphological taxonomists are critical.

Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Jefferson Monteiro Henriques ◽  
Guilherme José Costa Silva ◽  
Fernando Yuldi Ashikaga ◽  
Robert Hanner ◽  
Fausto Foresti ◽  
...  
Keyword(s):  
Species Identification ◽  
Species Concept ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Morphological Identification ◽  
Operational Taxonomic Units ◽  
Paulo State ◽  
Species Complexes ◽  
Definition Of

AbstractSpecies identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.

scholarly journals Sand fly identification and screening for Leishmania spp. in six provinces of Thailand

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Orawan Phuphisut ◽  
Chanyapat Nitatsukprasert ◽  
Nattaphol Pathawong ◽  
Boonsong Jaichapor ◽  
Arissara Pongsiri ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Distinct Species ◽  
Morphological Characters ◽  
Sand Fly ◽  
Morphological Identification ◽  
Sand Flies ◽  
Operational Taxonomic Units ◽  
Species Complexes ◽  
Human Leishmaniasis ◽  
Leishmania Spp

Abstract Background Phlebotomine sand flies are vectors of Leishmania spp. At least 27 species of sand flies have been recorded in Thailand. Although human leishmaniasis cases in Thailand are mainly imported, autochthonous leishmaniasis has been increasingly reported in several regions of the country since 1999. Few studies have detected Leishmania infection in wild-caught sand flies, although these studies were carried out only in those areas reporting human leishmaniasis cases. The aim of this study was therefore to identity sand fly species and to investigate Leishmania infection across six provinces of Thailand. Methods Species of wild-caught sand flies were initially identified based on morphological characters. However, problems identifying cryptic species complexes necessitated molecular identification using DNA barcoding in parallel with identification based on morphological characters. The wild-caught sand flies were pooled and the DNA isolated prior to the detection of Leishmania infection by a TaqMan real-time PCR assay. Results A total of 4498 sand flies (1158 males and 3340 females) were caught by trapping in six provinces in four regions of Thailand. The sand flies were morphologically classified into eight species belonging to three genera (Sergentomyia, Phlebotomus and Idiophlebotomus). Sergentomyia iyengari was found at all collection sites and was the dominant species at most of these, followed in frequency by Sergentomyia barraudi and Phlebotomus stantoni, respectively. DNA barcodes generated from 68 sand flies allowed sorting into 14 distinct species with 25 operational taxonomic units, indicating a higher diversity (by 75%) than that based on morphological identification. Twelve barcoding sequences could not be assigned to any species for which cytochrome c oxidase subunit I sequences are available. All tested sand flies were negative for Leishmania DNA. Conclusions Our results confirm the presence of several sand fly species in different provinces of Thailand, highlighting the importance of using DNA barcoding as a tool to study sand fly species diversity. While all female sand flies tested in this study were negative for Leishmania, the circulation of Leishmania spp. in the investigated areas cannot be ruled out. Graphical abstract

DNA Barcoding of Simulium asakoae (Diptera: Simuliidae) From Northern Thailand

2020 ◽  
Vol 57 (5) ◽  
pp. 1675-1678 ◽  
Author(s):  
Van Lun Low ◽  
Wichai Srisuka ◽  
Atiporn Saeung ◽  
Tiong Kai Tan ◽  
Zubaidah Ya’cob ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Genetic Divergence ◽  
Species Complex ◽  
Morphological Variability ◽  
Single Species ◽  
Genetic Distances ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Barcode Gap

Abstract Previous studies suggested the presence of species complex in the so-called Simulium asakoae Takaoka & Davies (Diptera: Simuliidae) in Thailand due to its high morphological variability and genetic divergence. To investigate whether the true S. asakoae is present in Thailand, we performed a detailed morphological identification of S. asakoae and compared its DNA barcodes with the morphospecies S. asakoae from Myanmar and the typical S. asakoae from Malaysia. Phylogenetic analysis revealed the Thai materials analyzed in this study were indeed genetically similar with those from Myanmar and Malaysia, though genetic distances 0–2.27% were observed. We tentatively regard this divergence as intraspecific variation, and the automatic barcode gap discovery analysis further supports them as a single species.

scholarly journals DNA barcoding of British mosquitoes (Diptera, Culicidae) to support species identification, discovery of cryptic genetic diversity and monitoring invasive species

ZooKeys ◽  
2019 ◽  
Vol 832 ◽  
pp. 57-76 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Victor A. Brugman ◽  
Nadya I. Nikolova ◽  
Ignacio Ruiz-Arrondo ◽  
Elsa Barrero ◽  
...  
Keyword(s):  
Invasive Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Mosquito Species ◽  
Extraction Methods ◽  
Control Programs ◽  
Species Groups ◽  
Dna Extraction Methods ◽  
The Uk ◽  
Cryptic Genetic Diversity

Correct mosquito species identification is essential for mosquito and disease control programs. However, this is complicated by the difficulties in morphologically identifying some mosquito species. In this study, variation of a partial sequence of the cytochromecoxidase unit I (COI) gene was used for the molecular identification of British mosquito species and to facilitate the discovery of cryptic diversity, and monitoring invasive species. Three DNA extraction methods were compared to obtain DNA barcodes from adult specimens. In total, we analyzed 42 species belonging to the generaAedesMeigen, 1818 (21 species),AnophelesMeigen, 1818 (7 species),CoquillettidiaTheobald, 1904 (1 species),CulexLinnaeus, 1758 (6 species),CulisetaFelt, 1904 (7 species), andOrthopodomyiaTheobald, 1904 (1 species). Intraspecific genetic divergence ranged from 0% to 5.4%, while higher interspecific divergences were identified betweenAedesgeminusPeus, 1971/Culisetalitorea(Shute, 1928) (24.6%) andAe.geminus/An.plumbeusStephens, 1828 (22.5%). Taxonomic discrepancy was shown betweenAn.daciaeLinton, Nicolescu & Harbach, 2004 andAn.messeaeFalleroni, 1828 indicating the poor resolution of theCOIDNA barcoding region in separating these taxa. Other species such asAe.cantans(Meigen, 1818)/Ae.annulipes(Meigen, 1830) showed similar discrepancies indicating some limitation of this genetic marker to identify certain mosquito species. The combination of morphology and DNA barcoding is an effective approach for the identification of British mosquitoes, for invasive mosquitoes posing a threat to the UK, and for the detection of hidden diversity within species groups.

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