scholarly journals DNA barcoding for identification of anuran species in the central region of South America

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10189
Author(s):  
Ricardo Koroiva ◽  
Luís Reginaldo Ribeiro Rodrigues ◽  
Diego José Santana
Keyword(s):  
South America ◽  
High Efficiency ◽  
Central Area ◽  
Coi Gene ◽  
Reference Database ◽  
Mato Grosso ◽  
Species Discovery ◽  
Mitochondrial Coi ◽  
Anuran Species ◽  
Specimen Identification

The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.

scholarly journals Molecular diversity of freshwater fishes of Bangladesh assessed by DNA barcoding

2020 ◽  
Vol 48 (1) ◽  
pp. 1-19
Author(s):  
Md Sagir Ahmed ◽  
Sujan Kumar Datta ◽  
Ayesha Akhter Zhilik
Keyword(s):  
Dna Barcoding ◽  
High Efficiency ◽  
Gc Content ◽  
Freshwater Fishes ◽  
Coi Gene ◽  
P Value ◽  
Base Pairs ◽  
Mitochondrial Coi ◽  
Interspecific Distance ◽  
The Mean

This study represents the comprehensive molecular identification of freshwater fishes of Bangladesh based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome. A total of 315 mitochondrial COI barcode sequences were obtained from 153 species,114 genera, 49 families and 16 orders of fishes. The mean length of the sequences was 652 base pairs. For all the samples, %G was significantly lower compared to the other nucleotides and %GC was lower compared to %AT (p-value ˂ 0.05). Also, a significantly lower %GC content was observed in second and third codon position compared to the first one in all the samples (1st>2nd>3rd, p-value˂ 0.05). The average K2P distances within species, genera, families and orders were 0.38%, 7.02%, 12.75% and 18.68%, respectively. The mean interspecific distance was 18-fold higher than the mean intraspecific distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species according to their taxonomic position. A total of 12 species were newly recorded in Bangladesh. High efficiency in species identification were demonstrated in the present study by DNA barcoding, and concluded that COI sequencing can be used as an authentic identification marker for freshwater fish species. Bangladesh J. Zool. 48(1): 1-19, 2020

scholarly journals Review of genetic diversification of bats in the Caribbean and biogeographic relationships to Neotropical species based on DNA barcodes

Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 65-73 ◽  
Author(s):  
Burton K. Lim
Keyword(s):  
Dominican Republic ◽  
Cryptic Species ◽  
Central America ◽  
Neotropical Region ◽  
Reference Database ◽  
Dna Barcodes ◽  
Species Discovery ◽  
Neotropical Species ◽  
The Caribbean ◽  
Specimen Identification

DNA barcoding is helping in discovering high levels of cryptic species and an underestimation of biodiversity in many groups of organisms. Although mammals are arguably the most studied and one of the least speciose taxonomic classes, the rate of species discovery is increasing and biased for small mammals on islands. An earlier study found bats in the Caribbean as a taxonomic and geographic deficiency in the International Barcode of Life initiative to establish a genetic reference database to enable specimen identification to species. Recent surveys in Dominican Republic, Jamaica, and Martinique have documented and barcoded half of the 58 bat species known from the Caribbean. I analyze all available barcode data of Caribbean bats to investigate biogeography and cryptic species in the Neotropical region. Analysis of the mitochondrial DNA gene cytochrome c oxidase subunit 1 results in a phylogenetic tree with all but one species as well-supported and reciprocally monophyletic. With a broader sampling across the Neotropics, there are also divergent lineages that exhibit biogeographic structuring: (i) a phylogenetic split between northern and southern Dominican Republic in three species, (ii) two taxa with cryptic species associated with higher degree of island endemism, (iii) populations of two widely distributed species with deep divergence between the Caribbean and North and Central America, and (iv) one species in the Caribbean with affinities to taxa in South America.

Angiostrongylus vasorum from South America and Europe represent distinct lineages

Parasitology ◽  
2009 ◽  
Vol 136 (1) ◽  
pp. 107-115 ◽  
Author(s):  
R. JEFFERIES ◽  
S. E. SHAW ◽  
M. E. VINEY ◽  
E. R. MORGAN
Keyword(s):  
South America ◽  
Taxonomic Revision ◽  
Single Species ◽  
Angiostrongylus Vasorum ◽  
Coi Gene ◽  
Separate Species ◽  
Domestic Species ◽  
Mitochondrial Coi ◽  
Rates Of Evolution ◽  
Evolutionary Event

SUMMARYAngiostrongylus vasorum is a nematode parasite of sylvan and domestic species of the family Canidae. It has a broad but patchy distribution worldwide, and there is evidence for geographical spread and increasing incidence of infection in recent years. While historically Angiostrongylus-like nematodes identified in dogs and foxes have been described as A. vasorum in Europe and Angiocaulus raillieti in South America, more recent taxonomic revision has amalgamated these into a single species, A. vasorum. Here we report, for the first time, the molecular characterization of isolates of A. vasorum from Germany, Portugal, Denmark and the United Kingdom on the basis of the mitochondrial COI gene and the second ribosomal internal transcribed spacer. When compared with isolates from Brazil, sequence analysis revealed 2 distinct genotypes. Estimated rates of evolution based on COI sequences for both nematode and host are consistent with the hypothesis that the presence of A. vasorum in South America is a result of an ancient evolutionary event. Angiostrongylus vasorum in South America potentially represents a separate species to that observed in Europe.

scholarly journals DNA Barcoding for Selected Mangrove-Based Estuary Fishes from Way Kambas National Park, Lampung Province, Indonesia

2021 ◽  
Vol 11 (2) ◽  
pp. 151-160
Author(s):  
Yanti Ariyanti ◽  
◽  
Ika Rini ◽  
Indah Oktaviani ◽  
Sovia Leksikowati ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
National Park ◽  
Conservation Status ◽  
Genetic Distances ◽  
Coi Gene ◽  
Species Discovery ◽  
Mitochondrial Coi ◽  
Identification Of Species ◽  
Way Kambas National Park

Over the past decade, DNA barcoding has provided new insight into fish ecology and biosystematics and led to new species' discovery. DNA barcoding is a method for the recognition and identification of species using short, standardised DNA fragments. The correct taxonomic identification of species is critical for the assessment and monitoring of biodiversity. This study applied DNA barcoding techniques to identify selected fish species from a mangrove-based estuary in Way Kambas National Park, Lampung Province, Indonesia. The gene encoding cytochrome c oxidase subunit I (COI) was amplified and bi-directionally sequenced from 22 specimens. The resulting 680 base pairs (bp) sequence was used to identify species, obtain phylogenetic information, and analyse genetic distances. A neighbour-joining tree was constructed based on the mitochondrial COI gene using the Kimura two-parameter model. This study also exhibits conservation status for those identified species. Our findings will facilitate future studies of fish species diversity in mangrove estuary-based ecosystems and provide preliminary data in policymaking in conservation areas such as National Park.

A Synopsis of Dicliptera (Acanthaceae) in Brazil, with the Description of Two New Species

2020 ◽  
Vol 45 (2) ◽  
pp. 340-348
Author(s):  
James Lucas da Costa-Lima ◽  
Earl Celestino de Oliveira Chagas
Keyword(s):  
New Species ◽  
South America ◽  
The State ◽  
Northeastern Brazil ◽  
Mato Grosso ◽  
The North ◽  
New Synonyms ◽  
Two New Species ◽  
Mato Grosso Do Sul ◽  
A New Species

Abstract—A synopsis of Dicliptera (Acanthaceae) for Brazil is presented. Six species are recognized: Dicliptera ciliaris, D. sexangularis, and D. squarrosa, widely distributed in South America; D. purpurascens, which ranges from the North Region of Brazil (in the state of Acre) to eastern Bolivia; D. gracilirama, a new species from the Atlantic Forest of northeastern Brazil; and D. granchaquenha, a new species recorded in dry and semideciduous forests in Bolivia and western Brazil, in the state of Mato Grosso do Sul. Furthermore, we propose new synonyms and designate lectotypes for eleven names. An identification key to the six accepted Dicliptera species in Brazil is provided.

Characterizing population structure of coral-associated fauna from mesophotic and shallow habitats in the Caribbean

2018 ◽  
Vol 99 (3) ◽  
pp. 619-629 ◽  
Author(s):  
Alex J. Veglia ◽  
Nicholas M. Hammerman ◽  
Carlos R. Rivera Rosaly ◽  
Matthew Q. Lucas ◽  
Alexandra Galindo Estronza ◽  
...  
Keyword(s):  
Population Structure ◽  
Puerto Rico ◽  
Marine Invertebrates ◽  
Geographic Distance ◽  
Harpacticoid Copepod ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Symbiotic Relationships ◽  
Harpacticoid Copepods ◽  
Obligate Symbiont

Symbiotic relationships are a common phenomenon among marine invertebrates, forming both obligatory and facultative dependencies with their host. Here, we investigate and compare the population structure of two crustacean species associated with both shallow and mesophotic ecosystems: an obligate symbiont barnacle (Ceratoconcha domingensis), of the coral Agaricia lamarcki and a meiobenthic, free-living harpacticoid copepod (Laophontella armata). Molecular analyses of the Cytochrome Oxidase Subunit I (COI) gene revealed no population structure between mesophotic and shallow barnacle populations within south-west Puerto Rico (ΦST = 0.0079, P = 0.33). The absence of population structure was expected due to the pelagic naupliar larvae of the barnacles and the connectivity patterns exhibited by the coral itself within the same region. Laophontella armata exhibited significant structure based on the mitochondrial COI gene between the mesophotic reef ecosystem of El Seco, Puerto Rico and mangrove sediments of Curaçao (ΦST = 0.2804, P = 0.0). The El Seco and Curaçao copepods shared three COI haplotypes despite the obligatory benthic development of harpacticoid copepods and the geographic distance between the two locations. Three other COI haplotypes from El Seco exhibited higher than expected (up to 7%) intra-species variability, potentially representing three new cryptic species of harpacticoid copepods or rare, deeply divergent lineages of L. armata. This result is evidence for the urgent need of a deeper investigation into the meiofauna diversity associated with mesophotic coral ecosystems (MCEs), arguably the most diverse metazoan component of MCEs.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

A review of the genus Forficuloecus Conci (Phthiraptera: Philopteridae) from parrots (Psittaciformes: Psittacidae), with descriptions of four new species

Zootaxa ◽  
2008 ◽  
Vol 1859 (1) ◽  
pp. 49 ◽  
Author(s):  
ROGER D. PRICE ◽  
KEVIN P. JOHNSON ◽  
RICARDO L. PALMA
Keyword(s):  
New Species ◽  
Coi Gene ◽  
Chewing Louse ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Genetic Distinctiveness

Ten species, including four new species, of the chewing louse genus Forficuloecus Conci, 1941, are recognized from Australasian parrots, and a key is given for their identification. The new species and their type hosts are: F. cameroni ex the Red-winged Parrot, Aprosmictus erythropterus (J.F. Gmelin, 1788); F. banksi ex the Mulga Parrot, Psephotus varius Clark, 1910; F. wilsoni ex the Northern Rosella, Platycercus venustus (Kuhl, 1820); and F. josephi ex the Bourke's Parrot, Neopsephotus bourkii (Gould, 1841). Partial sequences of the mitochondrial COI gene support the genetic distinctiveness of these new species.

Are Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara (Acari: Tetranychidae) one species? Morphological and molecular evidences for synonymy between these two spider mite species and a note on invasiveness of T. macfarlanei on okra and eggplant in India

2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda
Keyword(s):  
Spider Mite ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mite Species ◽  
Coi Gene ◽  
High Similarity ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
High Degree ◽  
Degree Of Similarity

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 

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