scholarly journals Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9680
Author(s):  
Pablo Viana Oliveira ◽  
Francine Alves Nogueira de Almeida ◽  
Magda Delorence Lugon ◽  
Karolinni Bianchi Britto ◽  
Janyra Oliveira-Costa ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequencing ◽  
High Resolution Melting ◽  
Coi Gene ◽  
Morphological Identification ◽  
Mitochondrial Coi ◽  
New Methods ◽  
Degraded Samples ◽  
Sequencing Technique ◽  
Coi Sequences

Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.

scholarly journals Combining old and new evidence to increase the known biodiversity value of the Sahamalaza Peninsula, Northwest Madagascar

2017 ◽  
Vol 86 (4) ◽  
pp. 273-295 ◽  
Author(s):  
Samuel G. Penny ◽  
Angelica Crottini ◽  
Franco Andreone ◽  
Adriana Bellati ◽  
Lovasoa M.S. Rakotozafy ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Taxonomy ◽  
Coi Gene ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Taxonomic Identification ◽  
Pitfall Trapping ◽  
Wet Season ◽  
Mitochondrial Coi ◽  
Coi Sequences

Prior herpetological surveys in 1996 and 2000 identified 14 species of amphibians and 32 species of reptiles from the Sahamalaza Peninsula. This work increases the total number of amphibian and reptile species known from this area to 20 and 43 respectively. To maximise our chances of species detection, survey effort covered the entire wet season and part of the dry season, and utilised a combination of opportunistic searching, transect searching, pitfall trapping, and acoustic recording. We identified species through an integrative taxonomic approach, combining morphological, bioacoustic and molecular taxonomy. Together, this enabled the detection of cryptic and seasonally inactive species that were missed in the shorter prior surveys that relied on morphological identification alone. The taxonomic identification of amphibians utilised a fragment of the mitochondrial 16S rRNA gene; taxonomic identification of reptiles utilised a fragment of the mitochondrial COI gene, and when necessary, also mitochondrial fragments of the 16S rRNA ND1, ND2, ND4 genes. All sequences were deposited in Genbank and COI sequences were also deposited in the BOLD database to foster taxonomic identification of malagasy reptiles. We report two new taxa: a species of Boophis, since described as B. ankarafensis, and a candidate new species of microhylid (genus: Stumpffia). We document range expansions of Boophis tsilomaro, Cophyla berara, Blaesodactylus ambonihazo beyond their type localities. Along with significant range expansions across a range of taxa, including Blommersia sp. Ca05, Boophys brachychir, Brookesia minima, Ebenavia inunguis, Geckolepis humbloti, Madascincus stumpffi, Pelomedus subrufa and Phelsuma kochi. Forest in the peninsula is under extreme pressure from human exploitation. Unless unsustainable agricultural and pastoral practices encroaching on these habitats halt immediately, both forest and the species that occur there, several of which appear to be local endemics, may be irreversibly lost.

New species of Sargassum-boring Limnoria Leach, 1814 (Crustacea, Isopoda, Limnoriidae) from Japan

Zootaxa ◽  
2021 ◽  
Vol 4970 (1) ◽  
pp. 119-130
Author(s):  
HIROKI YOSHINO ◽  
YURIKO KAMBARA ◽  
SHOTA KAJIWARA ◽  
TAKESHI A. OHSAWA
Keyword(s):  
New Species ◽  
The Other ◽  
Coi Gene ◽  
Congeneric Species ◽  
Japanese Species ◽  
Mitochondrial Coi ◽  
Chiba Prefecture ◽  
Mitochondrial Coi Gene ◽  
Mandibular Palp ◽  
Coi Sequences

A new marine Sargassum-boring species of Limnoria (Limnoriidae) is described on the basis of specimens obtained at Kamogawa-shi, Chiba Prefecture, Japan. Limnoria aspera sp. nov. shares a reduced mandibular palp to a seta, algal-feeding, and the clavate shaped epipod of the maxilliped with the other species of non-mandibular-palp group. L. aspera sp. nov. differs morphologically from the congeneric species by secondary unguis of pereopods and unique carinae of pleonite 5 and pleotelson. We describe the sequences of the mitochondrial COI gene and the nuclear 28S rDNA gene. L. aspera sp. nov. differs by 14.2–18.0% in p-distance based on COI sequences from other Japanese species, L. furca and L. nagatai. 

scholarly journals Identification of Megaselia scalaris (Diptera : Phoridae) based on morphology and mitochondrial 16S rRNA and COI gene sequences

2016 ◽  
Vol 25 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Mohammad Shamimul Alam ◽  
Khandaker Asif Ahmed ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
Model Organism ◽  
Coi Gene ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Neighbor Joining ◽  
Mitochondrial Coi ◽  
Molecular Approaches ◽  
Megaselia Scalaris ◽  
Rrna Sequences

Megaselia scalaris (Diptera: Phoridae), commonly known as scuttle fly, is widely distributed all over the world. It is easily cultured in the laboratory condition making it a potential model organism. Besides, it has forensic importance. However, no report from Bangladesh could be retrieved about this fly. So, in the present study, identification of this species was attempted using both morphological and molecular approaches. Characteristics of male hypopygium and legs played key roles in morphological identification. To strengthen identification, mitochondrial COI and 16S rRNA gene fragments were amplified and sequenced. Blast search at NCBI provided highest hits to available COI and 16S rRNA sequences of M. scalaris. A neighbor joining phylogenetic tree was built using sequences of respective COI gene region to show its relationship among other closely related dipteran flies. Dhaka Univ. J. Biol. Sci. 25(2): 149-159, 2016 (July)

New record of Thor hainanensis Xu & Li, 2014 and taxonomical remarks on Lysmata ternatensis de Man, 1902 (Decapoda: Thoridae & Lysmatidae) from the Lakshadweep Islands, India

Zootaxa ◽  
2019 ◽  
Vol 4624 (3) ◽  
pp. 351-364
Author(s):  
MANU MADHAVAN ◽  
P. PURUSHOTHAMAN ◽  
S. AKASH ◽  
S. BHARATHI ◽  
SHEENA JOSE ◽  
...  
Keyword(s):  
Related Species ◽  
New Record ◽  
Hainan Island ◽  
Morphological Identification ◽  
Closely Related Species ◽  
Mitochondrial Coi ◽  
Taxonomic Description ◽  
Coi Sequences ◽  
De Man ◽  
Relationship Of

The present study reports the new record of Thor hainanensis Xu & Li, 2014, on the basis of material from Agatti Islands in the Lakshadweep, India. This species was recently described from Hainan Island, China. Relationship of this species to two closely related species (T. paschalis and T. amboinensis) is discussed in this manuscript. Similarly, the present study also reports the rediscovery of other species, Lysmata ternatensis De Man, 1902 from the Lakshadweep waters with detailed taxonomic description. The present specimens were found to occur in the intertidal region in small crevices and rocks at a depth of 0.5-2.0 m. Genetic analysis using the mitochondrial COI sequences for both the species reveals close agreement for the morphological identification and showed the significant variation from the closely related species. 

scholarly journals Phortica eparmata species complex (Diptera, Drosophildae) from the Oriental Region, with DNA barcoding information of Chinese species

2018 ◽  
Author(s):  
Lin Zhu ◽  
Huiluo Cao ◽  
Hongwei Chen
Keyword(s):  
New Species ◽  
Species Complex ◽  
Coi Gene ◽  
Oriental Region ◽  
Mitochondrial Coi ◽  
Species Complexes ◽  
Mitochondrial Coi Gene ◽  
Coi Sequences ◽  
Two Parameter ◽  
A New Species

A new species complex, the eparmata complex, is established within the subgenus Phortica s. str., based on eight known and five new species, all of which are endemic to the Oriental Region: P. bipartita (Toda & Peng, 1992), P. eparmata (Okada, 1977), P. lanuginosa Chen & Toda, 2007, P. latipenis Chen & Gao, 2005, P. pangi Chen & Wen, 2005, P. setitabula Chen & Gao, 2005, P. unipetala Chen & Wen, 2005 and P. zeta Chen & Toda, 2007; P. jadete sp. nov., P. kava sp. nov., P. mengda sp. nov., P. wongding sp. nov. and P. yena sp. nov. A key to all species of this complex is provided. Barcoding sequences (mitochondrial COI gene) were obtained for 22 specimens of five known and the five above-mentioned new species. The intra- and inter-specific pairwise K-2P (Kimura’s two-parameter) distances of COI were determined. Phylogenetic analysis was performed using Bayesian inference based on COI sequences, confirming the monophyletic status of the eparmata complex, which is distinct from the species complexes of magna, omega, variegata and another two ungrouped species

scholarly journals Molecular Characterization of Anopheles sacharovi Based on Sequences of ITS2-rDNA Region and COI Gene in North of Iran

2019 ◽  
Author(s):  
Sahereh Gholami ◽  
Hasan Bakhshi ◽  
Seyyed Hassan Moosa-Kazemi ◽  
Alireza Zahraei-Ramazani ◽  
Alireza Chavshin ◽  
...  
Keyword(s):  
Sibling Species ◽  
Coi Gene ◽  
Its2 Region ◽  
Morphological Identification ◽  
Anopheles Mosquitoes ◽  
North Of Iran ◽  
Northwest Of Iran ◽  
Coi Sequences ◽  
West Azerbaijan ◽  
East Azerbaijan

Background: Malaria is an important mosquito-borne disease considered as one of the public health concerns across many countries. Anopheles mosquitoes are the main vectors of Plasmodium parasites, which cause malaria. Some of these vectors such as Anopheles maculipennis s.l. and Anopheles sacharovi are considered as complex of sibling species distributed in north of Iran. Methods: This study was conducted in north and northwest of Iran including East Azerbaijan, West Azerbaijan, Ar­dabil, Golestan and North Khorasan provinces with emphasis on the northern borders of the country during 2015–2016. Adult specimens were collected and subjected to morphological identification as well as molecular analysis. Results: Overall, 10405 mosquitoes were collected comprising 21 species. Culex pipiens and Cx. theileri were found as the most frequent species in whole study area. Morphological identification showed that out of 1455 female Anoph­eles specimens, 77% belonged to An. maculipennis Group. Out of the identified species, ITS2 region and COI gene sequences of 8 An. maculipennis s.s. and 31 An. sacharovi representing all provinces were obtained and submitted to GenBank. The COI sequences for An. sacharovi revealed the presence of 9 haplotypes with similarity of 98.17–100%. Conclusion: Some investigations have reported An. martinius as a member of sibling species of An. sacharovi among Iranian Anopheles genus; while based on our study, there was no evidence of the presence of this species in north and northwest of Iran.  

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.

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