Using hybridization capture to obtain mitochondrial genomes from forensically relevant North American canids: Assessing sequence variation for species identification

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.

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Complete Mitochondrial Genomes of the Cherskii’s SculpinCottus czerskiiand Siberian TaimenHucho taimenReveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

Evolutionary Bioinformatics ◽

10.1177/1176934317726783 ◽

2017 ◽

Vol 13 ◽

pp. 117693431772678 ◽

Cited By ~ 4

Author(s):

Evgeniy S Balakirev ◽

Pavel A Saveliev ◽

Francisco J Ayala

Keyword(s):

Mitochondrial Genome ◽

Species Identification ◽

Mitochondrial Genomes ◽

Complete Mitochondrial Genomes

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The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus

10.1101/2020.06.26.173625 ◽

2020 ◽

Author(s):

Jan-Niklas Macher ◽

Katerina Drakou ◽

Athina Papatheodoulou ◽

Berry van der Hoorn ◽

Marlen Vasquez

Keyword(s):

European Union ◽

Dna Barcoding ◽

Species Identification ◽

Aquatic Macroinvertebrates ◽

Mitochondrial Genomes ◽

Formal Description ◽

Aquatic Macroinvertebrate ◽

Molecular Approaches ◽

Reference Databases ◽

Macroinvertebrate Species

AbstractAquatic macroinvertebrates are often identified based on morphology, but molecular approaches like DNA barcoding, metabarcoding and metagenomics are increasingly used for species identification. These approaches require the availability of DNA references deposited in public databases. Here we report the mitochondrial genomes of 11 aquatic macroinvertebrates species from Cyprus, a European Union island country in the Mediterranean. Only three of the molecularly identified species could be assigned to a species name, highlighting the need for taxonomic work that leads to the formal description and naming of species, and the need for further genetic work to fill the current gaps in reference databases containing aquatic macroinvertebrates.Graphical Abstract

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Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)

Plant Science Today ◽

10.14719/pst.2019.6.sp1.697 ◽

2019 ◽

Vol 6 (sp1) ◽

pp. 635-638

Author(s):

Khushbu Anand ◽

Sonu Kumar ◽

Afroz Alam ◽

Asheesh Shankar

Keyword(s):

Genetic Variability ◽

Microsatellite Markers ◽

Species Identification ◽

In Silico ◽

Population Genetic ◽

Average Density ◽

Computational Approach ◽

Mitochondrial Genomes ◽

Genetic Studies ◽

Nucleotide Repeats

Microsatellites or SSRs are the markers of selection due to their reproducibility, degree of polymorphism, distribution throughout the genome and co-dominant nature. Microsatellites are used primarily to study the genetic variability in various species and marker aided selection. Since microsatellites can be readily amplified by PCR, they have been utilized most extensively. To reduce time and cost to a great extent, the computational approach for identifying and developing microsatellite markers by mining nucleotide sequences is preferred over the conventional methods. In the present analysis, an in-silico method was used to detect microsatellites effectively in mitochondrial genomes of Anomodon rugelii (Müll. Hal.) Keissl., Anomodon attenuatus (Hedw.) Hueb., Climacium americanum (Renauld & Cardot) Kindberg, and Hypnum imponens Hedw. (Bryopsida; Hypnales). A total of 101 perfect microsatellites were mined with an average density of 1 microsatellite/4.21 kb. The hexa-nucleotide repeats were not detected in mitochondrial genomes of studied taxa. Di-nucleotides were seen to be the most frequent repeats followed by tetra-nucleotides. The identified microsatellites were also checked for variability in length between species. The mined microsatellites will be used for gene tagging, species identification and population genetic studies.

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Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

Journal of Medical Entomology ◽

10.1093/jme/tjab152 ◽

2021 ◽

Author(s):

Shu-Tong Dai ◽

Dian-Xing Feng ◽

Da-Peng Sun

Keyword(s):

Mitochondrial Genome ◽

Species Identification ◽

Stop Codon ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genomes ◽

Base Pairs ◽

Protein Coding ◽

Phylogenetic Studies ◽

Rna Genes ◽

Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

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Correction Notice

North American Archaeologist ◽

10.1177/0197693118779642 ◽

2018 ◽

Vol 39 (2) ◽

pp. 165-167

Keyword(s):

Species Identification ◽

North American ◽

Archaeological Sites ◽

Transverse Diameter ◽

Specific Data ◽

Cambridge University ◽

Site Use ◽

Final Sentence ◽

Fish Taxon ◽

Adna Analysis

Ewonus, P. A. (2017). Assessing internal household relationships and site use: Zooarchaeological evidence from Dionisio Point, Galiano Island, Canada. North American Archaeologist, 38(4), 349–393. DOI: 10.1177/0197693117727392 In this article, which was published in volume 38, issue 4 of North American Archaeologist, the following corrections have been identified by the author: Abstract, line 7: The word “consisted” should be “comprised”. Figure 2: The image file layer containing the four archaeological sites referenced in this figure has been moved to underlay the base map layer. The revised figure is provided below. Page 357, line 3: The closing parenthesis should appear after “8.0mm” in the following sentence: “Examination of their data (Grier et al., 2013: 548–550) reveals that approximately half of this difference between salmon vertebra size in their overall sample (38.1%≥8.0 mm) and successful aDNA species identification (62.7%≥8.0 mm) is due to sampling that may be non-random (of the 149 vertebrae sampled for aDNA analysis with transverse diameter values presented in Grier et al. (2013), 75 (50.3%)≥8.0 mm).” Headings appearing on pages 363, 366, and page 367 are tertiary (H3), not primary headings (H1). Page 369, final line: “Comprised” was erroneously changed to “consisted”. The correct sentence should be: “Six other units, comprised of two that contain a major hearth (144N/116E, 147N/124E), … mammal remains.” Table 2: The fish taxon row title “ Theragra chalcogramma” was moved to page 362 in the table, while the specific data for this entry remains as the final row of the table page 361. Table 3: “Carnivora”, “Cetacea”, “Rodentia”, and “Miscellaneous” should be bolded headings. Table 4: “Anseriformes” (at top) should be bolded. Table 5: “Echinoidea” (at top) should be bolded. Page 376: In the following final sentence “remain” should read “remains”: “Of the fish elements recovered, only those from an individual 5 cm level in 10 excavation units were used in the assessment of horizontal faunal distributions (NISP = 3294, NSP = 6945). Mammal (NISP = 1451) and bird (NISP = 646) remain from all levels associated with the House 1 occupation, recovered in 6.4mm screens from 12 units, were examined for horizontal patterns (Frederick, 2012).” Page 381: The heading “Departure bay” should be “Departure Bay”. Pages 381, 384: Headings “Departure Bay”, “Tsawwassen VI, VII, and VIII”, and “Site comparison” should be tertiary headings (H3). Page 387, line 7: An unnecessary comma was inserted following the word Research in this final line of the Acknowledgments section. Page 393, Author biography: Inserting “the” before “Cambridge University” and “Vancouver Island University” was in error.

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Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections

PLoS ONE ◽

10.1371/journal.pone.0154363 ◽

2016 ◽

Vol 11 (4) ◽

pp. e0154363 ◽

Cited By ~ 31

Author(s):

E. Anne Chambers ◽

Paul D. N. Hebert

Keyword(s):

Natural History ◽

Species Identification ◽

North American ◽

Dna Barcodes ◽

Natural History Collections

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Fossil and genomic evidence constrains the timing of bison arrival in North America

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1620754114 ◽

2017 ◽

Vol 114 (13) ◽

pp. 3457-3462 ◽

Cited By ~ 30

Author(s):

Duane Froese ◽

Mathias Stiller ◽

Peter D. Heintzman ◽

Alberto V. Reyes ◽

Grant D. Zazula ◽

...

Keyword(s):

North America ◽

Sea Level ◽

Late Pleistocene ◽

North American ◽

Marine Isotope Stage ◽

Mitochondrial Genomes ◽

Subsequent Evolution ◽

Large Mammal ◽

Morphological Diversification ◽

Steppe Bison

The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada’s Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus. We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195–135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45–21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.

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