Accuracy of estimating genetic distance between species from short sequences of mitochondrial DNA.

The preliminary genetic study on Kalimantan false gharial from the wild was reported. Eleven tail scutes were collected from eleven individuals that originally consisting of two individuals from Kapuas River, one individual from Sentarum Lake, Jelai River, Mapam River, Perian Lake, and Lamandau River, two individuals from Barito River and three individuals from Mahakam River. PCR amplifying and sequencing 451 nucleotides in average that can be aligned at the same length of control region mitochondrial DNA. Among 11 individuals found eight polymorphic sites that consisted four haplotypes (A, B, C, and D) respectively, which is haplotype A is dominant. Based on phylogenetic tree that constructed by Tamura-Nei parameter, false gharial population in Kalimantan can be divided into two population groups; there were Central-Eastern Kalimantan population group and Western Kalimantan population group. Based on the hypothesis of landmasses separating between central-eastern Kalimantan and western Kalimantan that known as Schwaner Mountains, the genetic distance D = 1.53 percent was expected to be equal to 20 million years.

Download Full-text

Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.44.4.335-345 ◽

2019 ◽

Vol 44 (4) ◽

pp. 335

Author(s):

J. Jakaria ◽

T. Musyaddad ◽

S. Rahayu ◽

M. Muladno ◽

C. Sumantri

Keyword(s):

Mitochondrial Dna ◽

Genetic Distance ◽

Bos Taurus ◽

Bos Indicus ◽

Haplotype Diversity ◽

Complete Sequence ◽

Distance Method ◽

Mtdna Sequence ◽

D Loop ◽

Bali Cattle

This study aimed to investigate the diversity of the complete sequence of D-loop mitochondrial DNA (mtDNA) in Bali and Sumba Ongole (SO) cattlebreeds. A total of 24 blood samples were collected from Bali cattle (19 heads) and SO cattle (5 heads), and were extracted and then analyzed to obtain the sequence of D-loop mt DNA.Multiple alignments of the whole sequence of D-loop mtDNA were determined using clustal W. Genetic distance was calculated using a p-distance method, while the genetic tree was constructed using neighbor-joining (NJ) based on MEGA 6. Haplotype number, haplotype diversity (Hd) and nucleotide diversity (Pi) were analyzed using DnaSP version 6. As a result, the sequence of D-loop mtDNA in Bali cattle (921-1119 bp) and SO cattle (913 bp) was reported to have 8 and 4 haplotypes. Hd and Pi of Bali cattle reached 0.625±0.139 and 0.0266±0.0145, respectively, which wwere different from that of SO cattle, namely 0.900±0.1610 and 0.0064±0.0015, respectively. Specifically, we found 22 bp-repetitive nucleotide in Bali cattle, existing 3-9 times with a length of 66-198 bp present in D-loop mtDNA. This unique feature did not exist in SO cattle. Genetic distance and genetic tree determined according to sequence in hypervariability (HV-1) region of D-loop mtDNA (166 bp) resulted in satisfied separation, successfully classifying Bos javanicus, Bos indicus, and Bos taurus cluster.

Download Full-text

Karakteristik Molekuler Kelelawar (Microchiroptera), berdasarkan DNA Mitokondria (Gen COI) di Gua Sukabumi dan Sentul Jawa Barat

AL-Kauniyah Jurnal Biologi ◽

10.15408/kauniyah.v14i1.14147 ◽

2021 ◽

Vol 14 (1) ◽

pp. 20-28

Author(s):

Ismayati Afifah ◽

Dedy Duryadi Solihin ◽

Arzyana Sunkar

Keyword(s):

Mitochondrial Dna ◽

Genetic Distance ◽

Cytochrome Oxidase ◽

Dna Barcoding ◽

Cytochrome Oxidase I ◽

Genetic Identity ◽

Genetic Identification ◽

Coi Gene ◽

Genetic Characteristics ◽

Spin Column

AbstrakCytochrome Oxidase I (COI) merupakan salah satu gen mitokondria untuk membantu konstruksi dari pohon filogeni yang dapat bertindak sebagai gen marker. Gen COI memiliki keakuratan dalam mengidentifikasi spesies dan umumnya digunakan sebagai “DNA Barcoding”. Informasi mengenai karakteristik genetik berdasarkan DNA mitokondria pada kelelawar di Sukabumi dan Sentul belum banyak dilaporkan. Tujuan dari penelitian ini untuk mengetahui keragaman genetik kelelawar berdasarkan DNA mitokondria dengan penanda Cytochrome Oxidase I (COI) sebagai DNA barcoding. Isolasi DNA total dilakukan menggunakan Kit Dneasy® Blood and Tissue Kit cat no 69504 (50) berdasarkan prosedur Spin-Column Protocol dengan modifikasi. Hasil penelitian ini menunjukkan bahwa gen COI telah berhasil mengidentifikasi karakteristik spesies. Dua haplotipe didapatkan dari masing-masing populasi. Berdasarkan barcode DNA menunjukkan populasi Sukabumi merupakan spesies Chaerephon plicatus dengan nilai identitas genetik sebesar 97,08%, sedangkan populasi Sentul menunjukkan perbedaan secara genetik dengan spesies Hipposideros larvatus dengan nilai identitas genetik sebesar 94,85%. Identifikasi secara genetik dengan menggunakan gen COI menunjukkan bahwa kelelawar yang berasal Sukabumi adalah spesies Chaerephon plicatus dengan jarak genetik sebesar 3,1%. Kelelawar yang berasal dari Sentul memiliki kedekatan dengan spesies Hipposideros larvatus namun memiliki jarak genetik sebesar 5,2%. AbstractCytochrome Oxidase I (COI) is one of the mitochondrial genes to help the construction of phylogeny trees that can act as marker genes. The COI gene has accuracy in identifying species and is commonly used as "DNA Barcoding". Information about genetic characteristics based on mitochondrial DNA in bats in Sukabumi and Sentul has not been widely reported. The purpose of this study was to determine the genetic diversity of bats based on Mitochondrial DNA with Cytochrome Oxidase I (COI) markers as DNA barcoding. Total DNA isolation was carried out using the Dneasy® Blood and Tissue Kit paint no. 69504 (50) based on the Spin-Column Protocol procedure with modifications. The results of this study indicate that the COI gene has successfully identified species characteristics. Two haplotypes were obtained from each population. Based on DNA barcodes, the population of Sukabumi is a species of Chaerephon plicatus with a genetic identity value of 97.08%, while the Sentul population shows genetic differences with the Hipposideros larvatus species with a genetic identity value of 94.85%. Genetic identification using the COI gene shows that the bats originating from Sukabumi is a spesies Chaerephon plicatus with a genetic distance of 3.1%. The bats originating from Sentul are closely related to the species Hipposideros larvatus but have a genetic distance of 5.2%.

Download Full-text

Re-evaluation of the taxonomy of the Sri Lankan pigmy shrew Suncus fellowesgordoni (Soricidae: Crocidurinae) and its phylogenetic relationship with S. etruscus

Zootaxa ◽

10.11646/zootaxa.3187.1.5 ◽

2012 ◽

Vol 3187 (1) ◽

pp. 57 ◽

Cited By ~ 2

Author(s):

SUYAMA MEEGASKUMBURA ◽

MADHAVA MEEGASKUMBURA ◽

CHRISTOPHER J. SCHNEIDER

Keyword(s):

Mitochondrial Dna ◽

Sri Lanka ◽

Genetic Distance ◽

Nuclear Dna ◽

Morphological Data ◽

Sri Lankan ◽

Species Status ◽

Popula Tions ◽

Rag 1 ◽

Lower Incisors

The taxonomy of the pigmy shrews Suncus fellowesgordoni and S. etruscus is unclear and their phylogenetic relationshipsare unknown. Using molecular and morphological data, we confirm the species status of S. fellowesgordoni as being dis-tinct from S. etruscus, its probable sister species. Suncus fellowesgordoni is genetically distant from S. etruscus popula-tions in Sri Lanka and India, and Europe with a percent pairwise uncorrected genetic distance of 7.9–8.2% and 9.2–9.3%for cytochrome-b (mitochondrial DNA), respectively. The genetic distance between S. fellowesgordoni and S. etruscus ofSri Lanka and India for Rag 1 (nuclear DNA, exon) is 1.3–1.7%. The two species are also morphologically distinct by S. fellowesgordoni being larger in all dimensions, darker in hue and having two denticulations on the lower incisors.

Download Full-text

Phylogenetic Analysis of Rasbora spp. Based on the Mitochondrial DNA COI gene in Harapan Forest

JURNAL BIOLOGI TROPIS ◽

10.29303/jbt.v21i1.2351 ◽

2021 ◽

Vol 21 (1) ◽

pp. 89

Author(s):

Ahmad Subari ◽

Abdul Razak ◽

Ramadhan Sumarmin

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Genetic Distance ◽

Secondary Data ◽

Branch Length ◽

Coi Gene ◽

Lowland Tropical Forest ◽

Distance Analysis ◽

Relationship Of ◽

The Relationship

Harapan forest is the remaining lowland tropical forest in Sumatra which represents about 20 percent of the biodiversity on the island of Sumatra. There are several Rasbora species found in the Sungai Kapas Tengah River Refuge in the Harapan Jambi Forest that the relationship is not yet known.This research aims to know kinship and genetic distance several species of Rasbora from Sungai Kapas Tengah, Hutan Harapan Jambi. The method in this research using secondary data from the NCBI website ((National Center for Biotechnology Information). The data taken, namelynucleotide sequence from the Cytochrome Oxidase I (COI) gene in mitochondrial DNA. The Rasbora species analyzed were Rasbora from identification results in the Sungai Kapas Tengah River Refuge, Harapan Jambi Forest, consisting of, Rasbora bankanensis, R. caudimaculata, R. cf. sumatrana, R. dusonensis, R. elegans, R. sumatrana, and R. trilineata. Based on phylogenetic analysis, the location of the branch length in each Rasbora species, the closest kinship is owned byR. sumatrana and R. elegans species. Based on the results of genetic distance analysis, the closest genetic distance was the species R. elegans and R. sumatrana, with a distance value of 0.023 (2.3%). While the farthest genetic distance between R. bankanensis and R. caudimaculata, with a distance value of 0.172 (17.2%).Based on research results It can be concluded that R. bankanensis has a greater kinship and genetic distance value than other Rasbora species, so that this species forms a separate group. Meanwhile, 5 other species have kinship and the value of close genetic distance so that these species are united in the same group. For future researchers, it is hoped that some additional families of fish species will be analyzed for phylogenetic analysis in Sungai Kapas, Hutan Harapan Jambi, so that they can find out the relationship of several other species.

Download Full-text

Comparative Genetics Using Three mtDNA Markers in Aedes aegypti (Linnaeus) Populations from Four Municipalities in the Satate of Mato Grosso, Brazil.

10.21203/rs.3.rs-785088/v1 ◽

2021 ◽

Author(s):

Sandra Mariotto ◽

Mari Rose Oliveira Silva ◽

Cristina Márcia Menezes Butakka ◽

Lenicy Lucas Miranda Cerqueira ◽

Rosina Djunko Miyazaki ◽

...

Keyword(s):

Mitochondrial Dna ◽

Aedes Aegypti ◽

Genetic Distance ◽

Breeding Habitat ◽

Comparative Genetics ◽

Extrinsic Factors ◽

Mato Grosso ◽

Flow Investigation ◽

Nd5 Gene ◽

Mtdna Markers

Abstract Aedes aegypti mosquito has spread throughout the tropical and subtropical world and is currently the primary species responsible for transmitting dengue, urban yellow fever, Chikungunya, and Zika virus. This study aimed to investigate the inter- and intrapopulational genetic variability of Aedes aegypti through mitochondrial DNA, COI, ND4, and ND5 molecular markers in four municipalities in Mato Grosso. We used the Geneious software to build dendrograms for differentiating populations from each municipality. The interpopulational genetic distance obtained from sequence analysis showed a difference within populations through groups' formation in the ordering. Besides, we identified a difference in the interindividual genetic distance values, notably for the ND5 gene from the populations captured in the four municipalities. We recorded the smallest interindividual genetic distance within populations for populations from Chapada dos Guimarães. Extrinsic factors, including breeding habitat removal, can contribute to decreasing variability. Consequently, the dendrogram showed some similarities. Ovitrap monitoring, vector elimination, and genetic flow investigation stimulate actions to prevent transmitted diseases and support essential effective measures to control and fight Ae. aegypti.

Download Full-text

Identifikasi dan Analisis Filogenetik Portunus trituberculatus Dari Perairan Cirebon Menggunakan Barkode Gen COI Mitokondrial

Jurnal Kelautan Tropis ◽

10.14710/jkt.v21i2.3091 ◽

2018 ◽

Vol 21 (2) ◽

pp. 111

Author(s):

Subagiyo Subagiyo ◽

Retna Handayani ◽

Rahayu Rahayu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Cytochrome C ◽

Genetic Distance ◽

Cytochrome C Oxidase ◽

Nucleotide Diversity ◽

The Philippines ◽

Portunus Trituberculatus ◽

Gene Banks ◽

Phylogenetic Identification

Phylogenetic Identification and Analysis Portunus trituberculatus from Cirebon Coast Using the COI Barcode Mitochondrial Portunus trituberculatus spesimen from Cirebon coast were successfully identified using mitochondrial DNA cytochrome c oxydase subunit I (COI) genes. Analysis of haplotype distribution of P. trituberculatus along with the same species from China, Korea, India and the Philippines obtained from NCBI gene banks resulted 17 haplotypes from 25 specimens. Haploid diversity was 0.943 + 0.031 and nucleotide diversity was 0.04821 + 0.0139. The Cirebon specimen is in separated haplotipe from the others. The results of phylogenetic analysis showed that the 25 specimens were clustered into 3 clusters in 2 different lineages with percentages genetic distance were 12.76%, 14.24% and 14.33% respectively. The genetic distance within each cluster ranges from 0 - 2.92%. The Cirebon crab specimen is in the same cluster as the Philippine specimen with 1% genetic distance. Spesimen rajungan Portunus trituberculatus dari perairan Cirebon berhasil diidentifikasi menggunakan gen mitochondrial DNA cytochrome c oxidase subunit I (COI). Analisis distribusi haplotipe dengan data P trituberculatus yang berasal dari China, Korea, India dan Filipina yang diperoleh dari data genebank NCBI didapatkan 17 haplotipe dari 25 spesimen, dengan keragaman haploid 0,943 +0.031 dan keragaman nukleotida 0,04821+0.0139. Spesimen Cirebon merupakan haplotipe yang terpisah dari yang lainnya. Hasil kajian filogenetik menunjukkan 25 spesimen mengelompok ke dalam 3 kluster dari 2 garis keturunan yang berbeda dengan jarak genetik berturut turut 12,76 %, 14,24 % dan 14,33 %. Jarak genetik di dalam masing-masing kluster berkisar antara 0 – 2,92 %. Spesimen rajungan Cirebon berada pada garis keturunan dan kluster yang sama dengan spesimen Filipina dengan jarak genetik 1%.

Download Full-text

Microgeographic variation in allozymes and mitochondrial DNA of Microtus richardsoni, the water vole, in the Beartooth Mountains of Montana and Wyoming, U.S.A.

Canadian Journal of Zoology ◽

10.1139/z01-082 ◽

2001 ◽

Vol 79 (7) ◽

pp. 1286-1295 ◽

Cited By ~ 2

Author(s):

Marion Klaus ◽

Robert E Moore ◽

Ernest Vyse

Keyword(s):

Mitochondrial Dna ◽

Genetic Distance ◽

Restriction Enzymes ◽

Water Vole ◽

Sensitive Species ◽

Usda Forest Service ◽

Significant Difference ◽

Hardy Weinberg Equilibrium ◽

Microgeographic Variation ◽

A Site

Microtus richardsoni, the water vole, is listed as a sensitive species within region 2 of the USDA Forest Service. Because it is a sensitive species, the water vole's ability to disperse becomes an important management concern in terms of its population viability. Both allozyme and mitochondrial DNA analyses were used to study microgeographic population structure within a group of populations from four adjacent watersheds of the Beartooth Mountains of Montana and Wyoming. Of 31 protein loci examined, only ADH, EST-1, and SOD-1 were polymorphic. ADH and EST-1 were in HardyWeinberg equilibrium, but SOD-1 was not. Mitochondrial DNA was found to be polymorphic with 9 restriction enzymes. The size of the fragments produced by each restriction enzyme was estimated and ordered into a site map. In total, 51 sites were found with 9 restriction enzymes resulting in 29 different haplotypes from 142 individuals. Shared haplotypes were geographically contiguous except for one. There was no significant difference in genetic distance among water voles from the Beartooth Mountains, and only the outgroup from Togwotee Pass in the Absaroka Mountains of Wyoming had significant genetic distance. This suggests the possibility of dispersal between water voles from the contiguous watersheds of the Beartooth Mountains but not between the Beartooth Mountains and Togwotee Pass populations.

Download Full-text