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Journal articles on the topic 'Haplotype diversity'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Gariepy, Tara D., Dmitry L. Musolin, Aleksandra Konjević, et al. "Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia." NeoBiota 68 (September 15, 2021): 53–77. http://dx.doi.org/10.3897/neobiota.68.68915.

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The arrival, establishment and pest status of Halyomorpha halys in Europe and non-native countries in Asia have been well-documented, with thorough characterisation of the genetic diversity and occurrence of cytochrome oxidase I (COI) haplotypes in Switzerland, France, Hungary, Italy and Greece. However, a number of gaps exist in terms of the characterisation of the haplotype diversity and occurrence of H. halys along the invasion front that covers eastern Europe, western and central Asia. To contribute towards filling this gap, the COI haplotype diversity and distribution were investigated fo

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2

Gariepy, Tara D., Dmitry L. Musolin, Aleksandra Konjević, et al. "Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia." NeoBiota 68 (September 15, 2021): 53–77. https://doi.org/10.3897/neobiota.68.68915.

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The arrival, establishment and pest status of Halyomorpha halys in Europe and non-native countries in Asia have been well-documented, with thorough characterisation of the genetic diversity and occurrence of cytochrome oxidase I (COI) haplotypes in Switzerland, France, Hungary, Italy and Greece. However, a number of gaps exist in terms of the characterisation of the haplotype diversity and occurrence of H. halys along the invasion front that covers eastern Europe, western and central Asia. To contribute towards filling this gap, the COI haplotype diversity and distribution were investigated fo

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3

Kesik, Harun Kaya, Figen Celik, Seyma Gunyakti Kilinc, et al. "Genetic Diversity and Haplotype Analysis of Cattle Hydatid Cyst Isolates Using Mitochondrial Markers in Turkey." Pathogens 11, no. 5 (2022): 519. http://dx.doi.org/10.3390/pathogens11050519.

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Echinococcus granulosus sensu lato (s.l.) causes cystic echinococcosis in ungulates and humans. The current study was designed to find the genetic diversity and haplotypic profiles of hydatid cysts from the lungs of cattle in three provinces in eastern Turkey. Individual cyst isolates (n = 60) were collected from infected cattle lungs after slaughter and then samples were stored in ethanol (70%) until further use. From each isolate, total gDNA was extracted from the cysts’ germinal layers. A partial (875 bp) mt-CO1 gene was amplified by PCR and sequenced unidirectionally. The final size of the

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Sokolova, N. A., N. P. Korablev, P. N. Korablev, et al. "Mitochondrial Genetic Diversity of Eurasian Otter (<i>Lutra lutra</i>) from European Part of Russia and Transcaucasian Countries." Генетика 59, no. 7 (2023): 804–12. http://dx.doi.org/10.31857/s0016675823070111.

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In this study we examined mitochondrial DNA diversity of Eurasian otter from European part of Russia and Transcaucasian countries and compared it with other European populations. We used a fragment of mtDNA control region (255 bp) and also included previously detected haplotypes from NCBI. Six haplotypes were found in 75 samples from European part of Russia and Transcaucasian countries. Lut1 was the most common haplotype (62.1% of samples), Lut4 was detected in 17.6% of samples, other 4 haplotypes were newly detected. Haplotype diversity for European part of Russia and Transcaucasian countries

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Quan, Ke Thai, Thanh Nguyen Tuan, and Thi Thanh Pham Hien. "mtDNA haplotype network analysis: Exploring genetic relationships and diversity in dog haplogroups." GSC Biological and Pharmaceutical Sciences 24, no. 1 (2023): 224–32. https://doi.org/10.5281/zenodo.8265409.

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The genetic diversity and relationships of dog haplogroups were studied by analyzing the HV1 region of mitochondrial DNA. Previous studies have found six distinct haplogroups (A, B, C, D, E, and F) in dogs. Haplogroups A, B, and C were widely distributed, while haplogroups D, E, F were rare and distributed in restricted regions. In this study, HV1 sequences from global dog populations were collected, categorized into haplotypes, and used to construct haplotype networks. The results showed that haplogroup A was the most prevalent, comprising approximately 72.34% of dogs worldwide. Haplogroups A

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Arifin Zein, M. Syamsul, and Sri Sulandari. "Genetic diversity of Lombok chickens based on D-loop mitochondrial DNA sequences." Jurnal Ilmu Ternak dan Veteriner 13, no. 4 (2012): 308–14. https://doi.org/10.14334/jitv.v13i4.575.

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Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymorphic sites with polymorphism between nucleotides 200 and 400 contributing to 80% of the variation. Fuâ€™s Fs value was - 8.768 (all samples, P = 0), indicating high genetic diversity and population expansion, a conclusion supported by a neighborâ€“

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Anantaphruti, Malinee, Urusa Thaenkham, Teera Kusolsuk, et al. "Genetic Variation and Population Genetics ofTaenia saginatain North and Northeast Thailand in relation toTaenia asiatica." Journal of Parasitology Research 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/310605.

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Taenia saginatais the most common humanTaeniain Thailand. Bycox1sequences, 73 isolates from four localities in north and northeast were differentiated into 14 haplotypes, 11 variation sites and haplotype diversity of 0.683. Among 14 haplotypes, haplotype A was the major (52.1%), followed by haplotype B (21.9%). Clustering diagram of Thai and GenBank sequences indicated mixed phylogeny among localities. By MJ analysis, haplotype clustering relationships showed paired-stars-like network, having two main cores surrounded by minor haplotypes. Tajima’sDvalues were significantly negative inT. sagina

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Budhi Dharmayanthi, Anik, Achmad Muchsinin, Afriana Pulungan, and Moch Syamsul Arifin Zein. "Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta." Jurnal Biologi Indonesia 17, no. 2 (2021): 105–14. http://dx.doi.org/10.47349/jbi/17022021/105.

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Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates popul

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Koseniuk, Anna, and Ewa Słota. "Mitochondrial control region diversity in Polish sheep breeds." Archives Animal Breeding 59, no. 2 (2016): 227–33. http://dx.doi.org/10.5194/aab-59-227-2016.

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Abstract. The aim of the study was to determine the genetic variability of the Polish sheep breeds Świniarka, Wrzosówka, Pomorska, and Wielkopolska based on mitochondrial control region polymorphism. A comprehensive phylogenetic analysis and information about the genetic origin of the breeds were also obtained. The genetic variability of the breeds studied has been assessed based on the number of haplotypes, haplotype diversity, nucleotide diversity, the average number of nucleotide differences, the number of mutations, and phylogenetically informative sites. Sequence divergence between identi

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Ma, Peizhen, Chenxia Zuo, Shaojing Yan, et al. "Populations of the Invasive Mussel Mytella strigata in China Showed Lower Genetic Diversity in Autumn than in Spring." Biology 14, no. 1 (2024): 16. https://doi.org/10.3390/biology14010016.

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Native to tropical America, the charru mussel, Mytella strigata, has been spreading rapidly in the West Pacific Ocean, including the South China Sea. In order to study the adaptive evolution of M. strigata and examine the present status of invasion in China, the mitochondrial nad2 gene fragment was employed to analyze the genetic variations of seven populations sampled in both spring and autumn 2023. Results showed that all the populations had high haplotype diversity (>0.5) and low nucleotide diversity (<0.005), suggesting the ongoing rapid expansion following a genetic bottleneck. The

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Yang, Hongsheng, Donghong Yang, Xuewen Yang, et al. "Study on Genetic Diversity of Phellodendron amurense based on cpDNA." E3S Web of Conferences 271 (2021): 03059. http://dx.doi.org/10.1051/e3sconf/202127103059.

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In this study, 3 haplotypes were found in populations of Phellodendron amurense based on two combined cpDNA regions (psbA-trnH and trnT-trnL). Nucleotide diversity and haplotype diversity were 0.43×10-3 and 0.41, respectively at the level of species. The AMOVA revealed that only 8.53% of the variation was explained by differences among geographical groups, whereas inter-population and intrapopulation differences explained 18.32% and 71.35% of the variation, respectively. Phylogeographical relationships showed that all haplotypes were clustered into two lineages. Haplotype H1 and H2 cluster tog

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Dumaidi, Kamal, Hayah Qaraqe, Amer Al-Jawabreh, Rasmi Abu-Helu, Fekri Samarah, and Hanan Al-Jawabreh. "Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis A virus isolates from the West Bank, Palestine during the period between 2014 and 2016." PLOS ONE 15, no. 12 (2020): e0240339. http://dx.doi.org/10.1371/journal.pone.0240339.

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Background Hepatitis A virus (HAV) infection is one of the major causes of acute viral hepatitis. HAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide. Aims The aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West Bank, Palestine. Study design A cohort of 161 clinically and laboratory-confirmed HAV (IgM-positive) cases and 170 apparently healthy controls from all the districts of the West Bank, Palestine during the period of 2014 to 2016 were teste

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Thompson, Sarah M., Chris P. Johnson, Ashley Y. Lu, et al. "Genomes of ‘Candidatus Liberibacter solanacearum’ Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species." Phytopathology® 105, no. 7 (2015): 863–71. http://dx.doi.org/10.1094/phyto-12-14-0363-fi.

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‘Candidatus Liberibacter solanacearum’ contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found i

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14

Quan Ke Thai, Tuan Thanh Nguyen, and Hien Thi Thanh Pham. "mtDNA haplotype network analysis: Exploring genetic relationships and diversity in dog haplogroups." GSC Biological and Pharmaceutical Sciences 24, no. 1 (2023): 224–32. http://dx.doi.org/10.30574/gscbps.2023.24.1.0284.

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The genetic diversity and relationships of dog haplogroups were studied by analyzing the HV1 region of mitochondrial DNA. Previous studies have found six distinct haplogroups (A, B, C, D, E, and F) in dogs. Haplogroups A, B, and C were widely distributed, while haplogroups D, E, F were rare and distributed in restricted regions. In this study, HV1 sequences from global dog populations were collected, categorized into haplotypes, and used to construct haplotype networks. The results showed that haplogroup A was the most prevalent, comprising approximately 72.34% of dogs worldwide. Haplogroups A

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15

Popoola, Omoniyi Michael. "Genetic Differentiation and Molecular Phylogenetics of North African Catfish from Three Distinct Waterbodies." Croatian Journal of Fisheries 80, no. 3 (2022): 123–32. http://dx.doi.org/10.2478/cjf-2022-0013.

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Abstract The population structure and genetic variability of North African catfish Clarias gariepinus (Burchell 1822) were investigated using partial mitochondrial DNA cytochrome b region sequences. Fifty-four (54) samples were investigated from three geographically isolated rivers in Nigeria. The analysis of 53 haplotypes revealed greater haplotype diversity (0.99930) and nucleotide diversity (p) (0.07270). According to an analysis of molecular variance (AMOVA), the genetic diversity of North African catfish within populations is significantly higher than the genetic diversity across populati

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Gómez, A., E. Aguiriano, R. Alía, and M. A. Bueno. "Pinus pinea L. Spanish genetics resources characterization by chloroplast microsatellite markers." Forest Systems 11, no. 1 (2002): 145–54. http://dx.doi.org/10.5424/764.

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Gene conservation analysis in Pinus pinea L. was performed by chloroplast microsatellite markers. Genetic diversity and allelic richness of 10 Spanish populations belonging to diverse origin regions were determined using genetic variation at 9 cpSSR loci. Six amplified loci have been polymorphic. The variants detected at the cpSSR regions combined into 9 different haplotypes Most haplotypes are in common among populations. One haplotype has been detected in all populations included the population with the most reduced genetic base, in which all the samples showed the same haplotype. Number of

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Al Khatib, Hebah A., Muna A. Al Maslamani, Peter V. Coyle, et al. "Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes." Microorganisms 8, no. 1 (2020): 133. http://dx.doi.org/10.3390/microorganisms8010133.

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The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015–2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investig

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Wang, Dan, Yu Huang, Lu Rui, et al. "Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments." Genes 14, no. 9 (2023): 1754. http://dx.doi.org/10.3390/genes14091754.

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Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Gen

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Zhang, Yang, Qiang Bao, Zhi Cao, et al. "Chinese Domestic Ducks Evolved from Mallard Duck (Anas platyrhynchos) and Spot-Billed Duck (A. zonorhyncha)." Animals 13, no. 7 (2023): 1156. http://dx.doi.org/10.3390/ani13071156.

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China has a rich genetic resource in its 34 domestic duck breeds. In order to detect the genetic diversity and explore the origin of these indigenous duck populations, the mitochondrial DNA (mtDNA) control region was sequenced and analyzed for 208 individual ducks, including 22 domestic breeds, wild Mallards ducks, Eastern spot-billed ducks, White Muscovy ducks, and Black Muscovy ducks. The haplotype diversity (Hd) was 0.653 and the average nucleotide diversity (Pi) was 0.005, indicating moderate genetic diversity. Sixty haplotypes were detected, and the maximum-likelihood (ML) phylogenetic tr

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20

Kaul, Noyonika, Prem Lal Kashyap, Sudheer Kumar, Deepti Singh, and Gyanendra Pratap Singh. "Genetic Diversity and Population Structure of Head Blight Disease Causing Fungus Fusarium graminearum in Northern Wheat Belt of India." Journal of Fungi 8, no. 8 (2022): 820. http://dx.doi.org/10.3390/jof8080820.

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Head blight or scab caused by Fusarium graminearum (FG), once ranked as a minor disease in wheat, is now emerging as one of the economically important diseases in India. The present study represents the first in-depth population genetic analysis of the FG from the northern wheat belt of India. In this study, multiple conserved gene sequences comprised of β-tubulin (TUB), translation elongation factor 1-α (TEF), and histone-3 (HIS) regions were used for multi-locus phylogenetic analysis of 123 geographically distinct F. graminearum isolates collected from four different states (Haryana (HR), Pu

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EL-MABROUK, NADIA. "DERIVING HAPLOTYPES THROUGH RECOMBINATION AND GENE CONVERSION PATHWAYS." Journal of Bioinformatics and Computational Biology 02, no. 02 (2004): 241–56. http://dx.doi.org/10.1142/s0219720004000545.

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Retracing the trajectories of past genetic events is crucial to understand the structure of the genome, both in individuals and across populations. A haplotype describes a string of polymorphic sites along a DNA segment. Haplotype diversity is due to mutations creating new variants, and to recombinations and gene conversions that mix and redistribute these variants among individual chromosomes in populations. A number of studies have revealed a relatively simple pattern of haplotype diversity in the human genome, dominated by a few common haplotypes representing founder ancestral ones. New hap

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HARTATIK, TETY, DWI NUR HAPPY HARIYONO, and YUDI ADINATA. "Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences." Biodiversitas Journal of Biological Diversity 20, no. 1 (2018): 17–22. http://dx.doi.org/10.13057/biodiv/d200103.

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Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplo

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Arifin Zein, M. Syamsul, and S. Sulandari. "Genetic diversity and haplogroups distributions of Kampung chickens using hypervariable-I mitochondrial DNA control region." Jurnal Ilmu Ternak dan Veteriner 17, no. 2 (2013): 120–31. https://doi.org/10.14334/jitv.v17i2.686.

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Until now no studies evaluating the position of Kampung chickens in chicken clade of Asia. Thus studies based on molecular DNA sequence hipervariable-I on Kampung chicken is needed. Molecular studies based on DNA sequences hyper variable-I of Kampong chicken was done to confirm the results of previous evaluations conducted on 15 families of local chickens of Indonesia. An analysis of 210 individuals Kampung chicken (Aceh, North Sumatra, Lampung, Banten, Central Java, Lombok, Sulawesi, Ternate, Morotai and Halmahera) resulted in 51 haplotypes derived from 62 polymorphic sites. Polymorphic sites

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Noorhidayah, Mamat, Noor Azrizal-Wahid, Van Lun Low, and Norma-Rashid Yusoff. "Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842)." PLOS ONE 19, no. 4 (2024): e0301392. http://dx.doi.org/10.1371/journal.pone.0301392.

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Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovere

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Soberanes-Yepiz, Maritza L., Miriam V. Martín-Manzo, Marcel Martínez-Porchas, et al. "Diversity and genetic structure of <i>Macrobrachium americanum </i>(Bate, 1868) in two geographical areas of Mexico." Revista MVZ Córdoba 30, no. 2 (2025): e3388. https://doi.org/10.21897/rmvz.3388.

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Objetive. Analyze the population genetic with mitochondrial molecular markers (16S mtDNA and COI mtDNA) on the river prawn Macrobrachium americanum, in two different geographic areas of Mexico: Baja California Sur (San Pedro de la Presa and Guamuchil basins) and Guerrero (Aguas Blancas River). Materials and Methods. We calculated the number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (π), and the number of nucleotide differences (k) for each sampling site using the program Dnasp. To calculate the two phylogenetic networks (COI and 16s rDNA), we used the median-joining imp

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Joyce, Andrea L., Hannah Parolini, and Harry Brailovsky. "Distribution of Two Strains of Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) in the Western Hemisphere: Is L. zonatus a Potential Invasive Species in California?" Insects 12, no. 12 (2021): 1094. http://dx.doi.org/10.3390/insects12121094.

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The leaffooted plant bug, Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) is polyphagous and widely distributed in the Western Hemisphere. Although it has been recorded in California since around 1900, it has become a more common pest in almonds in the last decade. Other studies have shown that an established insect can become a pest when a new genotype is introduced. This study investigated the distribution of two lineages (strains) of L. zonatus in the Western Hemisphere. Specimens from the Leptoglossus collection in the national insect collection in Mexico were used to extract DNA and s

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CĂRĂBUŞ, Mihaela Cristina, Alexandru Lucian CURTU, Dragoș POSTOLACHE, Elena CIOCÎRLAN, and Neculae ŞOFLETEA. "Evidence of Low Chloroplast Genetic Diversity in Two Carpinus Species in the Northern Balkans." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 45, no. 1 (2017): 316–22. http://dx.doi.org/10.15835/nbha45110799.

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Genetic diversity and differentiation in two Carpinus species (C. betulus and C. orientalis) occurring in Romania was investigated by using three chloroplast Simple Sequence Repeat markers (cpSSRs). A total of 96 and 32 individuals were sampled in eighteen C. betulus and six C. orientalis populations, respectively. A total of four chloroplast haplotypes were observed. Two haplotypes were specific for C. betulus and two for C. orientalis. Most of C. betulus populations were fixed for the predominant haplotype (H1), which was observed in 82% of the individuals. All C. orientalis populations were

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Wei, Di, Sichen Zheng, Songlin Wang, et al. "Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers." Animals 13, no. 18 (2023): 2886. http://dx.doi.org/10.3390/ani13182886.

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China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with

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Alves, Paula D., Paulo Rohan, Rocio Hassan, and Eliana Abdelhay. "Lytic and Latent Genetic Diversity of the Epstein–Barr Virus Reveals Raji-Related Variants from Southeastern Brazil Associated with Recombination Markers." International Journal of Molecular Sciences 25, no. 9 (2024): 5002. http://dx.doi.org/10.3390/ijms25095002.

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Epstein–Barr virus (EBV) is a ubiquitous gammaherpesvirus etiologically associated with benign and malignant diseases. Since the pathogenic mechanisms of EBV are not fully understood, understanding EBV genetic diversity is an ongoing goal. Therefore, the present work describes the genetic diversity of the lytic gene BZLF1 in a sampling of 70 EBV-positive cases from southeastern Brazil. Additionally, together with the genetic regions previously characterized, the aim of the present study was to determine the impact of viral genetic factors that may influence EBV genetic diversity. Accordingly,

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Di Pietro, Romeo, Luca Quaranta, Claudia Mattioni, et al. "Chloroplast Haplotype Diversity in the White Oak Populations of the Italian Peninsula, Sicily, and Sardinia." Forests 15, no. 5 (2024): 864. http://dx.doi.org/10.3390/f15050864.

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A phylogeographic study on the chloroplast DNA of natural white oak forests (Quercus subgen. Quercus, sect. Quercus) was carried out to identify possible haplotype-structured distribution within the Italian Peninsula, Sicily, and Sardinia. Sixty white oak populations belonging to Q. frainetto, Q. robur and the collective groups Q. petraea and Q. pubescens were considered and analyzed by combining five Chloroplast Simple Sequence Repeat (cpSSR) markers. A total of 28 haplotypes were detected. Central and southern Italy displayed the highest variability (14 and 10 haplotypes, respectively), foll

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Garcia, Eric, Daniel Wright, Remy Gatins, et al. "Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks." PLOS ONE 16, no. 6 (2021): e0251878. http://dx.doi.org/10.1371/journal.pone.0251878.

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A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published m

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Emam, Ahmed Mostafa, Sandra Afonso, Pedro González-Redondo, et al. "Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis." World Rabbit Science 28, no. 2 (2020): 93. http://dx.doi.org/10.4995/wrs.2020.12219.

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<p>Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish local rabbit breed was Spanish common rabbit (SCR). Previous breeds were compared with European Wild Rabbit taken from Albacete, Spain (EWR). A total of 353 mutations, 290 polymorphic sites, 14 haplotypes, 0.06126 haplotype diversity and -1.900

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Pathak, Abhinaya, Yu-Cheng Hsu, Amir Sadaula, et al. "Reduced genetic diversity in greater one-horned rhinoceros in Chitwan National Park A new challenge and opportunity for rhino conservation in Nepal." Journal of Biological Studies 5, no. 4 (2022): 693–704. http://dx.doi.org/10.62400/jbs.v5i4.7111.

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Understanding the genetic diversity of a species is vital to improve the effectiveness of conservation management interventions. The greater one-horned rhinoceros (Rhinoceros unicornis) is one of the most iconic megaherbivores in South Asia but is classified as Vulnerable by the IUCN. The species is now broadly confined to two isolated populations in Chitwan National Park (CNP), Nepal and Northeast India, which are both constrained by poaching, and the loss or degradation of habitat. Since 2016, rhino mortalities have increased in CNP for unknown reasons. To assess the impact of any current or

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LeDuc, R. G., D. W. Weller, J. Hyde, et al. "Genetic differences between western and eastern gray whales (Eschrichtius robustus)." J. Cetacean Res. Manage. 4, no. 1 (2023): 1–5. http://dx.doi.org/10.47536/jcrm.v4i1.860.

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Molecular data were used to examine the differentiation between the western and eastern gray whale (Eschrichtius robustus) populations. Control region sequences were generated from samples collected in the western Pacific (n = 45) and eastern Pacific (n = 120). There were 36 unique haplotypes identified. Ten haplotypes were represented in the western samples, and 33 in the eastern samples. Seven of these haplotypes were shared between populations, leaving three haplotypes that were only seen in the western samples and 26 only in the eastern. Although there were no fixed (diagnostic) difference

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Knoll, Aleš, Lucie Langová, Antonín Přidal, and Tomáš Urban. "Haplotype Diversity in mtDNA of Honeybee in the Czech Republic Confirms Complete Replacement of Autochthonous Population with the C Lineage." Insects 15, no. 7 (2024): 495. http://dx.doi.org/10.3390/insects15070495.

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The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identifie

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Epifanio, John M., Bonnie L. Brown, Peter E. Smouse, and Carol J. Kobak. "Mitochondrial DNA divergence among popylations of American shad (Alosa sapidissima): how much variation is enough for mixed-stock analysis?" Canadian Journal of Fisheries and Aquatic Sciences 52, no. 8 (1995): 1688–702. http://dx.doi.org/10.1139/f95-761.

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We investigated the geographic distribution of the mitochondrial DNA (mtDNA) diversity of American shad from 15 North American rivers in 1992 with the intent of assessing sampling efficiency for future mixed-stock analysis. We observed 116 haplotypes among the 988 individuals assayed. Because no single or group of haplotypes completely discriminated river stocks or regional complexes, we investigated haplotype frequencies as stock descriptors. Analysis of four unique indices of haplotype divergence indicated that including rather than suppressing restriction site heteroplasmy increased resolut

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Mi̇Fsud, Clare Marie, and Adriana Vella. "Mitochondrial Genetic Diversity of Bat Species from the Maltese Islands and Applications for their Conservation." Natural and Engineering Sciences 4, no. 3 (2019): 276–92. https://doi.org/10.5281/zenodo.13441431.

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(Uploaded by Plazi for the Bat Literature Project) This work presents the first genetic species identification and phylogenetic analyses of all six bat species known to inhabit the Maltese archipelago. The results provide a DNA-based reference library of 12S rRNA, 16S rRNA, COI, Cytb and ND1 mitochondrial sequences for Maltese bat species. Phylogenetic analyses revealed that the Maltese bat populations do not harbour cryptic diversity. Analyses of genetic diversity for Maltese bat species showed contrasting matrilineal diversity between species, Hypsugo savii exhibited the highest haplotype di

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Mi̇Fsud, Clare Marie, and Adriana Vella. "Mitochondrial Genetic Diversity of Bat Species from the Maltese Islands and Applications for their Conservation." Natural and Engineering Sciences 4, no. 3 (2019): 276–92. https://doi.org/10.5281/zenodo.13441431.

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(Uploaded by Plazi for the Bat Literature Project) This work presents the first genetic species identification and phylogenetic analyses of all six bat species known to inhabit the Maltese archipelago. The results provide a DNA-based reference library of 12S rRNA, 16S rRNA, COI, Cytb and ND1 mitochondrial sequences for Maltese bat species. Phylogenetic analyses revealed that the Maltese bat populations do not harbour cryptic diversity. Analyses of genetic diversity for Maltese bat species showed contrasting matrilineal diversity between species, Hypsugo savii exhibited the highest haplotype di

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Mi̇Fsud, Clare Marie, and Adriana Vella. "Mitochondrial Genetic Diversity of Bat Species from the Maltese Islands and Applications for their Conservation." Natural and Engineering Sciences 4, no. 3 (2019): 276–92. https://doi.org/10.5281/zenodo.13441431.

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(Uploaded by Plazi for the Bat Literature Project) This work presents the first genetic species identification and phylogenetic analyses of all six bat species known to inhabit the Maltese archipelago. The results provide a DNA-based reference library of 12S rRNA, 16S rRNA, COI, Cytb and ND1 mitochondrial sequences for Maltese bat species. Phylogenetic analyses revealed that the Maltese bat populations do not harbour cryptic diversity. Analyses of genetic diversity for Maltese bat species showed contrasting matrilineal diversity between species, Hypsugo savii exhibited the highest haplotype di

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Mi̇Fsud, Clare Marie, and Adriana Vella. "Mitochondrial Genetic Diversity of Bat Species from the Maltese Islands and Applications for their Conservation." Natural and Engineering Sciences 4, no. 3 (2019): 276–92. https://doi.org/10.5281/zenodo.13441431.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) This work presents the first genetic species identification and phylogenetic analyses of all six bat species known to inhabit the Maltese archipelago. The results provide a DNA-based reference library of 12S rRNA, 16S rRNA, COI, Cytb and ND1 mitochondrial sequences for Maltese bat species. Phylogenetic analyses revealed that the Maltese bat populations do not harbour cryptic diversity. Analyses of genetic diversity for Maltese bat species showed contrasting matrilineal diversity between species, Hypsugo savii exhibited the highest haplotype di

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Mi̇Fsud, Clare Marie, and Adriana Vella. "Mitochondrial Genetic Diversity of Bat Species from the Maltese Islands and Applications for their Conservation." Natural and Engineering Sciences 4, no. 3 (2019): 276–92. https://doi.org/10.5281/zenodo.13441431.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) This work presents the first genetic species identification and phylogenetic analyses of all six bat species known to inhabit the Maltese archipelago. The results provide a DNA-based reference library of 12S rRNA, 16S rRNA, COI, Cytb and ND1 mitochondrial sequences for Maltese bat species. Phylogenetic analyses revealed that the Maltese bat populations do not harbour cryptic diversity. Analyses of genetic diversity for Maltese bat species showed contrasting matrilineal diversity between species, Hypsugo savii exhibited the highest haplotype di

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McConnell, Sean C., and Jill L. O. de Jong. "Diversity of Class I Major Histocompatibility Genes From Divergent Haplotypes in Zebrafish." Blood 120, no. 21 (2012): 1058. http://dx.doi.org/10.1182/blood.v120.21.1058.1058.

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Abstract Abstract 1058 The zebrafish is an important animal model for stem cell biology, cancer, and immunology research. Histocompatibility represents a key intersection of these disciplines, particularly in the context of transplantation experiments that distinguish between autologous and allogeneic tissues. Major histocompatibility (MH) genes are considered the most polymorphic genes in vertebrates, yet this immense variation occurs while maintaining conserved roles in antigen presentation. Histocompatibility in zebrafish remains poorly understood, requiring the identification of the classi

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Trang, Vu Thi, Tran Thi Thuy Ha, Tran Thi Kim Ngan, Nguyen Dinh Vinh, Pham Hong Nhat, and Vu Thi Huyen. "Genetic Diversity of Chanos Chanos (Forsskål, 1775) from Natural Populations in Vietnam." Vietnam Journal of Agricultural Sciences 5, no. 2 (2022): 1456–63. http://dx.doi.org/10.31817/vjas.2022.5.2.03.

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The genetic diversity of five natural populations of milkfish (Chanos chanos) collected in Nghe An, Quang Binh, Binh Dinh, Phu Yen, Khanh Hoa provinces in Vietnam was examined using COI gene sequence analysis. Twelve haplotypes were noted from a total of 50 sequences along with 12 variable sites and 6 parsimony informative sites. The Quang Binh milkfish population had the highest haplotype (0.889 ± 0.060) and nucleotide diversities (0.00301 ± 0.00049). Overall, haplotype and nucleotide diversities were 0.804 ± 0.036 and 0.00212 ± 0.00026, respectively. Genetic differentiation (FST) was high be

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Saville, Amanda, Melodi Charles, Suchitra Chavan, Miguel Muñoz, Luis Gómez-Alpizar, and Jean Beagle Ristaino. "Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations." Phytopathology® 107, no. 12 (2017): 1541–48. http://dx.doi.org/10.1094/phyto-02-17-0045-r.

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Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of popu

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Eamsobhana, P., H. S. Yong, S. L. Song, A. Prasartvit, S. Boonyong, and A. Tungtrongchitr. "Cytochrome c oxidase subunit I haplotype reveals high genetic diversity of Angiostrongylus malaysiensis (Nematoda: Angiostrongylidae)." Journal of Helminthology 92, no. 2 (2017): 254–59. http://dx.doi.org/10.1017/s0022149x17000244.

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AbstractThe rat lungworm Angiostrongylus malaysiensis is a metastrongyloid nematode parasite. It has been reported in Malaysia, Thailand, Laos, Myanmar, Indonesia and Japan. In this study, A. malaysiensis adult worms recovered from the lungs of wild rats in different geographical regions/provinces in Thailand were used to determine their haplotype by means of the mitochondrial partial cytochrome c oxidase subunit I (COI) gene sequence. The results revealed high COI haplotype diversity of A. malaysiensis from Thailand. The geographical isolates of A. malaysiensis from Thailand and other countri

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Criscione, Andrea, Serena Tumino, Marcella Avondo, Donata Marletta, and Salvatore Bordonaro. "Casein haplotype diversity in seven dairy goat breeds." Archives Animal Breeding 62, no. 2 (2019): 447–54. http://dx.doi.org/10.5194/aab-62-447-2019.

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Abstract. Selection, drift, gene flow and breeding have extensively shaped the genomic variability of domestic animals. In goat species, several mutations identified within the casein genes have been shown to affect the level of gene expression of milk production traits. The four casein genes – CSN1S1, CSN2, CSN1S2 and CSN3 – are organized in a cluster of 250 kb located in chromosome 6, and due to tight linkage, their genetic variability is well depicted by haplotypes which are transmitted to the progeny. Thirty single nucleotide polymorphisms (SNPs) located within the casein gene cluster were

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Liu, Jiahe, Xu Cai, Yufang Li, et al. "Selection on BrFLC1 Is Related to Intraspecific Diversity of Brassica rapa Vegetables." Horticulturae 7, no. 8 (2021): 247. http://dx.doi.org/10.3390/horticulturae7080247.

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Flowering time is important for Brassica rapa vegetables because premature bolting before harvest can lower yield and quality. FLOWERING LOCUS C (FLC) acts as a key repressor of flowering. In this study, we identified a nonsynonymous mutation at the 58th nucleotide of exon1 in BrFLC1 (named as Pe1+58 (A/C)) by screening resequencing data of 199 B. rapa accessions and verified this mutation as being related to flowering time variation. Strong linkage inheritance was detected between this locus and a previously reported splicing site mutation at intron 6 of BrFLC1 (Pi6+1 (G/A)), showing as co-oc

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Ashrifurrahman, Saruedi Simamora, Rusdiyan Ritonga, et al. "Mitochondrial CO1 gene haplotype diversity of Sumatran Tiger Panthera tigris sumatrae (Pocock, 1929) (Mammalia: Carnivora: Felidae)." Journal of Threatened Taxa 16, no. 4 (2024): 25019–28. http://dx.doi.org/10.11609/jott.8190.16.4.25019-25028.

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Sumatran Tigers Panthera tigris sumatrae inhabit 12 tiger conservation landscapes that stretch across Sumatra Island. Conservation efforts for these species require robust, information-based research, including a genetic approach. This study analyzed the haplotype diversity of P. t. sumatrae based on the mitochondrial CO1 (Cytochrome Oxidase Subunit 1) gene. Specifically, a nucleotide guanine at position 121 was found, distinguishing P. t. sumatrae from other tiger subspecies. Among the 17 sequences of P. t. sumatrae, two haplotypes were detected: 13 individuals were in haplotype 1 (Hap_1), an

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Putra, Widya Pintaka Bayu, Arif Wibowo, and Anang Hari Kristanto. "Haplotype Diversity in the Mitochondrial COI Gene of Barred Rainbowfish (Chilaterina fasciata) from Mamberamo River of Western New Guinea, Indonesia." HAYATI Journal of Biosciences 31, no. 1 (2023): 126–32. http://dx.doi.org/10.4308/hjb.31.1.126-132.

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A Barred rainbowfish (Chilatherina fasciata) is one of the native fish species found in Western New Guinea of Indonesia. This study aimed to observe the levels of haplotype diversity in the partial Cytochrome-c oxidase subunit I (COI) gene of Barred rainbowfish. For the DNA analysis, thirty (30) Barred rainbowfishes were caught from the Mamberamo River. Three (3) molecular packages of BioEdit, MEGA, and DNAsp were used to analyze twenty (30) forward sequences of the COI gene (502 bp). The research showed four (4) haplotypes for the examined population, a total of seven (7) mutations, and low g

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Saunders, Ginny C., Saira Cawthraw, Susan J. Mountjoy, et al. "Ovine PRNP untranslated region and promoter haplotype diversity." Journal of General Virology 90, no. 5 (2009): 1289–93. http://dx.doi.org/10.1099/vir.0.007997-0.

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The diversity and possible contribution of non-coding regions of the prion protein (PrP) gene (PRNP) to transmissible spongiform encephalopathy susceptibility and PrP regulation are not fully known. This study defined ten ovine PRNP promoters and five untranslated region (UTR) haplotypes found in atypical and classical scrapie cases and healthy control sheep. A greater diversity of promoter and UTR haplotypes was observed in conjunction with the ARQ PrP allele (seven promoter and four UTR haplotypes), while it was observed that the other alleles were linked with a limited number of haplotypes,

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