11 results on '"Vasiliev, Sergei K."'
Search Results
2. Genetic History of the Altai Breed Horses: From Ancient Times to Modernity.
- Author
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Kusliy, Mariya A., Yurlova, Anna A., Neumestova, Alexandra I., Vorobieva, Nadezhda V., Gutorova, Natalya V., Molodtseva, Anna S., Trifonov, Vladimir A., Popova, Kseniya O., Polosmak, Natalia V., Molodin, Vyacheslav I., Vasiliev, Sergei K., Semibratov, Vladimir P., Iderkhangai, Tumur-O., Kovalev, Alexey A., Erdenebaatar, Diimaajav, Graphodatsky, Alexander S., and Tishkin, Alexey A.
- Subjects
HORSE breeding ,HORSE breeds ,MITOCHONDRIAL DNA ,HYPERVARIABLE regions ,MODERNITY ,GENETIC markers - Abstract
This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia
- Author
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Buggiotti, Laura, primary, Yurchenko, Andrey A, additional, Yudin, Nikolay S, additional, Vander Jagt, Christy J, additional, Vorobieva, Nadezhda V, additional, Kusliy, Mariya A, additional, Vasiliev, Sergei K, additional, Rodionov, Andrey N, additional, Boronetskaya, Oksana I, additional, Zinovieva, Natalia A, additional, Graphodatsky, Alexander S, additional, Daetwyler, Hans D, additional, and Larkin, Denis M, additional
- Published
- 2021
- Full Text
- View/download PDF
4. High genetic diversity of ancient horses from the Ukok Plateau
- Author
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Vorobieva, Nadezhda V., primary, Makunin, Alexey I., additional, Druzhkova, Anna S., additional, Kusliy, Mariya A., additional, Trifonov, Vladimir A., additional, Popova, Kseniya O., additional, Polosmak, Natalia V., additional, Molodin, Vyacheslav I., additional, Vasiliev, Sergei K., additional, Shunkov, Michael V., additional, and Graphodatsky, Alexander S., additional
- Published
- 2020
- Full Text
- View/download PDF
5. The northernmost and latest occurrence of the fossil porcupine (Hystrix brachyura vinogradovi Argyropulo, 1941) in the Altai Mountains in the Late Pleistocene (ca. 32,000–41,000 cal BP)
- Author
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Kuzmin, Yaroslav V., primary, Kosintsev, Pavel A., additional, Vasiliev, Sergei K., additional, Fadeeva, Tatyana V., additional, and Hodgins, Gregory W.L., additional
- Published
- 2017
- Full Text
- View/download PDF
6. Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx:consequences on nucleotide misincorporation and methylation patterns
- Author
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Seguin-Orlando, Andaine, Hoover, Cindi A., Vasiliev, Sergei K., Ovodov, Nikolai D., Shapiro, Beth, Cooper, Alan, Rubin, Edward M., Willerslev, Eske, Orlando, Ludovic, Seguin-Orlando, Andaine, Hoover, Cindi A., Vasiliev, Sergei K., Ovodov, Nikolai D., Shapiro, Beth, Cooper, Alan, Rubin, Edward M., Willerslev, Eske, and Orlando, Ludovic
- Abstract
Recent developments in high-throughput sequencing (HTS) technologies have enabled the reconstruction of complete genome sequence and nucleosome and methylation maps from ancient individuals. A diversity of degradation reactions affect DNA molecules after an organism dies, introducing specific nucleotide misincorporation patterns in HTS data that are typically exploited to distinguish modern contaminants and authentic DNA templates. In this study, we used two different DNA polymerases to amplify Illumina TruSeq DNA libraries built on DNA extracts from ancient equines. The AmpliTaq Gold, widely used in ancient DNA studies, generated amplified libraries showing typical misincorporation patterns. Such patterns were partially lost following AccuPrime Pfx amplification, for which a two-fold reduction of endogenous content was also observed. This is explained by the inability of the AccuPrime Pfx to bypass uracils, which represent the most common post-mortem base modification and derive from the post-mortem deamination of cytosines. Our study, therefore, reveals that amplification of TruSeq DNA libraries with AccuPrime Pfx increases the cost of whole-genome sequencing for samples showing substantial levels of DNA degradation and creates atypical nucleotide misincorporation patterns for data authentication. The method can, however, be exploited to identify ancient methylation marks, and potentially, nucleosome occupancy maps. Statement of significance After an organism dies, DNA molecules are subjected to degradation resulting in fragmentation and bases modifications. After high- throughput sequencing (HTS), it is possible to detect the molecular signature of these damages, demonstrating that the data generated is authentic. DNA extracts from fossil remains indeed contain, besides endogenous ancient molecules, a variety of modern contaminants, but only the former generally exhibits molecular signatures typical of post-mortem damage. Our study reveals that these signature
- Published
- 2015
7. Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns
- Author
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Seguin-Orlando, Andaine, primary, Hoover, Cindi A., additional, Vasiliev, Sergei K., additional, Ovodov, Nikolai D., additional, Shapiro, Beth, additional, Cooper, Alan, additional, Rubin, Edward M., additional, Willerslev, Eske, additional, and Orlando, Ludovic, additional
- Published
- 2015
- Full Text
- View/download PDF
8. Mitochondrial phylogenomics of modern and ancient equids.
- Author
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Vilstrup, Julia T., Seguin-Orlando, Andaine, Stiller, Mathias, Ginolhac, Aurélien, Raghavan, Maanasa, Nielsen, Sandra C. A., Weinstock, Jacobo, Froese, Duane, Vasiliev, Sergei K., Ovodov, Nikolai D., Clary, Joel, Helgen, Kristofer M., Fleischer, Robert C., Cooper, Alan, Shapiro, Beth, Orlando, Ludovic, Vilstrup, Julia T., Seguin-Orlando, Andaine, Stiller, Mathias, Ginolhac, Aurélien, Raghavan, Maanasa, Nielsen, Sandra C. A., Weinstock, Jacobo, Froese, Duane, Vasiliev, Sergei K., Ovodov, Nikolai D., Clary, Joel, Helgen, Kristofer M., Fleischer, Robert C., Cooper, Alan, Shapiro, Beth, and Orlando, Ludovic
- Abstract
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
- Published
- 2013
9. Mitochondrial phylogenomics of modern and ancient equids
- Author
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Mouatt, Julia Thidamarth Vilstrup, Seguin-Orlando, Andaine, Stiller, Mathias, Ginolhac, Aurélien, Raghavan, Maanasa, Nielsen, Sandra Cathrine Abel, Weinstock, Jacobo, Froese, Duane, Vasiliev, Sergei K., Ovodov, Nikolai D., Clary, Joel, Helgen, Kristofer M., Fleischer, Robert C., Cooper, Alan, Shapiro, Beth, Orlando, Ludovic Antoine Alexandre, Mouatt, Julia Thidamarth Vilstrup, Seguin-Orlando, Andaine, Stiller, Mathias, Ginolhac, Aurélien, Raghavan, Maanasa, Nielsen, Sandra Cathrine Abel, Weinstock, Jacobo, Froese, Duane, Vasiliev, Sergei K., Ovodov, Nikolai D., Clary, Joel, Helgen, Kristofer M., Fleischer, Robert C., Cooper, Alan, Shapiro, Beth, and Orlando, Ludovic Antoine Alexandre
- Abstract
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
- Published
- 2013
10. Mitochondrial Phylogenomics of Modern and Ancient Equids
- Author
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Vilstrup, Julia T., primary, Seguin-Orlando, Andaine, additional, Stiller, Mathias, additional, Ginolhac, Aurelien, additional, Raghavan, Maanasa, additional, Nielsen, Sandra C. A., additional, Weinstock, Jacobo, additional, Froese, Duane, additional, Vasiliev, Sergei K., additional, Ovodov, Nikolai D., additional, Clary, Joel, additional, Helgen, Kristofer M., additional, Fleischer, Robert C., additional, Cooper, Alan, additional, Shapiro, Beth, additional, and Orlando, Ludovic, additional
- Published
- 2013
- Full Text
- View/download PDF
11. Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns
- Author
-
Seguin-Orlando, Andaine, Hoover, Cindi A., Vasiliev, Sergei K., Ovodov, Nikolai D., Shapiro, Beth, Cooper, Alan, Rubin, Edward M., Willerslev, Eske, and Orlando, Ludovic
- Abstract
Recent developments in high-throughput sequencing (HTS) technologies have enabled the reconstruction of complete genome sequence and nucleosome and methylation maps from ancient individuals. A diversity of degradation reactions affect DNA molecules after an organism dies, introducing specific nucleotide misincorporation patterns in HTS data that are typically exploited to distinguish modern contaminants and authentic DNA templates. In this study, we used two different DNA polymerases to amplify Illumina TruSeq DNA libraries built on DNA extracts from ancient equines. The AmpliTaq Gold, widely used in ancient DNA studies, generated amplified libraries showing typical misincorporation patterns. Such patterns were partially lost following AccuPrime Pfxamplification, for which a two-fold reduction of endogenous content was also observed. This is explained by the inability of the AccuPrime Pfxto bypass uracils, which represent the most common post-mortembase modification and derive from the post-mortemdeamination of cytosines. Our study, therefore, reveals that amplification of TruSeq DNA libraries with AccuPrime Pfxincreases the cost of whole-genome sequencing for samples showing substantial levels of DNA degradation and creates atypical nucleotide misincorporation patterns for data authentication. The method can, however, be exploited to identify ancient methylation marks, and potentially, nucleosome occupancy maps.Statement of significanceAfter an organism dies, DNA molecules are subjected to degradation resulting in fragmentation and bases modifications. After high- throughput sequencing (HTS), it is possible to detect the molecular signature of these damages, demonstrating that the data generated is authentic. DNA extracts from fossil remains indeed contain, besides endogenous ancient molecules, a variety of modern contaminants, but only the former generally exhibits molecular signatures typical of post-mortemdamage. Our study reveals that these signatures depend on the protocol used for amplifying DNA samples. It thus helps defining better guidelines for authenticating ancient HTS data. Our results also reveal one molecular approach that limits our ability to exploit the whole complexity of ancient DNA molecules preserved in fossil specimens but can help track ancient methylation marks.Data availabilityThe authors confirm that all data underlying the findings are fully available without restriction. All relevant data are contained within the paper.
- Published
- 2015
- Full Text
- View/download PDF
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