11 results on '"Dobrynin, Pavel"'
Search Results
2. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal
- Author
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Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J., Graphodatsky, Alexander, Koepfli, Klaus-Peter, Kliver, Sergei, Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J., Graphodatsky, Alexander, Koepfli, Klaus-Peter, and Kliver, Sergei
- Abstract
Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.
- Published
- 2023
3. GADMA2: more efficient and flexible demographic inference from genetic data
- Author
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Noskova, Ekaterina, primary, Abramov, Nikita, additional, Iliutkin, Stanislav, additional, Sidorin, Anton, additional, Dobrynin, Pavel, additional, and Ulyantsev, Vladimir I, additional
- Published
- 2022
- Full Text
- View/download PDF
4. A Study of the Genomic Variations Associated with Autistic Spectrum Disorders in a Russian Cohort of Patients Using Whole-Exome Sequencing
- Author
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Gibitova, Еkaterina А., primary, Dobrynin, Pavel V., additional, Pomerantseva, Ekaterina A., additional, Musatova, Elizaveta V., additional, Kostareva, Anna, additional, Evsyukov, Igor, additional, Rychkov, Sergey Y., additional, Zhukova, Olga V., additional, Naumova, Oxana Y., additional, and Grigorenko, Elena L., additional
- Published
- 2022
- Full Text
- View/download PDF
5. Insights from the rescue and breeding management of Cuvier's gazelle (Gazella cuvieri) through whole-genome sequencing
- Author
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Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas, Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Moreno, Eulalia, Lizano, Esther, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas, Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Moreno, Eulalia, and Lizano, Esther
- Abstract
Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier's gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier's gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier's gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.
- Published
- 2022
6. Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole-genome sequencing
- Author
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Rancho Santa Fe Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Smithsonian Institution, European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas F. K., Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marqués-Bonet, Tomàs, Moreno, Eulalia, Lizano, Esther, Rancho Santa Fe Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Smithsonian Institution, European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas F. K., Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marqués-Bonet, Tomàs, Moreno, Eulalia, and Lizano, Esther
- Abstract
Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier’s gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier’s gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier’s gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.
- Published
- 2022
7. Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae
- Author
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Derežanin, Lorena, Blažytė, Asta, Dobrynin, Pavel, Duchêne, David A., Grau, José Horacio, Jeon, Sungwon, Kliver, Sergei, Koepfli, Klaus-Peter, Meneghini, Dorina, Preick, Michaela, Tomarovsky, Andrey, Totikov, Azamat, Fickel, Jörns, Förster, Daniel W., Derežanin, Lorena, Blažytė, Asta, Dobrynin, Pavel, Duchêne, David A., Grau, José Horacio, Jeon, Sungwon, Kliver, Sergei, Koepfli, Klaus-Peter, Meneghini, Dorina, Preick, Michaela, Tomarovsky, Andrey, Totikov, Azamat, Fickel, Jörns, and Förster, Daniel W.
- Abstract
Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
- Published
- 2022
8. Insights from the rescue and breeding management of Cuvier’s gazelle ( Gazella cuvieri ) through whole‐genome sequencing
- Author
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Alvarez‐Estape, Marina, primary, Fontsere, Claudia, additional, Serres‐Armero, Aitor, additional, Kuderna, Lukas F. K., additional, Dobrynin, Pavel, additional, Guidara, Héla, additional, Pukazhenthi, Budhan S., additional, Koepfli, Klaus‐Peter, additional, Marques‐Bonet, Tomas, additional, Moreno, Eulalia, additional, and Lizano, Esther, additional
- Published
- 2022
- Full Text
- View/download PDF
9. GADMA2: more efficient and flexible demographic inference from genetic data.
- Author
-
Noskova, Ekaterina, Abramov, Nikita, Iliutkin, Stanislav, Sidorin, Anton, Dobrynin, Pavel, and Ulyantsev, Vladimir I
- Subjects
OPTIMIZATION algorithms ,GLOBAL optimization ,HISTORICAL source material ,RESEARCH personnel ,PARAMETER estimation - Abstract
Background Inference of complex demographic histories is a source of information about events that happened in the past of studied populations. Existing methods for demographic inference typically require input from the researcher in the form of a parameterized model. With an increased variety of methods and tools, each with its own interface, the model specification becomes tedious and error-prone. Moreover, optimization algorithms used to find model parameters sometimes turn out to be inefficient, for instance, by being not properly tuned or highly dependent on a user-provided initialization. The open-source software GADMA addresses these problems, providing automatic demographic inference. It proposes a common interface for several likelihood engines and provides global parameters optimization based on a genetic algorithm. Results Here, we introduce the new GADMA2 software and provide a detailed description of the added and expanded features. It has a renovated core code base, new likelihood engines, an updated optimization algorithm, and a flexible setup for automatic model construction. We provide a full overview of GADMA2 enhancements, compare the performance of supported likelihood engines on simulated data, and demonstrate an example of GADMA2 usage on 2 empirical datasets. Conclusions We demonstrate the better performance of a genetic algorithm in GADMA2 by comparing it to the initial version and other existing optimization approaches. Our experiments on simulated data indicate that GADMA2's likelihood engines are able to provide accurate estimations of demographic parameters even for misspecified models. We improve model parameters for 2 empirical datasets of inbred species. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
10. Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.
- Author
-
Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Serdyukova NA, Rayko M, Bulyonkova T, Cherkasov N, Pylev V, Peterfeld V, Penin A, Balanovska E, Lapidus A, Dna Zoo Consortium, OBrien SJ, Graphodatsky A, Koepfli KP, and Kliver S
- Subjects
- Animals, Karyotype, Lakes, Seals, Earless genetics
- Abstract
Pusa sibirica , the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.
- Published
- 2023
- Full Text
- View/download PDF
11. Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.
- Author
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Tamazian G, Dobrynin P, Zhuk A, Zhernakova DV, Perelman PL, Serdyukova NA, Graphodatsky AS, Komissarov A, Kliver S, Cherkasov N, Scott AF, Mohr DW, Koepfli KP, O'Brien SJ, and Krasheninnikova K
- Subjects
- Animals, Female, Genome, Genomics, Male, Molecular Sequence Annotation, Felidae, Puma genetics
- Abstract
The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification., (© The American Genetic Association. 2021.)
- Published
- 2021
- Full Text
- View/download PDF
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