| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Avetyan, D, et al.
(författare)
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Molecular Analysis of SARS-CoV-2 Lineages in Armenia
- 2022
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Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase were caused by the 20B clade, the third peak caused by the 20I (Alpha), while the last two peaks were caused by the 21J (Delta) and 21K (Omicron) variants. The functional analyses of mutations in sequences largely affected epitopes associated with protective HLA loci and did not cause the loss of the signal in PCR tests targeting ORF1ab and N genes as confirmed by RT-PCR. We also compared the performance of nanopore and Illumina short-read sequencing and showed the utility of nanopore sequencing as an efficient and affordable alternative for large-scale molecular epidemiology research. Thus, our paper describes new data on the genomic diversity of SARS-CoV-2 variants in Armenia in the global context of the virus molecular genomic surveillance.
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| 3. |
- Freitas, S., et al.
(författare)
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Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization
- 2022
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 76:5, s. 899-914
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.
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| 4. |
- Girnyk, Anastasiya E., et al.
(författare)
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Multiple interspecific hybridization and microsatellite mutations provide clonal diversity in the parthenogenetic rock lizard Darevskia armeniaca
- 2018
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Ingår i: BMC Genomics. - : BMC Genomics. - 1471-2164. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- The parthenogenetic Caucasian rock lizard Darevskia armeniaca, like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual Darevskia mixta and Darevskia valentini. Darevskia armeniaca was shown to consist of one widespread allozyme clone and a few rare ones, but notwithstanding the origin of clonal diversity remains unclear. We conduct genomic analysis of D. armeniaca and its parental sexual species using microsatellite and SNP markers to identify the origin of parthenogenetic clonal lineages. Four microsatellite-containing loci were genotyped for 111 specimens of D. armeniaca, 17 D. valentini, and four D. mixta. For these species, a total of 47 alleles were isolated and sequenced. Analysis of the data revealed 13 genotypes or presumptive clones in parthenogenetic D. armeniaca, including one widespread clone, two apparently geographically restricted clones, and ten rare clones. Comparisons of genotype-specific markers in D. armeniaca with those of its parental species revealed three founder-events including a common and two rare clones. All other clones appeared to have originated via post-formation microsatellite mutations in the course of evolutionary history of D. armeniaca. Our new approach to microsatellite genotyping reveals allele-specific microsatellite and SNP markers for each locus studied. Interspecies comparison of these markers identifies alleles inherited by parthenospecies from parental species, and provides new information on origin and evolution of clonal diversity in D. armeniaca. SNP analyses reveal at least three interspecific origins of D. armeniaca, and microsatellite mutations in these initial clones give rise to new clones. Thus, we first establish multiple origins of D. armeniaca. Our study identifies the most effective molecular markers for elucidating the origins of clonal diversity in other unisexual species that arose via interspecific hybridization.
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| 5. |
- Arakelyan, A., et al.
(författare)
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Multi-Phase Quadrature Domains and a Related Minimization Problem
- 2016
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Ingår i: Potential Analysis. - : Springer Netherlands. - 0926-2601 .- 1572-929X. ; , s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we introduce the multi-phase version of the so-called Quadrature Domains (QD), which refers to a generalized type of mean value property for harmonic functions. The well-established and developed theory of one-phase QD was recently generalized to a two-phase version, by one of the current authors (in collaboration). Here we introduce the concept of the multi-phase version of the problem, and prove existence as well as several properties of such solutions. In particular, we discuss possibilities of multi-junction points.
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| 6. |
- Arakelyan, A., et al.
(författare)
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Two-and multi-phase quadrature surfaces
- 2017
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Ingår i: Communications on Pure and Applied Analysis. - : American Institute of Mathematical Sciences. - 1534-0392 .- 1553-5258. ; 16:6, s. 2023-2045
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we shall initiate the study of the two-and multi-phase quadrature surfaces (QS), which amounts to a two/multi-phase free boundary problems of Bernoulli type. The problem is studied mostly from a potential theoretic point of view that (for two-phase case) relates to integral representation where dsx is the surface measure, μ = μ+-μ-is given measure with support in (a priori unknown domain) ω = ω+ [ω-, g is a given smooth positive function, and the integral holds for all functions h, which are harmonic on ω. Our approach is based on minimization of the corresponding two-and multiphase functional and the use of its one-phase version as a barrier. We prove several results concerning existence, qualitative behavior, and regularity theory for solutions. A central result in our study states that three or more junction points do not appear.
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| 7. |
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| 8. |
- Freitas, Susana N., et al.
(författare)
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The role of hybridisation in the origin and evolutionary persistence of vertebrate parthenogens: a case study of Darevskia lizards
- 2019
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 123, s. 795-808
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Tidskriftsartikel (refereegranskat)abstract
- Obligate parthenogenesis is found in only 0.1% of the vertebrate species, is thought to be relatively short lived and is typically of hybrid origin. However, neither the evolutionary persistence of asexuality in vertebrates, nor the conditions that allow the generation of new parthenogenetic lineages are currently well understood. It has been proposed that vertebrate parthenogenetic lineages arise from hybridisation between two divergent taxa within a specific range of phylogenetic distances (the ‘Balance Hypothesis’). Moreover, parthenogenetic species often maintain a certain level of hybridisation with their closest sexual relatives, potentially generating new polyploid hybrid lineages. Here we address the role of hybridisation in the origin and evolutionary lifespan of vertebrate parthenogens. We use a set of microsatellite markers to characterise the origins of parthenogens in the lizard genus Darevskia, to study the distinctiveness of sexual and asexual taxa currently in sympatry, and to analyse the evolutionary consequences of interspecific hybridisation between asexual females and sexual males. We find that parthenogens result from multiple past hybridisation events between species from specific lineages over a range of phylogenetic distances. This suggests that the Balance Hypothesis needs to allow for lineage-specific effects, as envisaged in the Phylogenetic Constraint Hypothesis. Our results show recurrent backcrossing between sexual and parthenogenic Darevskia but neither gene flow nor formation of new asexual lineages. We suggest that, along with their demographic advantage, parthenogens gain additional leverage to outcompete sexuals in nature when the retention of sexual reproductive machinery allows backcrossing with their sexual ancestors.
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| 9. |
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