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  • 1.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ljungvall, Ingrid
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Bhoumik, Priyasma
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland.;Swiss Fed Inst Technol, Sci & IT Serv, Basel Campus, Basel, Switzerland..
    Conn, Laura Bas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Murén, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ohlsson, Åsa
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Olsen, Lisbeth Hoier
    Univ Copenhagen, Dept Vet & Anim Sci, Copenhagen, Denmark..
    Engdahl, Karolina
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Hagman, Ragnvi
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Hanson, Jeanette
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Kryvokhyzha, Dmytro
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Grenet, Olivier
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Moggs, Jonathan
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Del Rio-Espinola, Alberto
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Epe, Christian
    Elanco Anim Hlth, Greenfield, IN USA.;Boehringer Ingelheim Anim Hlth, Ingelheim, Germany..
    Taillon, Bruce
    Elanco Anim Hlth, Greenfield, IN USA..
    Tawari, Nilesh
    Elanco Anim Hlth, Greenfield, IN USA..
    Mane, Shrinivas
    Elanco Anim Hlth, Greenfield, IN USA..
    Hawkins, Troy
    Elanco Anim Hlth, Greenfield, IN USA..
    Hedhammar, Åke
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Gruet, Philippe
    Novartis Anim Hlth, St Aubin, Switzerland..
    Häggström, Jens
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Cambridge, MA 02142 USA..
    The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels2021In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 17, no 9, article id e1009726Article in journal (Refereed)
    Abstract [en]

    Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a similar to 10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heartderived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.

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    FULLTEXT01
  • 2.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Salcedo, A.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wright, S. I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 616-629Article in journal (Refereed)
    Abstract [en]

    Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C.bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C.bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C.bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C.bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.

  • 3.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Paris Saclay, INRAE, AgroParisTech, GQE Le Moulon,CNRS, F-91190 Gif Sur Yvette, France..
    Tiret, Mathieu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Salcedo, Adriana
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Huang, Huirun R.
    Chinese Acad Sci, Key Lab Plant Resources Conservat & Sustainable U, South China Bot Garden, Guangzhou 510650, Peoples R China.;Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Guangzhou 510650, Peoples R China..
    Orsucci, Marion
    Swedish Univ Agr Sci, Dept Plant Biol, S-75007 Uppsala, Sweden..
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ge, Xue-Jun
    Chinese Acad Sci, Key Lab Plant Resources Conservat & Sustainable U, South China Bot Garden, Guangzhou 510650, Peoples R China.;Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Guangzhou 510650, Peoples R China..
    Stinchcombe, John R.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Rennes 1, UMR CNRS ECOBIO 6553, F-35042 Rennes, France..
    Wright, Stephen, I
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe2022In: AoB Plants, E-ISSN 2041-2851, Vol. 14, no 3, article id plac011Article in journal (Refereed)
    Abstract [en]

    The respective role of demography, plasticity and adaptation in the colonization success of plant species remains an intense topic of investigation in evolutionary ecology and genomics. A screening of phenotypic traits of hundreds of genotypes in large-scale common garden experiments in Eastern Asia and Europe shows that both demography and a high phenotypic plasticity underlie the success of the tetraploid and self-fertilizing species, Capsella bursa-pastoris, the shepherd's purse, at different stages of expansion. This study provides insight into the causes of the ecological success of a plant species during range expansion. The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity.

    Download full text (pdf)
    fulltext
  • 4.
    Dufresnes, Christophe
    et al.
    Univ Lausanne, Lab Conservat Biol, Biophore Bldg, CH-1015 Lausanne, Switzerland; Hintermann & Weber, Ave Alpes 25, CH-1820 Montreux, Switzerland.
    Mazepa, Glib
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Lausanne, Dept Ecol & Evolut, Biophore Bldg, CH-1015 Lausanne, Switzerland.
    Jablonski, Daniel
    Comenius Univ, Dept Zool, Ilkovicova 6, Bratislava 84215, Slovakia.
    Oliveira, Ricardo Caliari
    Katholieke Univ Leuven, Zool Inst, Lab Socioecol & Social Evolut, Naamsestr 59, B-3000 Leuven, Belgium.
    Wenseleers, Tom
    Katholieke Univ Leuven, Zool Inst, Lab Socioecol & Social Evolut, Naamsestr 59, B-3000 Leuven, Belgium.
    Shabanov, Dmytro A.
    Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkov, Ukraine.
    Auer, Markus
    Senckenberg Nat Hist Collect Dresden, Museum Zool, Konigsbrucker Landstr 159, D-01109 Dresden, Germany.
    Ernst, Raffael
    Senckenberg Nat Hist Collect Dresden, Museum Zool, Konigsbrucker Landstr 159, D-01109 Dresden, Germany.
    Koch, Claudia
    Leibniz Inst Biodiversitat Tiere, Zoolog Forschungsmuseum Alexander Koenig, Bonn, Germany.
    Ramirez-Chaves, Hector E.
    Univ Caldas, Dept Ciencias Biol, Fac Ciencias Exactas & Nat, Calle 65 26-10, Manizales, Caldas, Colombia;Univ Caldas, Museo Hist Nat, Ctr Museos, Calle 65 26-10, Manizales, Caldas, Colombia.
    Mulder, Kevin Patrick
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO InBIO, Campus Agr Vairao, P-4485661 Vairao, Portugal; Natl Zool Pk, Smithsonian Conservat Biol Inst, Ctr Conservat Genom, 3001 Connecticut Ave NW, Washington, DC 20008 USA; Natl Museum Nat Hist, Smithsonian Inst, Dept Vertebrate Zool, 10th St & Constitution Ave NW, Washington, DC 20560 USA.
    Simonov, Evgeniy
    Russian Acad Sci, Res Grp Physiol & Genet Hydrobionts, Siberian Branch, Inst Systemat & Ecol Anim, Novosibirsk 630091, Russia; Russian Acad Sci, Siberian Branch, Krasnoyarsk Sci Ctr, Fed Res Ctr,Lab Genom Res & Biotechnol, Krasnoyarsk 660036, Russia.
    Tiutenko, Arthur
    Univ Erlangen Nurnberg, Schlosspl 6, D-91054 Erlangen, Germany.
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wennekes, Paul L.
    Univ Reading, Sch Biol Sci, Plant Syst & Evolut, Philip Lyle Bldg 208, Reading RG6 6LA, Berks, England.
    Zinenko, Oleksandr I.
    Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkov, Ukraine; Kharkov Natl Univ, Museum Nat, Trinkler St 8, UA-61058 Kharkov, Ukraine.
    Korshunov, Oleksiy V.
    Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkov, Ukraine.
    Al-Johany, Awadh M.
    King Saud Univ, Dept Zool, Riyadh 11451, Saudi Arabia.
    Peregontsev, Evgeniy A.
    Zoocomplex MChJ, Gagarin Vil 14, Tashkent 100149, Uzbekistan.
    Masroor, Rafaqat
    Pakistan Museum Nat Hist, Garden Ave, Islamabad 44000, Pakistan.
    Betto-Colliard, Caroline
    Univ Lausanne, Dept Ecol & Evolut, Biophore Bldg, CH-1015 Lausanne, Switzerland.
    Denoel, Mathieu
    Univ Liege, Freshwater & OCean Sci Unit Res FOCUS, Behav Biol Grp, Lab Fish & Amphibian Ethol, Liege, Belgium.
    Borkin, Leo J.
    Russian Acad Sci, Zool Inst, Dept Herpetol, St Petersburg 199034, Russia.
    Skorinov, Dmitriy V.
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia.
    Pasynkova, Roza A.
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia.
    Mazanaeva, Lyudmila F.
    Dagestan State Univ, Makhachkala, Russia.
    Rosanov, Juriy M.
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia.
    Dubey, Sylvain
    Hintermann & Weber, Ave Alpes 25, CH-1820 Montreux, Switzerland; Univ Lausanne, Dept Ecol & Evolut, Biophore Bldg, CH-1015 Lausanne, Switzerland; Agrosustain SA, Route Duillier 50, CH-1260 Nyon, Switzerland.
    Litvinchuk, Spartak
    Russian Acad Sci, Inst Cytol, St Petersburg, Russia; Dagestan State Univ, Makhachkala, Russia.
    Fifteen shades of green: The evolution of Bufotes toads revisited2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 141, article id 106615Article in journal (Refereed)
    Abstract [en]

    The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopoly-ploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (< 6My), above which species barely admix and eventually evolve different mating calls (6-10My), or can successfully cross-breed through allopolyploidization (> 15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians.

  • 5.
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Genome evolution and adaptation of a successful allopolyploid, Capsella bursa-pastoris2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The term allopolyploid refers to an organism that originated through hybridization and increased its ploidy level by retaining the unreduced genomes of its parents. Both hybridization and polyploidy usually have negative consequences for the organism. However, there are species that not only survive these modifications but even thrive and can outcompete their diploid relatives. There are many intuitive explanations for the success of polyploids, but the number of empirical studies is limited.

    The shepherd's purse (Capsella bursa-pastoris) is an emerging model for studying a successful allopolyploid species. C. bursa-pastoris occurs worldwide, whereas its parental species, Capsella grandiflora and Capsella orientalis, have more limited distribution range. C. grandiflora is confined to Northern Greece and Albania, and C. orientalis is found only in the steppes of Central Asia. We described the genetic variation within C. bursa-pastoris and showed that it is not homogeneous across Eurasia but rather subdivided into three genetically distinct populations: one comprises accessions from Europe and Eastern Siberia, the second one is located in Eastern Asia and the third one groups accessions around the Middle East. Reconstruction of the colonization history suggested that this species originated in the Middle East and subsequently spread to Europe and Eastern Asia. This colonization was probably human-mediated. Interestingly, these three populations survive in different environmental conditions, and yet most gene expression differences between them could be explained by neutral processes. We also found that despite a common history within one species, the two subgenomes retained differences already present between the parental species. In particular, the genetic load was still higher on the subgenome inherited from C. orientalis than on the one inherited from C. grandiflora. The two subgenomes were also differentially influenced by introgression and selection in the three genetic clusters. Gene expression variation was highly correlated between the two subgenomes but the total level of expression showed variation in parental dominance across flower, leaf, and root tissues.

    This thesis for the first time shows that the evolutionary pathways of allopolyploids may differ not only on the species level but also between populations within one species. It also supports the theory that alloploidy provides an increased amount of genetic material that enables evolutionary flexibility.

    List of papers
    1. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)
    Open this publication in new window or tab >>Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)
    Show others...
    2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 616-629Article in journal (Refereed) Published
    Abstract [en]

    Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C.bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C.bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C.bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C.bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.

    Keywords
    Brassicaceae, time estimation, invasive species, dispersal, bottleneck, disomic inheritance, unphased SNP
    National Category
    Botany Genetics
    Identifiers
    urn:nbn:se:uu:diva-279642 (URN)10.1111/mec.13491 (DOI)000369530000013 ()26607306 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2016-03-08 Created: 2016-03-02 Last updated: 2022-01-29Bibliographically approved
    2. The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)
    Open this publication in new window or tab >>The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)
    Show others...
    2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1106-1121Article in journal (Refereed) Published
    Abstract [en]

    Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.

    Keywords
    adaptation, circadian rhythm, genetic drift, neutrality, population structure, RNA-Seq, transcriptome
    National Category
    Biochemistry and Molecular Biology Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-282478 (URN)10.1111/mec.13537 (DOI)000371433400007 ()26797895 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2016-04-05 Created: 2016-04-05 Last updated: 2022-01-29Bibliographically approved
    3. Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
    Open this publication in new window or tab >>Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
    Show others...
    2017 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size Ne, signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.

    Keywords
    allopolyploidy, genome evolution, introgression, selection, genetic load, demographic history
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-341706 (URN)10.1101/234096 (DOI)
    Available from: 2018-02-13 Created: 2018-02-13 Last updated: 2023-11-21Bibliographically approved
    4. Towards the new normal: Genomic and transcriptomic changes in the two subgenomes of a 100,000 years old tetraploid, Capsella bursa-pastoris
    Open this publication in new window or tab >>Towards the new normal: Genomic and transcriptomic changes in the two subgenomes of a 100,000 years old tetraploid, Capsella bursa-pastoris
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    2018 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression pattern still remains to be understood and put in a clear temporal perspective. Some studies have described important genomic and transcriptomic changes, whereas others detected a strong legacy from the parental species and much more subtle and concerted changes. These differences across studies could be the result of many factors such as age and demographic history of the alloploid species or extent of the divergence between the parental species. In the present study, we sequenced the transcriptomes of three tissues (root, leaf, and flower) and genomes of the tetraploid selfer C.bursa-pastoris, its two parental species C.grandiflora and C.orientalis, and its close relative C.rubella. In total 84 transcriptomes and 28 genomes were obtained. C.bursa-pastoris was created around 100,000 years ago and one would, therefore, expect the two subgenomes to be more similar in term of genetic polymorphism and their expression to have started to function together. However, at the genome level there was still a significant legacy effect on the number of deleterious genes carried by the two subgenomes of C.bursa-pastoris, with a higher accumulation of derived deleterious mutations in the C.orientalis subgenome. However, the overdispersion of the distribution of deleterious mutations was smaller than for synonymous ones, suggesting that both copies are needed and prevented to accumulate too many deleterious mutations. At the level of gene expression, one could still also detect a legacy effect but there were, however, significant differences among the three tissues with a more pronounced legacy effect of the  C.orientalis expression level in flower, a stronger C.grandiflora one in root and a more balanced situation in leaf. \hl{Flower tissues showed more evidence of trans regulation than leaf and root tissues. Finally, here was no association between expression levels and the number of deleterious mutations.

    Keywords
    allopolyploidy, gene expression, deleterious genes, parental legacy
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-341708 (URN)
    Available from: 2018-02-13 Created: 2018-02-13 Last updated: 2018-02-13
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  • 6.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Montpellier, CNRS IRD EPHE, ISEM UMR 5554, Inst Sci Evolut, Pl Eugene Bataillon, F-34075 Montpellier, France..
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, 25 Willcocks St, Toronto, ON M5S 3B2, Canada..
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1106-1121Article in journal (Refereed)
    Abstract [en]

    Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.

  • 7.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Orsucci, Marion
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes, CNRS, ECOBIO Ecosyst Biodivers Evolut UMR 6553, Rennes, France.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)2019In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 5, article id e1008131Article in journal (Refereed)
    Abstract [en]

    Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load.

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    fulltext
  • 8.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Salcedo, Adriana
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Eriksson, Mimmi C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tawari, Nilesh
    ASTAR, Genome Inst Singapore, Computat & Syst Biol Grp, Singapore, Singapore.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guerrina, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kreiner, Julia M.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Kent, Tyler V.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stinchcombe, John R.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes 1, CNRS, UMR 6553, ECOBIO,Ecosyst,Biodivers,Evolut, F-35000 Rennes, France.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)2019In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed)
    Abstract [en]

    Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cbp(Cg)) and the other one from the selfing and genetically depauperate Capsella orientalis (Cbp(Co)). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (N-e), signatures of positive and negative selection, and gene expression patterns. In all three regions, N-e of the two subgenomes decreased gradually over time and the Cbp(Co) subgenome accumulated more deleterious changes than Cbp(Cg). There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the Cbp(Cg) subgenome in Europe and the Middle East, and on the Cbp(Co) subgenome in Asia. In contrast, differences in expression were limited with the Cbp(Cg) subgenome slightly more expressed than Cbp(Co) in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions. Author summary Allopolyploid species have two or more sets of chromosomes that originate from hybridization of different species. It remains largely unknown how the two genomes evolve in the same organism and how strongly their evolutionary trajectory depends on the initial differences between the two parental species and the specific demographic history of the newly formed allopolyploid species. To address these questions, we analyzed the genomic and gene expression variation of the shepherd's purse, a recent allopolyploid species, in three regions of its natural range. After approximate to 100,000 generations of co-existence within the same species, the two subgenomes had still retained part of the initial difference between the two parental species in the number of deleterious mutations reflecting a history of mating system differences. This difference, as well as differences in patterns of positive selection and levels of gene expression, also strongly depended on the specific histories of the three regions considered. Most strikingly, and unexpectedly, the allopolyploid species showed signs of hybridization with different diploid relatives or multiple origins in different parts of its range. Regardless if it was hybridization or multiple origins, this profoundly altered the relationship between the two subgenomes in different regions. Hence, our study illustrates how both the genomic structure and ecological arena interact to determine the evolutionary trajectories of allopolyploid species.

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  • 9.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Salcedo, Adriana
    Eriksson, Mimmi C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Duan, Tianlin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tawari, Nilesh
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Guerrina, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kreiner, Julia M.
    Kent, Tyler V.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stinchcombe, John R.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wright, Stephen I.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)2017Manuscript (preprint) (Other academic)
    Abstract [en]

    Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size Ne, signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.

  • 10.
    Mezhzherin, Sergey, V
    et al.
    II Schmalhausen Inst Zool, Dept Evolutionary Genet & Fundamentals Systemat, Khmelnytskogo 15, UA-01030 Kiev, Ukraine..
    Tsyba, Anton A.
    II Schmalhausen Inst Zool, Dept Evolutionary Genet & Fundamentals Systemat, Khmelnytskogo 15, UA-01030 Kiev, Ukraine..
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. II Schmalhausen Inst Zool, Dept Evolutionary Genet & Fundamentals Systemat, Khmelnytskogo 15, UA-01030 Kiev, Ukraine.;Kharkov Natl Univ, Dept Zool & Anim Ecol, Svobody Sq 4, UA-61022 Kharkiv, Ukraine..
    Cryptic expansion of hybrid polyploid spined loaches Cobitis in the rivers of Eastern Europe2022In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 849, no 7, p. 1689-1700Article in journal (Refereed)
    Abstract [en]

    An expansion of a species range may happen unnoticed when an expanding species is similar in appearance to local species and distinguishable mainly by genetic methods. The morphological similarity of polyploid spined loaches of the hybrid complex Cobitis elongatoides-taenia-tanaitica with their diploid relatives makes their recent expansion in the rivers of Eastern Europe truly cryptic. We confirm this expansion and describe it in space and time by analyzing 20 museum collections from 1928 to 1985 and 92 recent sampling points from the Danube, Dniester, Southern Bug, Dnieper, Donets, and coastal rivers of the Sea of Azov. According to the museum collections, the numerical increase of polyploids relative to diploids occurred in the 1960-1980s that coincides with the time of intensive hydraulic construction when a series of reservoirs were created in the Middle Dnieper basin. Our sampling during 2000-2020 suggests that the trend toward the numerical increase of polyploids also continues in the twenty-first century. This expansion could have occurred under new ecological conditions, both due to the few clonal individuals that spread into the rivers of Eastern Europe as a result of postglacial recolonization, and due to invasions of polyploids from the Danube, Vistula, and Oder basins in the middle of the twentieth century. The expansion of polyploids is probably a consequence of their relatively high fitness in comparison with diploids in conditions of significant anthropogenization of river systems.

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