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Kryvokhyzha D, Salcedo A, Eriksson MC, Duan T, Tawari N, Chen J, Guerrina M, Kreiner JM, Kent TV, Lagercrantz U, Stinchcombe JR, Glemin S, Wright SI, and Lascoux M. 2019. Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid weed Capsella bursa-pastoris (Brassicaceae). PLOS Genetics, 15(2),
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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 (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. 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 CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo 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.
Kryvokhyzha D, Milesi P, Duan T, Orsucci M, Wright S, Glémin S, and Lascoux M. 2018. Towards the new normal: Transcriptomic and genomic changes in the two subgenomes of a 100,000 years old allopolyploid, Capsella bursa-pastoris. (Manuscript).
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 become more similar 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 suggests 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.
Cornille A, Salcedo A, Huang H, Kryvokhyzha D, Holm K, Ge XJ, Stinchcombe JR, Glemin S, Wright SI, and Lascoux M. 2018. Local adaptation and maladaptation during the worldwide range expansion of a self-fertilizing plant. (Manuscript).
Species having experienced rapid range expansion represent unique opportunities to evaluate the dynamics of adaptation during colonization of new environments. We investigated the consequences of range expansion on local adaptation of a successful worldwide colonizer, the shepherd’s purse Capsella bursa-pastoris. This species is an annual weed that originated recently in Eurasia and has now broadly colonized both temperate and subtropical areas. We assessed the performance, genetic diversity, and phenology of field-collected accessions belonging to three distinct genetic clusters of decreasing age (Middle East, Europe and Asia) in three common gardens in Europe, Asia and North America. To understand the genetic basis of local adaptation in this species, we also tested for correlation between SNP allele frequencies and environmental factors in Europe and Asia. Overall, we showed that patterns of local adaptation depended on population history: some older populations were weakly adapted to local conditions while those closer to the front of the colonization wave, far from the origin of the species, were maladapted whatever the common gardens. Altogether, our results have important consequences for the understanding of the evolution and adaptation of self-fertilizing plant during range expansion.
Kryvokhyzha D. 2018. Genome evolution and adaptation of a successful allopolyploid, Capsella bursa-pastoris. Ph.D. Thesis, Uppsala: Acta Universitatis Upsaliensis, 51 p.
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.
Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright S, Lagercrantz U, Lascoux M. 2016. The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology, 25(5), pp.1106–1121.
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 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 the regulation of flowering time.
Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright SI, Lascoux M. 2016 Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa-pastoris). Molecular Ecology, 25(2), pp.616–629.
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.
Kryvokhyzha D. 2014. Whole genome resequencing of Heliconius butterflies revolutionizes our view of the level of admixture between species. M.Sc. Thesis, Biology Education Centre, Uppsala University and Department of Organismic and Evolutionary Biology, Harvard University, 30 p.
The theory of “genomic islands of speciation” has been extensively debated during the last decade. This thesis not only supports this theory, but provides evidence that challenges previous beliefs on the level of admixture between species. The recently published Heliconius melpomene genome project reported apparent genomic paraphyly of H. pardalinus with regard to H. elevatus (Heliconius Genome Consortium 2012). Here, we investigate this pair of butterfly species more fully, firstly by using whole-genome resequence data, and secondly by analyzing additional geographic populations of both species, as well as outgroup taxa. Using a nuclear whole-genome phylogenetic analysis we also confirm that H. elevatus is paraphyletic. The genome-wide phylogenetic signal in H. pardalinus and H. elevatus does not indicate expected mutual monophyly of each species as it seems strongly distorted by a high level of admixture. However, several regions of the genome remain differentiated and do show the presumably original phylogenetic signal with mutual monophyly of H. pardalinus and H. elevatus. The genomic background is so homogenized that its level of differentiation (Fst ~ 0.03) virtually implies panmixia. The pattern of a high level of homogenization across the genome with several regions of differentiation was consistent with a number of other statistics such as absolute divergence Dxy, nucleotide polymorphism π, number of fixed differences and with a sliding window phylogeny. The identified genomic islands of divergence comprise genes responsible for wing-patterning and chemosensation in Heliconius and some of these genes are found to be under positive selection, suggesting possible candidates of speciation.
Shandikov G, Kryvokhyzha D, Slipko I. 2009. A first record of Caucasian dwarf Goby, Knipowitschia caucasica (Teleostei: Perciformes: Gobiidae), in the Severskiy Donets River drainage, Ukraine. Vestnik zoologii, 43(4), p.368.
The Caucasian dwarf goby Knipowitschia caucasica is a very little (commonly not exceeding 4 cm TL) Ponto-Caspian gobiid fish widely distributed in marine and brackish waters, rarely in freshwaters of coastal area in the basins of Caspian, Azov, Black, Adriatic and Aegean Seas. Recently, a female of this species has been sampled in Ukraine rather far from the mouth (about 380 km) in the lower part of the Middle Dnieper River near Zaporizhzha City. Our data show that freshwater area of K. caucasica in Ukraine extends for a great distance from the coastal area to the upper parts of big rivers. A ripe female of this species, TL 31.6 mm, SL 26.2 mm and weight 250 mg, was captured with a fine mesh net on a sandy slightly slimy bottom, at depths 0.5-1.0 m, in the Upper Siverskiy Donets River (about 1000 km from the shore of the Sea of Azov) in the vicinity of Village Haidary, Zmiev Distr., Kharkiv Region, 5.05.2009. The specimen has the following morphological characteristics: D1 VI, D2 I 8, A I 7, P 15/15 segmented rays; caudal fin symmetric, rounded, with 12 branched rays; head and back in front of D2 naked; scales on flanks of the body form 34 transversal rows and 8 longitudinal rows between origins of D2 and A. Anterior oculoscapular canal begins slightly behind of the anterior eye margin. Posterior oculoscapular canal is short. K. caucasica is considered to be an aboriginal species in the Upper Siverskiy Donets River, because there is no evidence of shipping traffic or any introduction. Since now, according the last faunistic reviews, the contemporary fish fauna of the Siverskiy Donets river system accounts about 60 species. Together with K. caucasica, 7 species and forms of fishes were captured: 2 invasive species of the Dnieper River fish fauna: Pungitius platygaster and Syngnathus abaster; and 5 native fishes: Rhodeus amarus, Cobitis melanoleuca and a polyploid form of spined loach – Cobitis “tanaitica”, Neozobius fluviatilis and Proterorhinus semilunaris.
Shandikov G, Kryvokhyzha D. 2008. To the question about species composition and some peculiarities of biology of spined loaches of the genus Cobitis (Teleostei: Cypriniformes: Cobitidae) in the Upper and Middle Severskiy Donets River, Ukraine. The Journal of V.N. Karazin Kharkiv National University. Series: Biology, 8(814), pp.91-118. [in Russian]
Six main morphotype-forms were determined for the spined loaches (genus Cobitis) in the Upper and Middle Severskiy Donets River, Kharkiv Region. Three of them turned out to be bisexual diploid species while the other 3 – asexual forms-biotypes with polyploid females exclusively. They were described due to both characteristic features of external morphology and ploidy additional data obtained by erythrocytes cytometry analysis. Two species – the Siberian spined loach, Cobitis melanoleuca, and Don spined loach, Cobitis cf. tanaitica, were discovered in the main riverbed of the Upper Severskiy Donets River, Zmiev District. The 3rd species of unclear taxonomic position that belongs to the species complex Cobitis taenia s. l. was found in the beginning of the Middle Severskiy Donets River and the area adjacent to the mouth of the Oskol River (both in Izyum District). Two triploid biotypes, named as C. ”tanaitica” and C. ”taenia”, from the Upper Severskiy Donets River differed significantly from all the other forms studied by their large size and coloration traits. The tetraploid female Cobitis “taenia s. l.” from the Lower Oskol River was the most similar to the diploid specimens of Cobitis taenia s. l. The detailed comparative morphological description of the discovered spined loaches forms and some traits of its biology (behavior, age, spawning and fecundity) are given. The peculiarities of reproduction of polyploid females with males of bisexual species are discussed; obviously they form diploid-polyploid complexes in the main riverbed of the Severskiy Donets River and in the Lower Oskol River. The problem of the reproduction strategy of unisexual group of triploid females C. ”tanaitica” in the Petchenezhskoe Reservoir, where during 2 years of studies no males have been discovered, needs additional investigation.