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Lascoux, Martin
Alternative names
Publications (10 of 84) Show all publications
Tahir, D., Glemin, S., Lascoux, M. & Kaj, I. (2019). Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree. Journal of Theoretical Biology, 461, 189-203
Open this publication in new window or tab >>Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree
2019 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 461, p. 189-203Article in journal (Refereed) Published
Abstract [en]

Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. In this work, we present a probabilistic modeling framework for binary trait, random species trees, in which the number of species and their traits are represented by an asymmetric, two-type, continuous time Markov branching process. The model involves a number of different parameters describing both character and molecular evolution on the so-called 'reduced' tree, consisting of only extant species at the time of observation. We expand our model by considering the impact of binary traits on dN/dS, the normalized ratio of nonsynonymous to synonymous substitutions. We also develop mechanisms which enable us to understand the substitution rates on a phylogenetic tree with regards to the observed traits. The properties obtained from the model are illustrated with a phylogeny of outcrossing and selfing plant species, which allows us to investigate not only the branching tree rates, but also the molecular rates and the intensity of selection.

Keywords
Branching processes, Irreversible transitions, Binary traits, Phylogenetic trees, Mutation rates
National Category
Evolutionary Biology Probability Theory and Statistics
Identifiers
urn:nbn:se:uu:diva-372749 (URN)10.1016/j.jtbi.2018.10.032 (DOI)000452245900018 ()30340056 (PubMedID)
Available from: 2019-01-15 Created: 2019-01-15 Last updated: 2019-04-25
Kryvokhyzha, D., Salcedo, A., Eriksson, M. C., Duan, T., Tawari, N., Chen, J., . . . Lascoux, M. (2019). Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae). PLoS Genetics, 15(2), Article ID e1007949.
Open this publication in new window or tab >>Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
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2019 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed) Published
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.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-379946 (URN)10.1371/journal.pgen.1007949 (DOI)000459970100033 ()30768594 (PubMedID)
Funder
Swedish Research Council, 2012-04999Swedish Research Council, 2015-03797
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-03-25Bibliographically approved
Kryvokhyzha, D., Milesi, P., Duan, T., Orsucci, M., Wright, S. I., Glemin, S. & Lascoux, M. (2019). Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris). PLoS Genetics, 15(5), Article ID e1008131.
Open this publication in new window or tab >>Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)
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2019 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 5, article id e1008131Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2019
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-387963 (URN)10.1371/journal.pgen.1008131 (DOI)000470208000025 ()31083657 (PubMedID)
Funder
Swedish Research Council, 2015-03797
Available from: 2019-06-27 Created: 2019-06-27 Last updated: 2019-06-27Bibliographically approved
Ma, T., Wang, K., Hu, Q., Xi, Z., Wan, D., Wang, Q., . . . Liu, J. (2018). Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex. Proceedings of the National Academy of Sciences of the United States of America, 115(2), E236-E243
Open this publication in new window or tab >>Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 2, p. E236-E243Article in journal (Refereed) Published
Abstract [en]

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
speciation, paraphyletic, genome divergence, natural selection, gene flow
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-341577 (URN)10.1073/pnas.1713288114 (DOI)000419686400019 ()29279400 (PubMedID)
Available from: 2018-02-14 Created: 2018-02-14 Last updated: 2018-02-14Bibliographically approved
Mendoza, S. P., Lascoux, M. & Glemin, S. (2018). Competitive ability of Capsella species with different mating systems and ploidy levels. Annals of Botany, 121(6), 1257-1264
Open this publication in new window or tab >>Competitive ability of Capsella species with different mating systems and ploidy levels
2018 (English)In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 121, no 6, p. 1257-1264Article in journal (Refereed) Published
Abstract [en]

Background and Aims

Capsella is a model genus for studying the transition from outcrossing to selfing, with or without change in ploidy levels. The genomic consequences and changes in reproductive traits (selfing syndrome) associated with these shifts have been studied in depth. However, potential ecological divergence among species of the genus has not been determined. Among ecological traits, competitive ability could be relevant for selfing evolution, as selfing has been shown to be statistically associated with reduced competitiveness in a recent meta-analysis.

Methods

We assessed the effect of competition on three Capsella species differing in their mating system and ploidy level. We used an experimental design where fitness related traits were measured in focal individuals with and without competitors.

Key Results

The diploid selfer (C. rubella) was most sensitive to competition, whereas the tetraploid selfer (C. bursa-pastoris) performed the best, with the diploid outcrosser (C. grandiflora) being intermediate.

Conclusions

These results add to the detailed characterization of Capsella species and highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species.

Keywords
Capsella, competition, mating system, outcrossing, ploidy, selfing
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-356872 (URN)10.1093/aob/mcy014 (DOI)000432059300017 ()29471370 (PubMedID)
Funder
Swedish Research Council
Available from: 2018-08-09 Created: 2018-08-09 Last updated: 2018-08-09Bibliographically approved
Svedberg, J., Hosseini, S., Chen, J., Vogan, A. A., Mozgova, I., Hennig, L., . . . Johannesson, H. (2018). Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements. Nature Communications, 9, Article ID 4242.
Open this publication in new window or tab >>Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements
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2018 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4242Article in journal (Refereed) Published
Abstract [en]

Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-368443 (URN)10.1038/s41467-018-06562-x (DOI)000447123000018 ()30315196 (PubMedID)
Funder
Swedish Research CouncilEU, Horizon 2020, 648143Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-12-07 Created: 2018-12-07 Last updated: 2018-12-07Bibliographically approved
Wang, X.-J., Hu, Q.-J., Guo, X.-Y., Wang, K., Ru, D.-F., German, D. A., . . . Liu, J.-q. (2018). Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum. Molecular Ecology, 27(14), 2943-2955
Open this publication in new window or tab >>Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum
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2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 14, p. 2943-2955Article in journal (Refereed) Published
Abstract [en]

The halophyte model plant Eutrema salsugineum (Brassicaceae) disjunctly occurs in temperate to subarctic Asia and North America. This vast, yet extremely discontinuous distribution constitutes an ideal system to examine long-distance dispersal and the ensuing accumulation of deleterious mutations as expected in expanding populations of selfing plants. In this study, we resequenced individuals from 23 populations across the range of E.salsugineum. Our population genomic data indicate that E.salsugineum migrated "out of the Altai region" at least three times to colonize northern China, northeast Russia and western China. It then expanded its distribution into North America independently from northeast Russia and northern China, respectively. The species colonized northern China around 33.7 thousand years ago (kya) and underwent a considerable expansion in range size approximately 7-8 kya. The western China lineage is likely a hybrid derivative of the northern China and Altai lineages, originating approximately 25-30 kya. Deleterious alleles accumulated in a stepwise manner from (a) Altai to northern China and North America and (b) Altai to northeast Russia and North America. In summary, E.salsugineum dispersed from Asia to North America and deleterious mutations accumulated in a stepwise manner during the expansion of the species' distribution.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
deleterious variant, Eutrema salsugineum, expansion, hybrid lineage, long-distance dispersal, migration
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-361100 (URN)10.1111/mec.14738 (DOI)000438352500004 ()29862594 (PubMedID)
Available from: 2018-09-21 Created: 2018-09-21 Last updated: 2018-09-21Bibliographically approved
Semerikova, S. A., Khrunyk, Y. Y., Lascoux, M. & Semerikov, V. L. (2018). From America to Eurasia: a multigenomes history of the genus Abies. Molecular Phylogenetics and Evolution, 125, 14-28
Open this publication in new window or tab >>From America to Eurasia: a multigenomes history of the genus Abies
2018 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 125, p. 14-28Article in journal (Refereed) Published
Abstract [en]

The origin of conifer genera, the main components of mountain temperate and boreal forests, was deemed to arise in the Mesozoic, although paleontological records and molecular data point to a recent diversification, presumably related to Neogene cooling. The geographical area(s) where the modern lines of conifers emerged remains uncertain, as is the sequence of events leading to their present distribution. To gain further insights into the biogeography of firs (Abies), we conducted phylogenetic analyses of chloroplast, mitochondrial and nuclear markers. The species tree, generated from ten single-copy nuclear genes, yielded probably the best phylogenetic hypothesis available for Abies. The tree obtained from five regions of chloroplast DNA largely corresponded to the nuclear species tree. Ancestral area reconstructions based on fossil calibrated chloroplast DNA and nuclear DNA trees pointed to repeated intercontinental migrations. The mitochondrial DNA haplotype tree, however, disagreed with nuclear and chloroplast DNA trees. It consisted of two clusters: one included mainly American haplotypes, while the other was composed of only Eurasian haplotypes. Presumably, this conflict is due to intercontinental migrations and introgressive hybridization, accompanied by the capture of the mitotypes from aboriginal species by the invading firs. Given that several species inhabiting Northeastern Asia carry American mitotypes and mutations typical for the American cluster, whereas no Asian mitotypes were detected within the American species, we hypothesize that Abies migrated from America to Eurasia, but not in the opposite direction. The direction and age of intercontinental migrations in firs are congruent with other conifers, such as spruces and pines of subsection Strobus, suggesting that these events had the same cause.

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018
Keywords
Abies, Multilocus phylogeny, Species tree, Molecular dating, Mitochondrial DNA capture, Introgressive hybridization, Intercontinental migrations, Bering Land Bridge
National Category
Biological Systematics Genetics
Identifiers
urn:nbn:se:uu:diva-356439 (URN)10.1016/j.ympev.2018.03.009 (DOI)000432583900002 ()29551520 (PubMedID)
Available from: 2018-07-31 Created: 2018-07-31 Last updated: 2018-07-31Bibliographically approved
Huang, H.-R., Liu, J.-J., Xu, Y., Lascoux, M., Ge, X.-J. & Wright, S. I. (2018). Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae). New Phytologist, 220(2), 624-635
Open this publication in new window or tab >>Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae)
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 220, no 2, p. 624-635Article in journal (Refereed) Published
Abstract [en]

Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa-pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low-altitude regions, a Western group from high-altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome-wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral drift may contribute to the population differentiation in the expression of the homeologues, and drive eventual gene loss over longer periods of time.

Keywords
duplication, homeologue-specific expression, neutral drift, polyploid, population structure
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-366946 (URN)10.1111/nph.15299 (DOI)000445194100025 ()30028022 (PubMedID)
Available from: 2018-11-28 Created: 2018-11-28 Last updated: 2018-11-28Bibliographically approved
Plomion, C., Aury, J.-M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., . . . Salse, J. (2018). Oak genome reveals facets of long lifespan. NATURE PLANTS, 4(7), 440-452
Open this publication in new window or tab >>Oak genome reveals facets of long lifespan
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2018 (English)In: NATURE PLANTS, ISSN 2055-026X, Vol. 4, no 7, p. 440-452Article in journal (Refereed) Published
Abstract [en]

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-364056 (URN)10.1038/s41477-018-0172-3 (DOI)000443221200016 ()29915331 (PubMedID)
Funder
EU, FP7, Seventh Framework ProgrammeEU, European Research CouncilSwedish Foundation for Strategic Research
Available from: 2018-12-07 Created: 2018-12-07 Last updated: 2018-12-07Bibliographically approved
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