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Lascoux, Martin
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Publications (10 of 75) Show all publications
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
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
Hantemirova, E. V., Heinze, B., Knyazeva, S. G., Musaev, A. M., Lascoux, M. & Semerikov, V. L. (2017). A new Eurasian phylogeographical paradigm?: Limited contribution of southern populations to the recolonization of high latitude populations in Juniperus communis L.(Cupressaceae). Journal of Biogeography, 44(2), 271-282
Open this publication in new window or tab >>A new Eurasian phylogeographical paradigm?: Limited contribution of southern populations to the recolonization of high latitude populations in Juniperus communis L.(Cupressaceae)
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2017 (English)In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 44, no 2, p. 271-282Article in journal (Refereed) Published
Abstract [en]

AimThe aims of this population genetics study of the common juniper across Eurasia were to (1) assess the contribution of southern mountain ranges to the post-glacial recolonization of high latitudes and (2) test whether recent expansion or high gene flow could explain the low genetic differentiation in Northern Eurasia. LocationNorthern Eurasia and mountain regions of Central Europe and Asia. MethodsSix hundred and twenty-two individuals were sampled in 42 populations. Two chloroplast DNA (cpDNA) fragments were investigated (trnT-trnL and 16S-trnA). Analyses of the distribution of haplotypes across the continent included a suite of phylogeographical and phylogenetic tests. Putative geographical distribution in the past was reconstructed using environmental niche modelling. ResultsEighty-four haplotypes clustered into four main clades (GL1-GL4). The largest clade, GL3, corresponds to populations from the Alps, northern Europe, Western Caucasus and Siberia. These populations were moderately differentiated (28%) compared to the total range (76%) and Fu's F-s statistic was negative, indicating a population expansion. Some haplotypes within GL3 form subclades with a restricted geographical distribution, suggesting a local origin of the mutation and limited dispersal. In line with these findings, modelling of ecological niches found no significant reduction in the expected range during the LGM. Remarkably, populations from the eastern part of North Caucasus, the Himalayas, Tien Shan and south Siberia were distinctly different from populations in the rest of the range. Main conclusionsAs in Siberian larch species, the pattern of genetic diversity at cpDNA across the natural range of J. communis suggests that colonization of northern Europe and Siberia started from a limited area and predated the last glaciation. It is likely that juniper survived the subsequent glacial epoch at high latitudes in cryptic refugia serving as secondary centres of recolonization. Southern mountain refugia contribution to the recolonization of high latitudes was, at best, limited.

Keywords
chloroplast DNA, common juniper, Cupressaceae, Eurasia, glacial cycles, phylogeography
National Category
Ecology Physical Geography
Identifiers
urn:nbn:se:uu:diva-317959 (URN)10.1111/jbi.12867 (DOI)000393570500004 ()
Available from: 2017-03-31 Created: 2017-03-31 Last updated: 2018-01-13Bibliographically approved
Bodare, S., Ravikanth, G., Ismail, S. A., Patel, M. K., Spanu, I., Vasudeva, R., . . . Tsuda, Y. (2017). Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India. Conservation Genetics, 18(1), 1-15
Open this publication in new window or tab >>Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India
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2017 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 18, no 1, p. 1-15Article in journal (Refereed) Published
Abstract [en]

Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, which is the world's most densely populated biodiversity hotspot. In this study, we used variation at ten nuclear simple sequence repeat loci to investigate genetic diversity and fine scale spatial genetic structure (FSGS) in seedlings and adults of D. malabaricum from four forest patches in the northern part of the Western Ghats. When genetic variation was compared between seedlings and adults across locations, significant differences were detected in allelic richness, observed heterozygosity, fixation index (F (IS)), and relatedness (P < 0.05). Reduced genetic diversity and increased relatedness at the seedling stage might be due to fragmentation and disturbance. There was no FSGS at the adult stage and FSGS was limited to shorter distance classes at the seedling stage. However, there was clear spatial genetic structure at the landscape level (< 50 km), regardless of age class, due to limited gene flow between forest patches. A comparison of the distributions of size classes in the four locations with published data from a more southern area, showed that large trees (diameter at breast height, DBH, > 130 cm) are present in the southern sacred forests but not in the northern forest reserves. This pattern is likely due to stronger harvesting pressure in the north compared to the south, because in the north there are no cultural taboos regulating the extraction of natural resources. The implications for forest conservation in this biodiversity hotspot are discussed.

Place, publisher, year, edition, pages
SPRINGER, 2017
Keywords
Dysoxylum malabaricum, Fragmentation, Disturbance, Land use, Spatial genetic structure, Western Ghats
National Category
Ecology Genetics
Identifiers
urn:nbn:se:uu:diva-319106 (URN)10.1007/s10592-016-0877-7 (DOI)000394253300001 ()
Funder
Sida - Swedish International Development Cooperation Agency
Available from: 2017-04-03 Created: 2017-04-03 Last updated: 2017-11-29Bibliographically approved
Chen, J., Glemin, S. & Lascoux, M. (2017). Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species. Molecular biology and evolution, 34(6), 1417-1428
Open this publication in new window or tab >>Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species
2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1417-1428Article in journal (Refereed) Published
Abstract [en]

A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, pi(S), and nonsynonymous sites, pi(N), and a measure of the efficacy of selection, the ratio pi(N)/pi(S), in 34 animal and 28 plant species using full genome data. We then evaluated the relationship of nucleotide diversity and selection efficacy with effective population size, the distribution of fitness effect and life history traits. In animals, our data confirm that longevity and propagule size are the variables that best explain the variation in pi(S) among species. In plants longevity also plays a major role as well as mating system. As predicted by the nearly neutral theory of molecular evolution, the log of pi(N)/pi(S) decreased linearly with the log of pi(S) but the slope was weaker in plants than in animals. This appears to be due to a higher mutation rate in long lived plants, and the difference disappears when pi(S) is rescaled by the mutation rate. Differences in the distribution of fitness effect of new mutations also contributed to variation in pi(N)/pi(S) among species.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
effective population size, distribution of fitness effects, purifying selection, life history traits, nearly neutral theory
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-326224 (URN)10.1093/molbev/msx088 (DOI)000402061700010 ()28333215 (PubMedID)
Funder
Swedish Research Council FormasSwedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2017-07-04 Created: 2017-07-04 Last updated: 2017-07-04Bibliographically approved
Salojarvi, J., Smolander, O.-P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., . . . Kangasjarvi, J. (2017). Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics, 49(6), 904-+
Open this publication in new window or tab >>Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
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2017 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 49, no 6, p. 904-+Article in journal (Refereed) Published
Abstract [en]

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2017
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-327136 (URN)10.1038/ng.3862 (DOI)000402062300015 ()28481341 (PubMedID)
Available from: 2017-08-30 Created: 2017-08-30 Last updated: 2017-08-30Bibliographically approved
Tsuda, Y., Semerikov, V., Sebastiani, F., Vendramin, G. G. & Lascoux, M. (2017). Multispecies genetic structure and hybridization in the Betula genus across Eurasia. Molecular Ecology, 26(2), 589-605
Open this publication in new window or tab >>Multispecies genetic structure and hybridization in the Betula genus across Eurasia
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2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 2, p. 589-605Article in journal (Refereed) Published
Abstract [en]

Boreal and cool temperate forests are the major land cover of northern Eurasia, and information about continental-scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetic studies of forest tree species have been conducted in Europe or Eastern Asia, continental-scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of two tetraploid and four diploid species collected from Iceland to Japan. All individuals were genotyped at seven to 18 nuclear simple sequence repeats (nSSRs). Pairwise <mml:msubsup>FST</mml:msubsup> among the six species ranged from 0.285 to 0.903, and genetic differentiation among them was clear. structure analysis suggested that Betula pubescens is an allotetraploid and one of the parental species was Betula pendula. In both species pairs of B.pendula and B.plathyphylla, and B.pubescens and B.ermanii, genetic diversity was highest in central Siberia. A hybrid zone was detected around Lake Baikal for eastern and western species pairs regardless of ploidy level. Approximate Bayesian computation suggested that the divergence of B.pendula and B.platyphylla occurred around the beginning of the last ice age (36300years BP, 95% CI: 15330-92700) and hybridization between them was inferred to have occurred after the last glacial maximum (1614years BP, 95% CI: 561-4710), with B.pendula providing a higher contribution to hybrids.

Place, publisher, year, edition, pages
WILEY-BLACKWELL, 2017
Keywords
allotetraploid, Betula, demographic history, Eurasia, genetic structure, species delimitation
National Category
Biochemistry and Molecular Biology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-318616 (URN)10.1111/mec.13885 (DOI)000393944000014 ()27763698 (PubMedID)
Funder
Swedish Research Council
Available from: 2017-03-27 Created: 2017-03-27 Last updated: 2017-11-29Bibliographically approved
Bartoszek, K., Glemin, S., Kaj, I. & Lascoux, M. (2017). Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations. Journal of Theoretical Biology, 429, 35-45
Open this publication in new window or tab >>Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations
2017 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 429, p. 35-45Article in journal (Refereed) Published
Abstract [en]

The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.

Keywords
Migration, Ornstein-Uhlenbeck process, Phylogenetic comparative methods, Species interactions, Trait evolution
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-333740 (URN)10.1016/j.jtbi.2017.06.011 (DOI)000407873100003 ()28619246 (PubMedID)
Available from: 2017-11-16 Created: 2017-11-16 Last updated: 2018-05-31Bibliographically approved
Zhao, L., Lascoux, M. & Waxman, D. (2016). An informational transition in conditioned Markov chains: Applied to genetics and evolution. Journal of Theoretical Biology, 402, 158-170
Open this publication in new window or tab >>An informational transition in conditioned Markov chains: Applied to genetics and evolution
2016 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 402, p. 158-170Article in journal (Refereed) Published
Abstract [en]

In this work we assume that we have some knowledge about the state of a population at two known times, when the dynamics is governed by a Markov chain such as a Wright-Fisher model. Such knowledge could be obtained, for example, from observations made on ancient and contemporary DNA, or during laboratory experiments involving long term evolution. A natural assumption is that the behaviour of the population, between observations, is related to (or constrained by) what was actually observed. The present work shows that this assumption has limited validity. When the time interval between observations is larger than a characteristic value, which is a property of the population under consideration, there is a range of intermediate times where the behaviour of the population has reduced or no dependence on what was observed and an equilibrium-like distribution applies. Thus, for example, if the frequency of an allele is observed at two different times, then for a large enough time interval between observations, the population has reduced or no dependence on the two observed frequencies for a range of intermediate times. Given observations of a population at two times, we provide a general theoretical analysis of the behaviour of the population at all intermediate times, and determine an expression for the characteristic time interval, beyond which the observations do not constrain the population's behaviour over a range of intermediate times. The findings of this work relate to what can be meaningfully inferred about a population at intermediate times, given knowledge of terminal states.

Keywords
Random genetic drift, Population genetics theory, Frequency trajectories, Conditional distribution, Ancient DNA
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-299544 (URN)10.1016/j.jtbi.2016.04.021 (DOI)000377623700016 ()27105672 (PubMedID)
Available from: 2016-07-25 Created: 2016-07-22 Last updated: 2017-11-28Bibliographically approved
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