Pascal Milesi

Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Zhou, Qiujie; Karunarathne, Piyal; Andersson-Li, Lili; Chen, Chen et al.

Part of Molecular Ecology, 2024

• DOI for Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles
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Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests

Karunarathne, Piyal; Zhou, Qiujie; Lascoux, Martin; Milesi, Pascal

Part of Global Change Biology, 2024

• DOI for Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests
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Resilience of genetic diversity in forest trees over the Quaternary

Milesi, Pascal; Kastally, Chedly; Dauphin, Benjamin; Cervantes, Sandra et al.

Part of Nature Communications, 2024

• DOI for Resilience of genetic diversity in forest trees over the Quaternary
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A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection

Karunarathne, Piyal; Zhou, Qiujie; Schliep, Klaus; Milesi, Pascal

Part of Molecular Ecology Resources, p. 1772-1789, 2023

• DOI for A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection
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BioRssay: an R package for analyses of bioassays and probit graphs

Karunarathne, Piyal; Pocquet, Nicolas; Labbe, Pierrick; Milesi, Pascal

Part of Parasites & Vectors, 2022

• DOI for BioRssay: an R package for analyses of bioassays and probit graphs
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Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes

Milesi, Pascal; Claret, Jean-Loup; Unal, Sandra; Weill, Mylène et al.

Part of Parasites & Vectors, 2022

• DOI for Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes
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Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees

Milesi, Pascal; Berlin, Mats; Chen, Jun; Orsucci, Marion et al.

Part of Evolutionary Applications, p. 1946-1959, 2019

• DOI for Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees
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The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation

Milesi, Pascal; Assogba, Benoit S.; Atyame, Celestine M.; Pocquet, Nicolas et al.

Part of Molecular Ecology, p. 493-507, 2018

• DOI for The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation
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When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species

Herrera-Egoavil, Maria del Pilar; Leal, Luis; Zhou, Qiujie; Milesi, Pascal et al.

Part of Molecular Ecology, 2026

• DOI for When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species
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Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management

Söderquist, Linus; Joffard, Nina; Scofield, Douglas; Milesi, Pascal et al.

Part of Ecography, 2025

• DOI for Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management
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When numbers matter: Rethinking the role of gene duplication on short evolutionary timescales

Lindstedt, Freja; Zhou, Qiujie; Milesi, Pascal

Part of American Journal of Botany, 2025

• DOI for When numbers matter: Rethinking the role of gene duplication on short evolutionary timescales
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The genetic architecture of repeated local adaptation to climate in distantly related plants

Whiting, James R.; Booker, Tom R.; Rougeux, Clement; Lind, Brandon M. et al.

Part of Nature Ecology & Evolution, 2024

• DOI for The genetic architecture of repeated local adaptation to climate in distantly related plants
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Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes

Claret, Jean-Loup; Di-Liegro, Marion; Namias, Alice; Assogba, Benoit et al.

Part of Heredity, p. 179-191, 2024

• DOI for Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes
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When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species

Herrera-Egoavil, Maria del Pilar; Leal, Luis; Zhou, Qiujie; Milesi, Pascal et al.

Part of Molecular Ecology, 2026

• DOI for When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species
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Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management

Söderquist, Linus; Joffard, Nina; Scofield, Douglas; Milesi, Pascal et al.

Part of Ecography, 2025

• DOI for Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management
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When numbers matter: Rethinking the role of gene duplication on short evolutionary timescales

Lindstedt, Freja; Zhou, Qiujie; Milesi, Pascal

Part of American Journal of Botany, 2025

• DOI for When numbers matter: Rethinking the role of gene duplication on short evolutionary timescales
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The genetic architecture of repeated local adaptation to climate in distantly related plants

Whiting, James R.; Booker, Tom R.; Rougeux, Clement; Lind, Brandon M. et al.

Part of Nature Ecology & Evolution, 2024

• DOI for The genetic architecture of repeated local adaptation to climate in distantly related plants
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Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes

Claret, Jean-Loup; Di-Liegro, Marion; Namias, Alice; Assogba, Benoit et al.

Part of Heredity, p. 179-191, 2024

• DOI for Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes
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Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Zhou, Qiujie; Karunarathne, Piyal; Andersson-Li, Lili; Chen, Chen et al.

Part of Molecular Ecology, 2024

• DOI for Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles
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Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests

Karunarathne, Piyal; Zhou, Qiujie; Lascoux, Martin; Milesi, Pascal

Part of Global Change Biology, 2024

• DOI for Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests
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Resilience of genetic diversity in forest trees over the Quaternary

Milesi, Pascal; Kastally, Chedly; Dauphin, Benjamin; Cervantes, Sandra et al.

Part of Nature Communications, 2024

• DOI for Resilience of genetic diversity in forest trees over the Quaternary
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Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Leal, J Luis; Milesi, Pascal; Hodková, Eva; Zhou, Qiujie et al.

Part of Systematic Biology, p. 392-418, 2024

• DOI for Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles
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A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection

Karunarathne, Piyal; Zhou, Qiujie; Schliep, Klaus; Milesi, Pascal

Part of Molecular Ecology Resources, p. 1772-1789, 2023

• DOI for A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection
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Between but Not Within-Species Variation in the Distribution of Fitness Effects

James, Jennifer; Kastally, Chedly; Budde, Katharina B.; Gonzalez-Martinez, Santiago C. et al.

Part of Molecular biology and evolution, 2023

• DOI for Between but Not Within-Species Variation in the Distribution of Fitness Effects
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Diversity and enrichment of breeding material for resilience in European forests

Olsson, Sanna; Dauphin, Benjamin; Jorge, Veronique; Grivet, Delphine et al.

Part of Forest Ecology and Management, 2023

• DOI for Diversity and enrichment of breeding material for resilience in European forests
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Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences

Leal, Luis J.; Milesi, Pascal; Salojarvi, Jarkko; Lascoux, Martin

Part of Systematic Biology, p. 372-390, 2023

• DOI for Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences
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Divergent selection predating the Last Glacial Maximum mainly acted on macro‐phenotypes in Norway spruce

Tiret, Mathieu; Olsson, Lars; Grahn, Thomas; Karlsson, Bo et al.

Part of Evolutionary Applications, p. 163-172, 2023

• DOI for Divergent selection predating the Last Glacial Maximum mainly acted on macro‐phenotypes in Norway spruce
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Genomics and adaptation in forest ecosystems

Neophytou, Charalambos; Heer, Katrin; Milesi, Pascal; Peter, Martina et al.

Part of Tree Genetics & Genomes, 2022

• DOI for Genomics and adaptation in forest ecosystems
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The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe

Cornille, Amandine; Tiret, Mathieu; Salcedo, Adriana; Huang, Huirun R. et al.

Part of AoB Plants, 2022

• DOI for The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe
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BioRssay: an R package for analyses of bioassays and probit graphs

Karunarathne, Piyal; Pocquet, Nicolas; Labbe, Pierrick; Milesi, Pascal

Part of Parasites & Vectors, 2022

• DOI for BioRssay: an R package for analyses of bioassays and probit graphs
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Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes

Milesi, Pascal; Claret, Jean-Loup; Unal, Sandra; Weill, Mylène et al.

Part of Parasites & Vectors, 2022

• DOI for Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes
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Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

Li, Lili; Milesi, Pascal; Tiret, Mathieu; Chen, Jun et al.

Part of New Phytologist, p. 1976-1987, 2022

• DOI for Teasing apart the joint effect of demography and natural selection in the birth of a contact zone
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Norway spruce postglacial recolonization of Fennoscandia

Nota, Kevin; Klaminder, Jonatan; Milesi, Pascal; Bindler, Richard et al.

Part of Nature Communications, 2022

• DOI for Norway spruce postglacial recolonization of Fennoscandia
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How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus

Zhang, Zebin; Kryvokhyzha, Dmytro; Orsucci, Marion; Glemin, Sylvain et al.

Part of New Phytologist, p. 2344-2357, 2022

• DOI for How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus
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Killing two enemies with one stone?: Genomics of resistance to two sympatric pathogens in Norway spruce

Capador‐Barreto, Hernán D.; Bernhardsson, Carolina; Milesi, Pascal; Vos, Ingrid et al.

Part of Molecular Ecology, p. 4433-4447, 2021

• DOI for Killing two enemies with one stone?: Genomics of resistance to two sympatric pathogens in Norway spruce
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The GenTree Leaf Collection: Inter- and intraspecific leaf variation in seven forest tree species in Europe

Benavides, Raquel; Carvalho, Barbara; Bastias, Cristina C.; Lopez-Quiroga, David et al.

Part of Global Ecology and Biogeography, p. 590-597, 2021

• DOI for The GenTree Leaf Collection: Inter- and intraspecific leaf variation in seven forest tree species in Europe
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis

Chen, Zhi-Qiang; Zan, Yanjun; Milesi, Pascal; Zhou, Linghua et al.

Part of Genome Biology, 2021

• DOI for Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
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The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Opgenoorth, Lars; Benjamin, Dauphin; Benavides, Raquel; Heer, Katrin et al.

Part of GigaScience, 2021

• DOI for The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species
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Shift in ecological strategy helps marginal populations of shepherd's purse (Capsella bursa-pastoris) to overcome a high genetic load

Orsucci, Marion; Milesi, Pascal; Hansen, Johanna; Girodolle, Johanna et al.

Part of Proceedings of the Royal Society of London. Biological Sciences, 2020

• DOI for Shift in ecological strategy helps marginal populations of shepherd's purse (Capsella bursa-pastoris) to overcome a high genetic load
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High genetic diversity but no geographical structure of Aedes albopictus populations in Réunion Island

Latreille, Anne C.; Milesi, Pascal; Magalon, Hélène; Mavingui, Patrick et al.

Part of Parasites & Vectors, 2019

• DOI for High genetic diversity but no geographical structure of Aedes albopictus populations in Réunion Island
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Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees

Milesi, Pascal; Berlin, Mats; Chen, Jun; Orsucci, Marion et al.

Part of Evolutionary Applications, p. 1946-1959, 2019

• DOI for Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees
• Download full text (pdf) of Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees

Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce

Chen, Jun; Li, Lili; Milesi, Pascal; Jansson, Gunnar et al.

Part of Evolutionary Applications, p. 1539-1551, 2019

• DOI for Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce
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Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

Kryvokhyzha, Dmytro; Milesi, Pascal; Duan, Tianlin; Orsucci, Marion et al.

Part of PLOS Genetics, 2019

• DOI for Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)
• Download full text (pdf) of Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation

Milesi, Pascal; Assogba, Benoit S.; Atyame, Celestine M.; Pocquet, Nicolas et al.

Part of Molecular Ecology, p. 493-507, 2018

• DOI for The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation
• Download full text (pdf) of The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation

Recent introductions, ancient recolonization events and local adaptation: a first fine-scale mapping of the population genetic structure of Norway spruce across Sweden

Li, Lili; Milesi, Pascal; Chen, Jun; Baison, John et al.

Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management

Söderquist, Linus; Joffard, Nina; Scofield, Douglas; Milesi, Pascal et al.

Conserved Evolutionary Response to Whole Genome Duplication in Angiosperms Revealed Using High Resolution Gene Expression Profiling

Leal, J. Luis; Hodková, Eva; Billhardt, Anja; Eklund, Magnus et al.

rCNV2: A composite-likelihood ratio method for robust detection of CNVs from SNPs data

Zhou, Qiujie; Lindstedt, Freja; Karunarathne, Piyal; Milesi, Pascal

Gene copy number variations are untaped key players in adaptation along environmental gradient

Zhou, Qiujie; Lascoux, Martin; Milesi, Pascal