The Experts below are selected from a list of 52911 Experts worldwide ranked by ideXlab platform
Emmanuelle D'alençon - One of the best experts on this subject based on the ideXlab platform.
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Molecular determinism of Ecological Adaptation and speciation in the Lepidoptera Spodoptera frugiperda
2017Co-Authors: Emmanuelle D'alençonAbstract:Molecular determinism of Ecological Adaptation and speciation in the Lepidoptera [i]Spodoptera frugiperda [/i]. at the International Conference on Management of Destructive Agricultural Pests Spodoptera (Noctuidae)
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Molecular determinism of Ecological Adaptation and speciation in two strains of the Lepidoptera Spodoptera frugiperda
2017Co-Authors: Emmanuelle D'alençonAbstract:Molecular determinism of Ecological Adaptation and speciation in two strains of the Lepidoptera [i]Spodoptera frugiperda[/i]. Congres de genomique environnementale
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Molecular determinism of Ecological Adaptation and speciation in two strains of the Lepidoptera Spodoptera frugiperda
2017Co-Authors: Emmanuelle D'alençonAbstract:Molecular determinism of Ecological Adaptation and speciation in two strains of the Lepidoptera [i]Spodoptera frugiperda[/i]. Congrès de génomique environnementale
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Molecular determinism of Ecological Adaptation and speciation in the Lepidoptera Spodoptera frugiperda
2017Co-Authors: Emmanuelle D'alençonAbstract:Molecular determinism of Ecological Adaptation and speciation in the Lepidoptera [i]Spodoptera frugiperda[/i]. Réunion de travail au laboratoire iEES
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Ecological Adaptation and speciation of Spodoptera frugiperda host-plant strains: a comparative transcriptomic and epigenetic approach
2015Co-Authors: Emmanuelle D'alençonAbstract:Ecological Adaptation and speciation of [i]Spodoptera frugiperda[/i] host-plant strains: a comparative transcriptomic and epigenetic approach. Arthropod Genomics Symposium
William A Cresko - One of the best experts on this subject based on the ideXlab platform.
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ancient genomic variation underlies repeated Ecological Adaptation in young stickleback populations
Evolution letters, 2018Co-Authors: Thomas C Nelson, William A CreskoAbstract:Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on Ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local Adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We extend restriction site-associated DNA sequencing (RAD-seq) to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel Adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by dXY , reaches tenfold higher than background levels and genomic variation is structured into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback (Pungitius pungitius), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local Adaptation in stickleback has therefore been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on Ecological timescales is a result of genome evolution over geological timescales, and vice versa.
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ancient genomic variation underlies repeated Ecological Adaptation in young stickleback populations
bioRxiv, 2017Co-Authors: Thomas C Nelson, William A CreskoAbstract:Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on Ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local Adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish ( Gasterosteus aculeatus ) as a model. We extend the popular restriction site-associated DNA sequencing (RAD-seq) method to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel Adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by d XY , reaches ten-fold higher than background levels and structures genomic variation into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback ( Pungitius pungitius ), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local Adaptation in stickleback has actually been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on Ecological timescales is a result of genome evolution over geological timescales, and vice versa .
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ancient genomic variation underlies recent and repeated Ecological Adaptation
bioRxiv, 2017Co-Authors: Thomas C Nelson, William A CreskoAbstract:Adaptation in the wild often involves the use of standing genetic variation (SGV), allowing rapid responses to selection on Ecological timescales. Despite increasing documentation of evolutionarily important SGV in natural populations, we still know little about how the genetic and genomic structure and molecular evolutionary history of SGV relate to Adaptation. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We demonstrate that adaptive genetic variation is structured genome-wide into distinct marine and freshwater haplogroups. This divergent variation averages six million years old, nearly twice the genome-wide average, but has been evolving over the 15-million-year history of the species. Divergent marine and freshwater genomes maintain regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries about ancient SGV demonstrate the intertwined nature of selection on Ecological timescales and genome evolution over geological timescales.
Mats E. Pettersson - One of the best experts on this subject based on the ideXlab platform.
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Ecological Adaptation in european eels is based on phenotypic plasticity
Proceedings of the National Academy of Sciences of the United States of America, 2021Co-Authors: Erik D Enbody, Mats E. Pettersson, Grace C Sprehn, Stefan Palm, Hakan Wickstrom, Leif AnderssonAbstract:The relative role of genetic Adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across Ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic Adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.
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Ecological Adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci.
eLife, 2020Co-Authors: Fan Han, Mats E. Pettersson, Minal Jamsandekar, Brian W Davis, Dorte Bekkevold, Florian Berg, Michele Casini, Angela P. Fuentes-pardo, Geir DahleAbstract:Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic Adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying Ecological Adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying Ecological Adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.
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the genetic architecture underlying Ecological Adaptation in atlantic herring is not consistent with the infinitesimal model
bioRxiv, 2020Co-Authors: Fan Han, Mats E. Pettersson, Minal Jamsandekar, Angela P Fuentespardo, Brian W Davis, Dorte Bekkevold, Florian Berg, Michele Casini, Geir DahleAbstract:Abstract Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic Adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying Ecological Adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying Ecological Adaptation in the herring is in conflict with the infinitesimal model for complex traits because of the large shifts in allele frequencies at hundreds of loci under selection.
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a chromosome level assembly of the atlantic herring detection of a supergene and other signals of selection
bioRxiv, 2019Co-Authors: Mats E. Pettersson, Christina M Rochus, Xiaoning Hong, Leanne Haggerty, Qiwu Xu, Ola Wallerman, Junfeng Chen, Jason Hill, He Zhang, Toby HuntAbstract:The Atlantic herring is a model species for exploring the genetic basis for Ecological Adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo PacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying Ecological Adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with Ecological Adaptation in the Atlantic herring.
Humberto Quesada - One of the best experts on this subject based on the ideXlab platform.
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Population genomics of parallel evolution in gene expression and gene sequence during Ecological Adaptation
Scientific reports, 2018Co-Authors: María José Rivas, María Saura, Andrés Pérez-figueroa, Marina Panova, Tomas Johansson, Carl André, Armando Caballero, Emilio Rolán-alvarez, Kerstin Johannesson, Humberto QuesadaAbstract:Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel Ecological Adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
Thomas C Nelson - One of the best experts on this subject based on the ideXlab platform.
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ancient genomic variation underlies repeated Ecological Adaptation in young stickleback populations
Evolution letters, 2018Co-Authors: Thomas C Nelson, William A CreskoAbstract:Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on Ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local Adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We extend restriction site-associated DNA sequencing (RAD-seq) to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel Adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by dXY , reaches tenfold higher than background levels and genomic variation is structured into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback (Pungitius pungitius), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local Adaptation in stickleback has therefore been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on Ecological timescales is a result of genome evolution over geological timescales, and vice versa.
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ancient genomic variation underlies repeated Ecological Adaptation in young stickleback populations
bioRxiv, 2017Co-Authors: Thomas C Nelson, William A CreskoAbstract:Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on Ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local Adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish ( Gasterosteus aculeatus ) as a model. We extend the popular restriction site-associated DNA sequencing (RAD-seq) method to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel Adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by d XY , reaches ten-fold higher than background levels and structures genomic variation into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback ( Pungitius pungitius ), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local Adaptation in stickleback has actually been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on Ecological timescales is a result of genome evolution over geological timescales, and vice versa .
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ancient genomic variation underlies recent and repeated Ecological Adaptation
bioRxiv, 2017Co-Authors: Thomas C Nelson, William A CreskoAbstract:Adaptation in the wild often involves the use of standing genetic variation (SGV), allowing rapid responses to selection on Ecological timescales. Despite increasing documentation of evolutionarily important SGV in natural populations, we still know little about how the genetic and genomic structure and molecular evolutionary history of SGV relate to Adaptation. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We demonstrate that adaptive genetic variation is structured genome-wide into distinct marine and freshwater haplogroups. This divergent variation averages six million years old, nearly twice the genome-wide average, but has been evolving over the 15-million-year history of the species. Divergent marine and freshwater genomes maintain regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries about ancient SGV demonstrate the intertwined nature of selection on Ecological timescales and genome evolution over geological timescales.
