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626 results on '"Wright, Stephen I"'

1. The genetic architecture of repeated local adaptation to climate in distantly related plants

Author

Whiting, James R., Booker, Tom R., Rougeux, Clément, Lind, Brandon M., Singh, Pooja, Lu, Mengmeng, Huang, Kaichi, Whitlock, Michael C., Aitken, Sally N., Andrew, Rose L., Borevitz, Justin O., Bruhl, Jeremy J., Collins, Timothy L., Fischer, Martin C., Hodgins, Kathryn A., Holliday, Jason A., Ingvarsson, Pär K., Janes, Jasmine K., Khandaker, Momena, Koenig, Daniel, Kreiner, Julia M., Kremer, Antoine, Lascoux, Martin, Leroy, Thibault, Milesi, Pascal, Murray, Kevin D., Pyhäjärvi, Tanja, Rellstab, Christian, Rieseberg, Loren H., Roux, Fabrice, Stinchcombe, John R., Telford, Ian R. H., Todesco, Marco, Tyrmi, Jaakko S., Wang, Baosheng, Weigel, Detlef, Willi, Yvonne, Wright, Stephen I., Zhou, Lecong, and Yeaman, Sam

Published
2024
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4. Long-term balancing selection drives evolution of immunity genes in Capsella.

Author

Koenig, Daniel, Hagmann, Jörg, Li, Rachel, Bemm, Felix, Slotte, Tanja, Neuffer, Barbara, Wright, Stephen I, and Weigel, Detlef

Subjects
Capsella, Adaptation, Biological, Evolution, Molecular, Genes, Plant, Genetic Variation, Selection, Genetic, NB-LRR, balancing selection, bottleneck, disease resistance, evolutionary biology, genetics, genomics, immunity, selfing, Adaptation, Biological, Evolution, Molecular, Genes, Plant, Selection, Genetic, Biochemistry and Cell Biology
Abstract

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

Published
2019

7. Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulus

Author

Sacchi, Bianca, primary, Humphries, Zoë, additional, Kružlicová, Jana, additional, Bodláková, Markéta, additional, Pyne, Cassandre, additional, Choudhury, Baharul, additional, Gong, Yunchen, additional, Bačovský, Václav, additional, Hobza, Roman, additional, Barrett, Spencer C H, additional, and Wright, Stephen I, additional

Published
2024
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20. Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulus

Author

Sacchi, Bianca M., primary, Humphries, Zoë, additional, Kružlicová, Janka, additional, Bodláková, Markéta, additional, Pyne, Cassandre, additional, Choudhury, Baharul, additional, Gong, Yunchen, additional, Bačovský, Václav, additional, Hobza, Roman, additional, Barrett, Spencer C.H., additional, and Wright, Stephen I., additional

Published
2023
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21. Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

Author

Ross-Ibarra, Jeffrey, Wright, Stephen I., Foxe, John Paul, Kawabe, Akira, DeRose-Wilson, Leah, Gos, Gesseca, Charlesworth, Deborah, and Gaut, Brandon S.

Abstract

BackgroundMany of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation.Principal FindingsWe studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events.ConclusionsOur results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata.

Published
2008

29. Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus

Author

Kreiner, Julia M., Hnatovska, Solomiya, Stinchcombe, John R., Wright, Stephen I., Kreiner, Julia M., Hnatovska, Solomiya, Stinchcombe, John R., and Wright, Stephen I.

Abstract

Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences—individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.

Published
2023
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31. The butterfly plant arms-race escalated by gene and genome duplications

Author

Edger, Patrick P., Heidel-Fischer, Hanna M., Bekaert, Michaël, Rota, Jadranka, Glöckner, Gernot, Platts, Adrian E., Heckel, David G., Der, Joshua P., Wafula, Eric K., Tang, Michelle, Hofberger, Johannes A., Smithson, Ann, Hall, Jocelyn C., Blanchette, Matthieu, Bureau, Thomas E., Wright, Stephen I., dePamphilis, Claude W., Schranz, M. Eric, Barker, Michael S., Conant, Gavin C., Wahlberg, Niklas, Vogel, Heiko, Pires, J. Chris, and Wheat, Christopher W.

Published
2015

40. Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha.

Author

Sandler, George, Agrawal, Aneil F, and Wright, Stephen I

Subjects
LIVERWORTS, GENOMICS, VEGETATIVE propagation, GENETIC variation, ASEXUAL reproduction, GENE flow, SUBSPECIES
Abstract

The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction. [ABSTRACT FROM AUTHOR]

Published
2023
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