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Patterns of selection at the phytochrome A locus in European aspen (Populus tremula)
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (Evolutionary Ecology)
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (Evolutionary Ecology)
(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

When a phenotype with a higher fitness arises in the population the underlying alleles are swept through the population until they reach fixation. The area surrounding the locus of the beneficial allele hitchhikes with the allele under selection, and the size of the area affected depends on the strength of selection. In Populus tremula a < 20kb region on linkage group 13 shows great reduction in synonymous diversity and an increase in rare and derived alleles as indicated by low negative values of Tajima's D and Fay and Wu's H. There is also an increase in associations between allleles at SNP sites in this region. We find that the sweep peaks in exon 2 of the phytochrome A gene. PHYA has not only undergone rapid protein evolution, it also show higher divergence in P. tremula than other plants examined, where it is unusually conserved, further pointing to adaptive significance of the increased rate of protein evolution seen in P. tremula.

Keyword [en]
selective sweep, hitch-hiking, natural selection, nuclotide diversity, populus
National Category
Ecology
Research subject
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-30357OAI: oai:DiVA.org:umu-30357DiVA: diva2:281821
Available from: 2009-12-17 Created: 2009-12-17 Last updated: 2015-11-13
In thesis
1. Tracing selection and adaptation along an environmental gradient in Populus tremula
Open this publication in new window or tab >>Tracing selection and adaptation along an environmental gradient in Populus tremula
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.

Place, publisher, year, edition, pages
Umeå: Institutionen för Ekologi, miljö och geovetenskap, Umeå universitet, 2009. 42 p.
Keyword
Local adaptation, Selection, genetic differentiation, QST, FST, Association study, frequency spectra, recurrent hitchhiking, selective sweep, Tree, Populus, natural selection, quantitative genetics
National Category
Ecology
Research subject
Population Biology; Genetics
Identifiers
urn:nbn:se:umu:diva-30123 (URN)978-91-7264-907-1 (ISBN)
Public defence
2010-01-16, Stora Hörsalen KBC, KB3B1, Umeå Universitet, KBC, Linnaeus väg 6, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2009-12-17 Created: 2009-12-07 Last updated: 2010-02-01Bibliographically approved

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Hall, DavidIngvarsson, Pär

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