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Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
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2006 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 174, no 4, 2095-2105 p.Article in journal (Refereed) Published
Abstract [en]

DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico-Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively.

Place, publisher, year, edition, pages
2006. Vol. 174, no 4, 2095-2105 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-24392DOI: 10.1534/genetics.106.065102ISI: 000243284500033PubMedID: 17057229OAI: oai:DiVA.org:uu-24392DiVA: diva2:52166
Available from: 2007-02-12 Created: 2007-02-12 Last updated: 2017-12-07Bibliographically approved
In thesis
1. Population Genetics and Genome Organization of Norway Spruce
Open this publication in new window or tab >>Population Genetics and Genome Organization of Norway Spruce
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the underlying genetic causes of adaptation to local conditions is one of the main goals of population genetics. A strong latitudinal cline in the phenotypic trait of bud set is observed in present day populations of Norway spruce (Picea abies (L.) Karst). The first step towards determining how this strong selection on adaptive traits translates at the loci underlying the trait was to use multilocus sequence data to gain information on the fundamental population genetic properties of Norway spruce. We determined that the level of LD was low and genetic diversity was in the low range. Coalescent simulations revealed a demographic scenario of a fairly old and severe bottleneck as consistent with the observed data. To examine the role of selection at genes putatively involved in the control of bud set we, again, used a multilocus data set to test for deviations from neutrality and demographic scenarios inferred from background loci. Different candidate genes were identified by using different approaches, highlighting the difficulty in predicting how local adaptation will manifest itself on different time scales and in rangewide samples. When examining properties important in the design of association studies, the inevitable next step in identifying genes involved in local adaptation, we found that previous estimates of a low level of LD were highly influenced by the joint analysis of several loci over a large distribution range and that estimates of LD was in fact heterogeneous across loci and increased within populations. In addition, we found that within species tests for deviations from neutral expectations were highly sensitive to sample size. Additional genomic sequence characterization in Norway spruce is necessary to provide more comprehensive sets of markers for association studies, also including gene promoters and non-genic regions of the genome. In the final paper we show that the HMPR method is effective in constructing libraries enriched for the single copy fraction of the genome when applied to the large and dominantly repetitive genome of Norway spruce.

In summary, the studies presented in this thesis together constitute a foundation for future studies on adaptive evolution in Norway spruce.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 44 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 969
Keyword
Picea abies, demographic history, linkage disequilibrium, HMPR
National Category
Genetics Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Functional Genomics
Identifiers
urn:nbn:se:uu:diva-180370 (URN)978-91-554-8465-1 (ISBN)
Public defence
2012-10-19, Zootissalen, Evolutionsbiologiskt Centrum (EBC), Villavägen 9, Uppsala, 10:00 (English)
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Supervisors
Available from: 2012-09-28 Created: 2012-09-05 Last updated: 2013-01-23Bibliographically approved

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