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doi:10.1534/genetics.106.065102
A more recent version of this article appeared on December 1, 2006.
REGULAR RESEARCH PAPERS |
Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce (Picea abies (L.) Karst)
Myriam Heuertz 1, Emanuele De Paoli 2, Thomas Källman 3, Hanna Larsson 3, Irina Jurman 2, Michele Morgante 2, Martin Lascoux 3* and Niclas Gyllenstrand 3
1 Universite Libre de Bruxelles
2 University of Udine
3 University of Uppsala
* To whom correspondence should be addressed. E-mail: martin.lascoux{at}ebc.uu.se.
Submitted on August 20, 2006
Revised on September 13, 2006
Accepted on 2 October 2006
DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce (Picea abies (L.) Karst.) haplotypes sampled in 7 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 thousand 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.
Key Words: DNA polymorphism, Picea abies, bottleneck, coalescent, linkage disequilibrium
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