Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea Abies (L.) Karst]

By Heuertz, Myriam; De Paoli, Emanuele et al. | Genetics, December 2006 | Go to article overview

Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea Abies (L.) Karst]


Heuertz, Myriam, De Paoli, Emanuele, Källman, Thomas, Larsson, Hanna, et al., Genetics


ABSTRACT

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.

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LEVEL of nucleotide polymorphism, extent and pattern of linkage disequilibrium (LD), and degree of population differentiation are fundamental population genetics parameters that are strongly influenced by evolutionary forces that acted in the past. Their analysis can therefore be used to infer past demographic history and selection events. Solid reconstructions of past demographic events based on a large number of loci are needed to detect genomic areas that are under selection since, if the population departs from the standard neutral model, current neutrality tests that compare the observed polymorphism pattern to that expected under the standard neutral model cannot be used (see, for example, THORNTON and ANDOLFATTO 2005). In a few intensively studied species, the availability of extensive genomic data and powerful coalescent-based estimation methods are enabling such reconstructions, thereby greatly facilitating the detection of loci under selection in genome scans (e.g., AKEY et al. 2002; SCHAFFNER et al. 2005; WRIGHT et al. 2005). In other organisms, while such fine-tuned reconstructions are still out of reach, more limited surveys of nucleotide variation, coupled to coalescent simulations still do allow the evaluation of different demographic models. For example, HADDRILL et al. (2005) used multilocus neutrality tests, measures of linkage disequilibrium, and coalescent simulations to show that simple bottleneck models were sufficient to account for most, if not all, polymorphism features of Drosophila melanogaster. Such approaches have not yet been applied to conifer species, although they may be the key to the understanding of some of the intriguing patterns of nucleotide polymorphism that have emerged from initial surveys. Estimates of nucleotide diversity reported so far in conifers have been much lower than expected on the basis of their life-history traits and the high heterozygosity levels observed at allozyme loci for these species (HAMRICK and GODT 1996). The average π silent was 0.0064 in Pinus taeda (BROWN et al. 2004) and ~0.0041 in P. sylvestris (DVORNYK et al. 2002; GARCÍA- GIL et al. 2003). In Norway spruce, nucleotide diversity seems also low (π^sub s^ = 0.0041 for 21 EST loci sequenced across 12 individuals; S. degli Ivanissevich and M. Morgante, unpublished data). In P. taeda, BROWN et al. (2004) concluded that the low nucleotide diversity could be the result of a particularly low mutation rate (on the order of 1.7 × 10^sup -10^/bp/year, i.e., an order of magnitude lower than in angiosperms) combined with a low effective population size (5.6 × 10^sup 5^) due to population fluctuations during the late Pleistocene and the Holocene. …

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