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

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 BalticoNordic 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.

Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Lastly, the F ST values of SNPs did not deviate significantly from neutral expectations based on the Bayesian F ST test. Our results are in line with recent data obtained in various species, in which differentiation of CGs was compared with differentiation of neutral markers and of the target trait (Eveno et al (2008) in P. pinaster; Pyhäjärvi et al (2008) in P. sylvestris; Heuertz et al (2006) in Picea abies; Hall et al (2007) and Luquez et al (2007) in P. tremula). In all these case studies, the mean differentiation of genes was of the same level as differentiation of the neutral markers and far less than differentiation of the target trait.…”

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

“…For instance, Heuertz et al (2006) found that across large geographic distances, Picea abies is strongly differentiated across large geographic barriers, with F ST estimates approaching those that we found among genetic groupings. Therefore, even though many forest trees have extensive potential for long-distance dispersal (Savolainen et al, 2007), they can still develop strong neutral genetic structure across large spatial scales and geographic barriers.…”

“…Other North American tree species support the hypothesis of impacts of past climate on population sizes and distributions. In a latitudinally oriented study of Picea sitchensis, Holliday et al (2010) found support for an historical bottleneck and expansion, and also found negative Tajima's D, as did a study of Picea aibes in Eurasia (Heuertz et al, 2006). In P. trichocarpa of the central and northern Pacific Northwest, populations have expanded rapidly since the LGM (Zhou et al, 2014).…”

Population genomics of the eastern cottonwood (Populus deltoides)

“…It can also be the consequence of demographic changes influencing diversity in the entire genome, like population growth after an ancient bottleneck (Holliday, Yuen, Ritland, & Aitken, 2010). Population size reduction during the last glacial period and population growth after this bottleneck has shaped demography in other tree species (Heuertz et al., 2006; Holliday et al., 2010; Ingvarsson, 2008; Pyhäjärvi et al., 2007; Zhou et al., 2014) and is also a plausible scenario for P. deltoides , but demography has not been assessed in this species to date. In the absence of a demographic study in P. deltoides and because demography can confound signatures of selection causing false‐positive Tajima's D outliers, this statistic was used to complement the information obtained with other tests.…”