Comparative Nucleotide Diversity Across North American and European Populus Species

Abstract

Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.

Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa

“…The rapid decay of LD in this population also means that high marker density will be required for association analysis to avoid missing possible significant markers or functional variations. However, the decline of LD with distance within PtoCesA3 extended over longer distances than the LD decline observed for candidate genes in several related species of Populus, where a rapid decay of LD occurs within a few hundred base pairs (Ingvarsson 2005(Ingvarsson , 2008Wegrzyn et al 2010;Ismail et al 2012). Previous studies conducted by Olson et al (2010) and Guerra et al (2013) reported that LD decayed over significantly longer distances in P. balsamifera and P. nigra genes.…”

Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

“…Much higher overall nucleotide diversity levels in a conifer were uncovered for P. taeda (π = 0.00398; [86]). Among the studied poplars, interestingly, the European species, P. tremula, showed the highest nucleotide diversity (π = 0.007 [87] or even π = 0.0111 [88], dependent on the surveyed genes), but differences in diversity were also consistent with its different and complex demographic history. However, nucleotide diversity is best interpreted on a gene-by-gene basis, as population history and selection affect these mutation rates more specifically [40,89].…”

Identification of single nucleotide polymorphisms (SNPs) at candidate genes involved in abiotic stress in two Prosopis species of hybrids

“…Populus (Ismail et al, 2012), Pinus (González Martinez et al, 2006;Wachowiak et al, 2011) and Quercus (Derory et al, 2012).…”