title: 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.
authors.affiliation: Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. mohamed.ismail@agr.menofia.edu.eg
authors.forename: Mohamed
authors.initials: M
authors.lastname: Ismail
authors.forename: Raju Y
authors.initials: RY
authors.lastname: Soolanayakanahally
authors.forename: Pär K
authors.initials: PK
authors.lastname: Ingvarsson
authors.forename: Robert D
authors.initials: RD
authors.lastname: Guy
authors.forename: Stefan
authors.initials: S
authors.lastname: Jansson
authors.forename: Salim N
authors.initials: SN
authors.lastname: Silim
authors.forename: Yousry A
authors.initials: YA
authors.lastname: El-Kassaby
mesh_terms: D003198:Computer Simulation; D005060:Europe; D005787:Gene Frequency / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D017711:Nonlinear Dynamics; D009656:North America; D009711:Nucleotides / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032107:Populus / Q000235:genetics*; D013045:Species Specificity; D013997:Time Factors
chemical_list: D009711:Nucleotides