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Journal of Molecular Evolution

, Volume 74, Issue 5–6, pp 257–272 | Cite as

Comparative Nucleotide Diversity Across North American and European Populus Species

  • Mohamed IsmailEmail author
  • Raju Y. Soolanayakanahally
  • Pär K. Ingvarsson
  • Robert D. Guy
  • Stefan Jansson
  • Salim N. Silim
  • Yousry A. El-Kassaby
Article

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.

Keywords

Populus Nucleotide diversity Linkage disequilibrium Selection Divergence 

Supplementary material

239_2012_9504_MOESM1_ESM.docx (22 kb)
Supplementary material 1 (DOCX 22 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Mohamed Ismail
    • 1
    • 2
    Email author
  • Raju Y. Soolanayakanahally
    • 1
    • 3
  • Pär K. Ingvarsson
    • 4
  • Robert D. Guy
    • 1
  • Stefan Jansson
    • 5
  • Salim N. Silim
    • 6
  • Yousry A. El-Kassaby
    • 1
  1. 1.Department of Forest SciencesUniversity of British ColumbiaVancouverCanada
  2. 2.Department of Genetics, Faculty of AgricultureMinufiya UniversityShebin El-KomEgypt
  3. 3.Agri-Environment Services BranchAgriculture and Agri-Food CanadaIndian HeadCanada
  4. 4.Department of Ecology and Environmental Science, Umeå Plant Science CentreUmeå UniversityUmeåSweden
  5. 5.Department of Plant Physiology, Umeå Plant Science CentreUmeå UniversityUmeåSweden
  6. 6.Agri-Environment Services BranchAgriculture and Agri-Food CanadaOttawaCanada

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