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Comparative Nucleotide Diversity Across North American and European Populus Species

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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.

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  1. Mohamed Ismail

    Present address: Department of Genetics, Faculty of Agriculture, Minufiya University, Minufiya, Shebin El-Kom, Egypt

Authors and Affiliations

  1. Department of Forest Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Mohamed Ismail, Raju Y. Soolanayakanahally, Robert D. Guy & Yousry A. El-Kassaby

  2. Agri-Environment Services Branch, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada

    Raju Y. Soolanayakanahally

  3. Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden

    Pär K. Ingvarsson

  4. Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden

    Stefan Jansson

  5. Agri-Environment Services Branch, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada

    Salim N. Silim

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Ismail, M., Soolanayakanahally, R.Y., Ingvarsson, P.K. et al. Comparative Nucleotide Diversity Across North American and European Populus Species. J Mol Evol 74, 257–272 (2012). https://doi.org/10.1007/s00239-012-9504-5

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