Limits...
Mountain pine beetle host-range expansion threatens the boreal forest.

Cullingham CI, Cooke JE, Dang S, Davis CS, Cooke BJ, Coltman DW - Mol. Ecol. (2011)

Bottom Line: We were able to accurately classify simulated individuals, and hence applied these markers to identify the ancestry of attacked trees.This once unsuitable habitat is now a novel environment for MPB to exploit, a potential risk which could be exacerbated by further climate change.The consequences of host-range expansion for the vast boreal ecosystem could be significant.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada. cathy.cullingham@ualberta.ca

Show MeSH

Related in: MedlinePlus

Work-flow for generating genotypes for simulations to assess the capability of 12 microsatellite loci to resolve the species identify of jack pine, lodgepole pine and their hybrids.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3116149&req=5

fig03: Work-flow for generating genotypes for simulations to assess the capability of 12 microsatellite loci to resolve the species identify of jack pine, lodgepole pine and their hybrids.

Mentions: The detection of hybrid classes will depend on the degree of differentiation between the parental species and the loci used (Anderson & Thompson 2002; Vähä & Primmer 2006). Previous studies that have assessed hybrid zones and the resolving capacity of microsatellites have included only first (F1) and second generation hybrids (F2, F1 backcrosses) in their simulations (Thulin et al. 2006; Vähä & Primmer 2006; Burgarella et al. 2009; Quintela et al. 2010). We also included a third generation of hybrids (F2 backcrosses and F1 double backcrosses) to assess our ability to resolve advanced introgression. We simulated five datasets using Hybridlab ver. 1.0 (Nielsen et al. 2006). Hybridlab was developed to create artificial parental and hybrid genotypes to evaluate the power to correctly identify hybrids. As input, we used genetic profiles from 100 jack pine from Ontario and Saskatchewan and 100 lodgepole pine from British Columbia (we selected samples far removed from the hybrid zone) to represent the microsatellite allele frequency variation for each species. For each dataset we simulated profiles for 300 jack pine and 300 lodgepole pine; we chose 300 as we felt this would simulate our dataset closely. Using these 600 simulated genotypes we generated 100 F1 hybrids. With these hybrid profiles we were able to simulate F2 hybrids, F1 × jack pine (F1Pj), F1 × lodgepole pine (F1Pl), F2 × jack pine (F2Pj), F2 × lodgepole pine (F2Pl), F1-jackpine × jack pine (F1Pj-Pj), and F1-lodgepole pine × lodgepole pine (F1Pl-Pl) (Fig. 3). Each dataset for hybrid analysis was comprised of simulated genotypes for 300 jack pine and 300 lodgepole pine and 10 individuals from each hybrid class: F1, F2, F1Pj, F1Pl, F2Pj, F2Pl, F1Pj-Pj and F1Pl-Pl. We then analysed these datasets with two different Bayesian methods (Structure and Newhybrids) to establish a threshold (QT) for assigning parental and hybrid status. We used both Bayesian methods in our approach to maximize the accuracy of assigning individuals (Thulin et al. 2006; Vähä & Primmer 2006; Burgarella et al. 2009).


Mountain pine beetle host-range expansion threatens the boreal forest.

Cullingham CI, Cooke JE, Dang S, Davis CS, Cooke BJ, Coltman DW - Mol. Ecol. (2011)

Work-flow for generating genotypes for simulations to assess the capability of 12 microsatellite loci to resolve the species identify of jack pine, lodgepole pine and their hybrids.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116149&req=5

fig03: Work-flow for generating genotypes for simulations to assess the capability of 12 microsatellite loci to resolve the species identify of jack pine, lodgepole pine and their hybrids.
Mentions: The detection of hybrid classes will depend on the degree of differentiation between the parental species and the loci used (Anderson & Thompson 2002; Vähä & Primmer 2006). Previous studies that have assessed hybrid zones and the resolving capacity of microsatellites have included only first (F1) and second generation hybrids (F2, F1 backcrosses) in their simulations (Thulin et al. 2006; Vähä & Primmer 2006; Burgarella et al. 2009; Quintela et al. 2010). We also included a third generation of hybrids (F2 backcrosses and F1 double backcrosses) to assess our ability to resolve advanced introgression. We simulated five datasets using Hybridlab ver. 1.0 (Nielsen et al. 2006). Hybridlab was developed to create artificial parental and hybrid genotypes to evaluate the power to correctly identify hybrids. As input, we used genetic profiles from 100 jack pine from Ontario and Saskatchewan and 100 lodgepole pine from British Columbia (we selected samples far removed from the hybrid zone) to represent the microsatellite allele frequency variation for each species. For each dataset we simulated profiles for 300 jack pine and 300 lodgepole pine; we chose 300 as we felt this would simulate our dataset closely. Using these 600 simulated genotypes we generated 100 F1 hybrids. With these hybrid profiles we were able to simulate F2 hybrids, F1 × jack pine (F1Pj), F1 × lodgepole pine (F1Pl), F2 × jack pine (F2Pj), F2 × lodgepole pine (F2Pl), F1-jackpine × jack pine (F1Pj-Pj), and F1-lodgepole pine × lodgepole pine (F1Pl-Pl) (Fig. 3). Each dataset for hybrid analysis was comprised of simulated genotypes for 300 jack pine and 300 lodgepole pine and 10 individuals from each hybrid class: F1, F2, F1Pj, F1Pl, F2Pj, F2Pl, F1Pj-Pj and F1Pl-Pl. We then analysed these datasets with two different Bayesian methods (Structure and Newhybrids) to establish a threshold (QT) for assigning parental and hybrid status. We used both Bayesian methods in our approach to maximize the accuracy of assigning individuals (Thulin et al. 2006; Vähä & Primmer 2006; Burgarella et al. 2009).

Bottom Line: We were able to accurately classify simulated individuals, and hence applied these markers to identify the ancestry of attacked trees.This once unsuitable habitat is now a novel environment for MPB to exploit, a potential risk which could be exacerbated by further climate change.The consequences of host-range expansion for the vast boreal ecosystem could be significant.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada. cathy.cullingham@ualberta.ca

Show MeSH
Related in: MedlinePlus