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Cross-species outlier detection reveals different evolutionary pressures between sister species.

Cullingham CI, Cooke JE, Coltman DW - New Phytol. (2014)

Bottom Line: To better understand this we aim to identify genetic regions that have adaptive potential.We found contrasting relationships between environmental variation and genetic diversity for the species.Using rigorous criteria we have been able to identify potential outlier SNPs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada.

No MeSH data available.


Comparison of the number of outlier loci identified using seven different approaches on three data sets: species data (white bars), pure lodgepole pine (Pinus contorta var. latifolia; grey bars), and pure jack pine (Pinus banksiana; black bars). The methods used were the island and hierarchic demographic models in arelquin (Arelquin and Arelquin_ST, respectively), bayescan with and without prior odds (only the BaySCAN_prior is shown here), matsam, bayenv and introgress.
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fig01: Comparison of the number of outlier loci identified using seven different approaches on three data sets: species data (white bars), pure lodgepole pine (Pinus contorta var. latifolia; grey bars), and pure jack pine (Pinus banksiana; black bars). The methods used were the island and hierarchic demographic models in arelquin (Arelquin and Arelquin_ST, respectively), bayescan with and without prior odds (only the BaySCAN_prior is shown here), matsam, bayenv and introgress.

Mentions: We identified 21 and 17 outliers in lodgepole pine using the island and hierarchical demographic models in arlequin, respectively (Fig. 1). Fourteen loci were identified in both models; of these, all but two loci exhibited signals of positive selection. We identified 10 and 11 outliers in jack pine using the island and hierarchical models, respectively. Only three of these loci were shared between the models at the 0.01 significance level, while an additional four loci were shared at the 0.05 level. The three commonly identified loci had signals of positive selection. For the combined subset, we identified 204 and 14 loci using the island and hierarchical models, respectively. All 14 loci identified with the hierarchical model were also identified with the island model. Six of the 14 loci had signals of negative selection. One locus was identified in both jack pine and the combined subset, but no loci were identified across all subsets.


Cross-species outlier detection reveals different evolutionary pressures between sister species.

Cullingham CI, Cooke JE, Coltman DW - New Phytol. (2014)

Comparison of the number of outlier loci identified using seven different approaches on three data sets: species data (white bars), pure lodgepole pine (Pinus contorta var. latifolia; grey bars), and pure jack pine (Pinus banksiana; black bars). The methods used were the island and hierarchic demographic models in arelquin (Arelquin and Arelquin_ST, respectively), bayescan with and without prior odds (only the BaySCAN_prior is shown here), matsam, bayenv and introgress.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4260136&req=5

fig01: Comparison of the number of outlier loci identified using seven different approaches on three data sets: species data (white bars), pure lodgepole pine (Pinus contorta var. latifolia; grey bars), and pure jack pine (Pinus banksiana; black bars). The methods used were the island and hierarchic demographic models in arelquin (Arelquin and Arelquin_ST, respectively), bayescan with and without prior odds (only the BaySCAN_prior is shown here), matsam, bayenv and introgress.
Mentions: We identified 21 and 17 outliers in lodgepole pine using the island and hierarchical demographic models in arlequin, respectively (Fig. 1). Fourteen loci were identified in both models; of these, all but two loci exhibited signals of positive selection. We identified 10 and 11 outliers in jack pine using the island and hierarchical models, respectively. Only three of these loci were shared between the models at the 0.01 significance level, while an additional four loci were shared at the 0.05 level. The three commonly identified loci had signals of positive selection. For the combined subset, we identified 204 and 14 loci using the island and hierarchical models, respectively. All 14 loci identified with the hierarchical model were also identified with the island model. Six of the 14 loci had signals of negative selection. One locus was identified in both jack pine and the combined subset, but no loci were identified across all subsets.

Bottom Line: To better understand this we aim to identify genetic regions that have adaptive potential.We found contrasting relationships between environmental variation and genetic diversity for the species.Using rigorous criteria we have been able to identify potential outlier SNPs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada.

No MeSH data available.