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2.
Figure 3

Figure 3. Performance of , , HKA, and Tajima's under the demographic models in with selection parameter and dominance parameter .. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

The first column is the divergence model in . The second column is the divergence model in with a recent bottleneck within the ingroup species. The third column is the divergence model in with recent population growth within the ingroup species.

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.
3.
Figure 4

Figure 4. Performance of , , HKA, and Tajima's under the demographic models in with selection parameter and dominance parameter .. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

The first column is the divergence model in . The second column is the divergence model in with a recent bottleneck within the ingroup species. The third column is the divergence model in with recent population growth within the ingroup species.

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.
4.
Figure 8

Figure 8. Signal of balancing selection at the FANK1 gene for the CEU (blue) and YRI (orange) populations using the test statistic.. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

From bottom to top, the horizontal dotted gray lines indicate the , , , and empirical cutoffs, respectively. SNPs (rsIDs) correspond to markers showing significant levels of transmission distortion within the Meyer et al. study .

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.
5.
Figure 2

Figure 2. Demographic models used in simulations in which a selected allele arises after the split a pair of species.. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

(A) Divergence model. Model parameters are a diploid effective population size , divergence time of the ingroup and outgroup species, and the time when the selected allele arises. (B) Divergence model with a recent bottleneck within the ingroup species. Additional model parameters are the diploid effective population size during the bottleneck, the time when the bottleneck began, and the time when the bottleneck ended. (C) Divergence model with recent population growth within the ingroup species. Additional model parameters are the current diploid effective population size after recent growth and the time when the growth occurred.

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.
6.
Figure 5

Figure 5. Performance of , , HKA, and Tajima's under the bottleneck and growth demographic models in with selection parameter and dominance parameter .. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

The left panel is the divergence model in with a recent bottleneck within the ingroup species. The right panel is the divergence model in with recent population growth within the ingroup species. The population sizes for the bottleneck and growth demographic histories have been scaled so that they produce the same number of segregating sites as a constant size population with diploid effective size individuals.

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.
7.
Figure 6

Figure 6. Performance of , , HKA, and Tajima's under the bottleneck and growth demographic models in with selection parameter and dominance parameter .. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

The left panel is the divergence model in with a recent bottleneck within the ingroup species. The right panel is the divergence model in with recent population growth within the ingroup species. The population sizes for the bottleneck and growth demographic histories have been scaled so that they produce the same number of segregating sites as a constant size population with diploid effective size individuals.

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.
8.
Figure 1

Figure 1. Calculation of probabilities of polymorphism and substitution under a model of balancing selection and the incorporation of these probabilities into a genome scan.. From: A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data.

(A) Relationship among tree length , tree height and inter-specific coalescence time . (B) A site is polymorphic if a mutation occurred on the length of branches until the most recent common ancestor of the ingroup sample (red region). (C) A site is a substitution if a mutation occurred on the length of branches that represent the divergence between the outgroup species and the most recent common ancestor of the ingroup species (blue region). (D) Height and length of genealogies in relationship to their spatial proximity to a selected site and how the shapes of these genealogies affect the pattern of polymorphism around the site. The composite likelihood ratio is high near a selected site as there is an excess of polymorphisms close to the site and a deficit far from the site.

Michael DeGiorgio, et al. PLoS Genet. 2014 Aug;10(8):e1004561.

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