It thereby differs from previous approaches (e.g., [51]) in that Bayesian skyline plots fully parameterize both the mutation model (including relaxed clock models) and the genealogical process, whereas prior methods relied on generating estimates from summary statistics (e.g. the use of pairwise differences by [51]).
Interestingly, the phenotypes of human glaucoma mutation-based mouse models including myocilin Y423H (20, 17), optineurin E50K (12) and Wdr36 Del605-607 (Figs 2– 4) all involve loss of peripheral RGCs accompanied by peripheral retinal degeneration.
Two raters independently coded mutation-containing propositions for 30% of all models that incorporated mutation (n = 176 models, including 66 from the midterm exam and 110 from the final exam).
The program BOTTLENECK, v.1.2.02 [ 157] was used to test for recent bottlenecks using the Wilcoxon test and mode-shift tests with 104 replications, with the two phase mutation model (TPM, including 10% infinite alleles model) and the single step mutation model (SMM).
At midterm, most students failed to represent mutation as the mechanism causing variation: only 39% of all models included the concept of mutation, and an even smaller subset of these clearly represented mutation as the origin of variation (Table 3).
The most probable genetic models included either a mutation within a maternally imprinted domain or a chromosomal structural rearrangement.
Model 4: final backwards stepwise model including mutation data and MGMT methylation status, MGMT hemizygous deletion patients only.
Model 2: addition of MGMT methylation status to Model 1. Model 3: final backwards stepwise model including mutation data and MGMT methylation status.
Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection.
The FEL model revealed a total of 23 sites under selection using this model, including a mutation in the highly conserved small peptide ASARM (from aspartate to glicine).
