Sequence and phylogenetic analyses showed that most Old World monkeys shared five classes of KIR loci: i) KIR2DL5/3DL20 in the most centromeric region, followed by ii) the single Ig domain-encoding locus KIR1D, iii) the pseudogene KIR2DP, iv) the conserved KIR2DL4, and v) the highly diversified KIR3DL/H loci in the telomeric half of the cluster.
Thus, the annotations of these two classes of MIR loci (i.e. variant and siRNA-like) should be reconsidered.
Differentially expressed genes in three comparison groups with no-interaction at Sa and Sb pollen sterility loci (i.e. harboring neutral genes at Sa and Sb loci).
Hemimethylated loci (i.e. loci with fragments present in EcoRI/HpaII digestions but absent in EcoRI/MspI digestions) were excluded from genetic and epigenetic analysis.
All trace files were visually scanned for overlapping peaks as indicators of amplification from multiple loci (i.e. paralogs).
We defined a triplet-based distance between each pair of forests F i and F j, where F i and F j were, respectively, the forests of 100 bootstrap trees obtained for loci i and j.
The covariance of the expected number of opposing homozygotes between loci i and j is equal to the probability that two animals have opposing homozygotes both at locus i and j.
We follow this approach introducing two new steps to asses the matching between CN and GE loci: (i) first, a signal correlation analysis; (ii) second, an alteration frequency analysis.
Using the iterative projection method, and in order to limit error propagation, the projection process started with the map that presents the more stable framework and well ordered and spread loci i. e. the map derived from the DYDH population.
A combined likelihood surface was then constructed by multiplying likelihoods at each grid point across all loci i and all summary statistics j (2) where f λ is the observed marginal coalescent likelihood of ϕ ij.
For our model, it can be shown that these disequilibria are (13) where r ij is the recombination rate between loci i and j, and that the between-generation change in the p i is (14) to first order in γ. (A Mathematica notebook with the detailed derivation of these equations is available from the lead author).
