Some lambruscos are made using the so-called ancestral method, in which yeasts are left in the bottle to create a fizz and leave sediment.
For each ortholog, we inferred the nucleotide sequences of ancestral species by using the likelihood method (Yang et al. 1995) and counted the numbers of substitutions at paired (A U, G C, and G U pairs) and unpaired sites (all other pairs) separately.
In addition to using the naïve ancestral state reconstruction methods described in the previous section, the biogeographic method Lagrange [ 89] was used to reconstruct the history of the 'Plate II' tectonic plate character.
Ancestral sequences were estimated using the ML method (MEGA).
Reconstruction of ancestral genomes using the maximum parsimony method predicts that the last common ancestor of all sequenced CVs encoded at least 297 protein families, including 155 core CV protein families plus 142 families that were lost in one or more modern CV genomes.
The phylogenetic positions of individual mutations were determined by ancestral sequence reconstruction, using the joint ML method (Pupko et al., 2000) with the GTR+ Γ nucleotide substitution model implemented in HYPHY v1.0b (Pond et al., 2005).
Go has previously predicted the numbers of ancestral T2R genes using the linearized tree method [ 15], and identified some lineage-specific gene expansions and contractions that occurred throughout vertebrate evolution.
Ancestral ranges were reconstructed using the dispersal extinction cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics.
We reconstructed ancestral areas of mustelids using the likelihood reconstruction method [ 86, 130] implemented in Mesquite v1.12 [ 131].
Ancestral sequences were determined using the maximum likelihood method from PAMLv3.15 [ 34] under a Poisson model of amino acid evolution.
