Exact(5)
We note that the deep divergence time of lineage 1, substantially present within all lake samples, is consistent with long-term isolation of Ace Lake.
Let d (i, j ) be the time of lineage divergence, the time at which the lineages cease to exist within the same host (see Figure 1).
For the former, we can assume that the number of SNPs arising from the time of lineage divergence d (i, j ) until observation follows a Poisson distribution with mean μ (t i s + t j s − 2 d (i, j ) ).
The time of lineage coexistence, evolutionary distance between transfer partners, and quantity of transferred substitutions corresponded to appropriate edge lengths in the phylogenies of figure 1 (see Materials and Methods for details).
Under an assumed or hypothesized set of transmission routes, the time of lineage divergence d (i, j ) is known, and the rate of lineage coalescence can be derived from the specification of a model of within-host population dynamics and transmission.
Similar(55)
In this context the divergence time of lineages is of interest and dating of the split of the "cave haplogroup" based on genetic distances would be desirable.
To infer the time of the two branches where positive selection was detected (branches B and C in Figure 2), we estimated the divergence time of lineages of interest using the mitochondrial sequences.
To date the time frame, in which positive selection is predicted, the divergence time of lineages of interest was inferred from the phylogeny of the mitochondrial genome constructed here.
For TEs shared among species, times of lineage divergence place upper bounds on the insertion times: no insertion older than 12 MYA is recognizable.
However, our aim was to provide an approximation (not precise dating) for times of lineage splitting.
The species have a well-documented phylogenetic relationship as noted in Figure 1 of [ 3], and this figure can be consulted for details such as times of lineage splitting, chromosome composition, etc.
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