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Figure 3 | BMC Ecology

Figure 3

From: Conservation genetics of a rare Gerbil species: a comparison of the population genetic structures and demographic histories of the locally rare Pygmy Gerbil and the common Anderson's Gerbil

Figure 3

A Bayesian skyline plot derived from an alignment of concatenated CR+CO2 sequences of G. henleyi (a) and G. a. allenbyi (b). The x-axis is in units of years before present, and the y-axis is equal to Neτ (the product of the effective population size and the generation length in years). The thick solid line is the median estimate, and the dashed lines show the 95% highest posterior density (HPD) interval. Sequences were simulated down the tree using the general time-reversible (GTR) model and empirical base frequencies, while also allowing for a heterogeneous (four-category gamma distribution) mutation rate among sites. The number of groups (m) was set to 20 for G. henleyi, and 5 for G. a. allenbyi. MCMC chains were run for 10,000,000 iterations of which the first 10% were discarded to allow for burn-in. Genealogies and model parameters were sampled every 1,000 iterations. Utilizing a strict molecular clock model, evolutionary rate was expressed in mutations per site per year, assuming it is normally distributed with a mean equal to 27.4 × 10-9 [42], and a standard deviation of 10 × 10-9.

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