The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution.
Bayesian inference produced an estimate across all seven loci of 4Nem = 12.26 (95th percentile = 5.93 15.27) from primary to logged forest and 4Nem = 2.04 (95th percentile = 1.05 3.40) from logged to primary forest.
The chief concern of phylogenetics, in contrast, is to produce a concrete inference of historical evolutionary relationships and to characterize the statistical support for that inference.
Nonetheless, these experiments show that our statistical method, when combined with the types and quantities of data we have available, can produce a reliable inference.
Without too much biophysical a priori information, our analysis will produce a quantitative inference of heterogeneous selection in the HA1 domain: nonsynonymous epitope changes are predominantly under positive selection, nonsynonymous changes outside the epitopes are predominantly under negative selection, and synonymous changes evolve near neutrality.
Bayesian inference of migration rates produced an estimate for mtDNA of 2Nfm = 8.20 (95th percentile = 1.64 24.56) from primary to logged forest and 2Nfm = 3.35 (95th percentile = 0.07 13.46) from logged to primary forest.
ML analysis and Bayesian inference produced a similar topology (Fig. 2).
In each case, the inference process produced a narrow posterior, relative to the prior, with clear similarity to the actual value of g ¯ for each starting parameter set.
While none of the three nuclear loci examined in this study was completely sorted with regard to LAB and RAB groups of R. marina, a Bayesian species tree inference method produced a high posterior probability (P = 1.0) for their sister-taxa relationship.
Their siliceous cell walls are often preserved in lake sediments with sufficient fidelity to allow taxonomic identifications and ecological inferences, thus producing an archive of limnological history.
