First, we employed the McDonald-Kreitman test (MKT), which is a two-population neutrality test that compares the ratio of fixed nonsynonymous to synonymous differences to the ratio of polymorphic nonsynonymous to synonymous differences [ 22].
These statistical tests [68], [69] (Tajima's D and Fu-Li's D* and F*) are based on the proportion of rare and common polymorphisms expected in a population under neutrality, and this proportion is informative about natural selection.
Theta values were comparable across Caribbean populations, and neutrality tests (Tajima's D, Fu and Li's F and D, mismatch analysis and R2) do not suggest significant deviations from neutral expectations including population bottlenecks or expansions, except in the Bahamas and Turks and Caicos Islands where R2 was significant.
Additionally, selection was investigated using population-based neutrality tests.
The widely used simulator ms (Hudson, 2002) is a powerful tool for genealogies in general structured populations under neutrality, with high performance and an easy to use interface.
There is a high probability (P > 0.05) that nuclear genes would be fixed in these populations under neutrality, suggesting that drift cannot be rejected as a possibility for morphological divergence [Additional file 3].
When branch lengths were reduced four times, an s value of 3 occurred in none of simulated trees, suggesting that there is a very low probability (P < 0.0001) that nuclear genes would be fixed in different populations under neutrality [Additional file 3].
In the presence of mutation, we used simulation to determine the range of the population size under neutrality.
Therefore, the population size under neutrality (N e ) that has the same variance in allele frequency as the population under selection can be determined using numerical iteration.
The corresponding N e is defined here as the population size under neutrality that will increase F from F0 to F t n e a r l y f i x e d between t = 0 and t = t nearlyfixed.
