Table 2.

popGenHMM Model Comparison

Chrom	States	LogLik	Params.	Obs	BIC
2L	2	− 402,659.796	6	2,884,699	805,408.842
	3	− 401,712.001	13	2,884,699	803,617.375
X	2	− 253,841.601	6	2,567,728	507,771.752
	3	− 252,722.130	13	2,567,728	505,636.121

NOTE.—Chrom is the chromosome for the given region of data. States is the number of states in the popGenHMM trained. LogLik is the final trained log likelihood of the popGenHMM. Params. is the number of free parameters in the model. Obs is the number of observations used for training. BIC is the Bayesian information criterion. Models with lower values of BIC are preferred. For both the chromosomes X and 2L, the three-state popGenHMM fits the data significantly better.