Methods focused on the statistical inference of the set of present species as well as the estimation of their relative proportions, incorporate knowledge from all reads to assign each individual read to a species.
First, the analyses of cross-sectional design preclude causal inference in the present study.
Methods that relied on shorter sequences (i.e., trimmed alignments or protein sequences) or simpler models of sequence evolution (i.e., neighbor-joining or parsimony) tended to yield weaker support for the earlier diverging lineages, but none of our analyses were in significant conflict with the key inferences of the phylogeny presented in Figure 2 or Additional file 11: Figure S8.
Methods that relied on shorter sequences (i.e., trimmed alignments or protein sequences) or simpler models of sequence evolution (i.e., neighbor-joining or parsimony) tended to yield weaker support for the earlier diverging lineages, but none of our analyses were in significant conflict with the key inferences of the phylogeny presented in Figure 3.
Ultimately, the historian's task is to shed light on the what, why, and how of the past, based on inferences from the evidence of the present.
A consideration of the merits of this general idea of explanatory or abductive inference is beyond the scope of the present article.
Detailed population genetic inference is not a focus of the present study, but we present basic summaries of genetic diversity and structure, as well as patterns of admixture into sub-Saharan African populations from cosmopolitan populations.
The observational results of the present study support the inference of Lieberman ([1998]).
Because the cross-sectional nature of the present study precludes any causal inferences, however, further studies using prospective designs are required to clarify these relationships.
The cross-sectional and correlational nature of the present study does not allow causal inferences.
