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Analysis of human genome variation may focus on one of two possible goals: understanding the genome region under study or solving historical and evolutionary questions specific to the population(s) analyzed. Understanding of variation of a given genome region has a genetic interest because it is a consequence of the dynamics of the genome and thus the evolutionary forces (mutation, selection in its varieties, drift, recombination, … ) may be understood. It is thus a way to understand the mechanisms that produce variation in the genome. On the other hand, when genetic variation is being analyzed, random individuals from specific populations offer the possibility to trace back their origin beyond the limitation of the genome region sampled. The goal then may be the evolutionary reconstitution of specific populations or, for a global sampling, the origin of our species. The underlying idea is very simple: if we are able to trace back the coalescence of genomic regions from an ample worldwide sample, we can infer the phylogeny of humans. The rationale can be sketched as follows: (i) The evolutionary dynamics of the genome region is known in pattern and tempo. (ii) From the extant variation the past can be inferred and the coalescence process reconstructed; in some cases just part of the genetic information is being used, and analyses do not fully exploit the information contained in the data. (iii) Translate the genetic process into a process of individuals that reproduce (the population), and the time and place of the ancestral individual (carrying the ancestral genome) may be recognized. (iv) If the geographic distribution of derivative genetic stages is known, the expansion process may be dissected as migratory waves and events. (v) The structure of the genetic variation may reveal demographic characteristics such as population size and subdivision as well as ancient …

Genome, diversity, and origins: The Y chromosome as a storyteller