Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome

Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci map ping on the nonrecombining portion of the human Y chromosome have been type d in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to charact erize the stable backgrounds or haplogroups of Y chromosomes that prevail i n this geographic region. Variation in the more rapidly mutating genetic ma rkers (STRs) has been used both to estimate the time to the most recent com mon ancestor for STR variability within these stable backgrounds and to exp lore whether STR differentiation among haplogroups still retains informatio n about their phylogeny. When analysis of molecular variance was used to st udy the apportionment of STR variation among both genetic backgrounds (i.e. , those defined by haplogroups) and population backgrounds, we found STR va riability to be clearly structured by haplogroups. More than 80% of the gen etic variance was found among haplogroups, whereas only 3.72% of the geneti c variation could be attributed to differences among populations-that is, g enetic variability appears to be much more structured by lineage than by po pulation. This was confirmed when two population samples from the Iberian P eninsula were added to the analysis. The deep structure of the genetic vari ation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population m ay be better understood as an association of lineages from a deep and popul ation-independent gene genealogy, rather than as a complete evolutionary un it.