Still Not the Same: Human Genetic Variation on the Rise
In doing so, the scientists estimate that humans generally share 99% of the genome, rather than the 99.9% of the genome that is traditionally claimed to be held in common. This PLOS Biology study appears to be quite detailed and comprehensive, in terms of what the scientists were looking for.
Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants.Full text here
Previous CNV mapping has suggested that human genomes may vary by as much as 10% (rather than the above estimation of 1% from the PLOS study).
UPDATE: The authors did take a cursory look at CNVs in the assembly. But they were looking for more "micro-variations" rather than CNV variations at a higher level of analysis. This difference in "logical levels" of ways of grouping data can be confusing. Future research should clarify any confusion, however.
Comparing the method behind the 10% estimate with the method behind the 1% estimate is like comparing apples to oranges. But in terms of real world significance in describing behavioural and other phenotypic differences between populations (and within populations), it will almost certainly be fruitful for future research to look at all sources of variation.
Human civilisations and cultures vary significantly from population to population. The underlying reasons for these significant differences are a matter for debate. All of the many conflicting books, articles, theses, etc. seeking to explain the relative prosperity and productivity of different cultures and populations illustrates the huge distances between premises and philosophies of the humans who attempt to explain "why some populations are wealthy and intellectually prodigious, and why some are impoverished and intellectually moribund."