AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 139:23–34 (2009) Human DNA Sequences: More Variation and Less Race Jeffrey C. Long,1* Jie Li,1 and Meghan E. Healy2 1Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618 2Department of Anthropology, University of New Mexico, Albuquerque, NM 87131 KEY WORDS race; DNA sequence; short tandem repeat; diversity; hierachical models ABSTRACT Interest in genetic diversity within and sity is one of nested subsets, such that the diversity in between human populations as a way to answer questions non-Sub-Saharan African populations is essentially a sub- about race has intensified in light of recent advances in set of the diversity found in Sub-Saharan African popula- genome technology. The purpose of this article is to apply tions. The actual pattern of DNA diversity creates some a method of generalized hierarchical modeling to two unsettling problems for using race as meaningful genetic DNA data sets. The first data set consists of a small sam- categories. For example, the pattern of DNA diversity ple of individuals (n 5 32 total, from eight populations) implies that some populations belong to more than one who have been fully resequenced for 63 loci that encode a race (e.g., Europeans), whereas other populations do not total of 38,534 base pairs. The second data set consists of belong to any race at all (e.g., Sub-Saharan Africans). As a large sample of individuals (n 5 928 total, from 46 popu- Frank Livingstone noted long ago, the Linnean classifica- lations) who have been genotyped at 580 loci that encode tion system cannot accommodate this pattern because short tandem repeats. The results are clear and somewhat within the system a population cannot belong to more surprising. We see that populations differ in the amount than one named group within a taxonomic level. Am J of diversity that they harbor. The pattern of DNA diver- Phys Anthropol 139:23–34, 2009. VC 2009 Wiley-Liss, Inc. Richard Lewontin was the first researcher to apply study found that the component of allelic diversity measures of genetic variability within and between between major geographic regions accounted for only human populations to questions about human races 4.3% of the total. However, the study’s findings present (Lewontin, 1972). He found in an analysis of blood group us with a paradox because it was possible to use these and protein allele frequencies that relative to the total genotypes to classify individuals back to their regional diversity for our species, the within groups component is populations. Others have argued that Rosenberg and col- 85.4%, the component for populations within races is leagues should have measured STR diversity using a dif- 8.3%, and the interracial component is only 6.3%. On ferent statistic, and offer that their favored statistic this basis, Lewontin concluded that human races are of yields a higher component of diversity between major ge- virtually no genetic or taxonomic significance. His find- ographic regions, that is, 9.2% (Excoffier and Hamilton, ings have had lasting impact, and many later studies 2003). However, neither 4.3% nor 9.2% is very different produced similar results using a similar model of popula- from Lewontin’s 6.3%, and the high classification success tion structure with different sources of data and differ- in Rosenberg’s study is counter intuitive in comparison ent statistical methods (Michalakis and Excoffier, 1996; with all such measures of diversity. We must now judge Barbujani et al., 1997; Jorde et al., 2000; Romualdi taxonomic significance on a different basis than the com- et al., 2002; Li et al., 2008). ponent of diversity between populations. Geneticists have renewed their interest in the variabil- We know less about the pattern of diversity for non- ity within and between groups in light of advances in ge- repeated DNA sequences; however, studies reporting on nome technology (Bamshad et al., 2003; Burchard et al., DNA sequence diversity in noncoding autosomal genomic 2003; Cooper et al., 2003). Our current methods in genomics have several advantages relative to the meth- ods of the 1970s. They reveal exact DNA sequence changes, can yield data in amounts that were unimagin- Additional Supporting Information may be found in the online able even a few decades ago, and allow us to make com- version of this article. parisons across related species. There is no ascertain- Grant sponsor: The National Science Foundation; Grant number: ment bias associated with the patterns of diversity NSF 0321610; Grant sponsor: The University of Michigan Endow- detected in DNA sequencing studies (Clark et al., 2005; ment for Biological Sciences. Keinan et al., 2007), whereas the patterns of diversity in single nucleotide polymorphism (SNP) marker studies *Correspondence to: Jeffrey C. Long, Department of Human reflect the methods of SNP discovery as well as evolu- Genetics, University of Michigan, Ann Arbor, MI 48109, USA. tionary differences between populations. Studies at the E-mail: [email protected] DNA level are providing new insights into genetic diver- sity within and between human populations. Received 31 March 2008; accepted 2 December 2008 Rosenberg and colleagues analyzed 377 short tandem repeat (STR) DNA loci in a sample of 1,052 people DOI 10.1002/ajpa.21011 (Rosenberg et al., 2002). These individuals came from 52 Published online 18 February 2009 in Wiley InterScience populations with locations throughout the world. This (www.interscience.wiley.com). VC 2009 WILEY-LISS, INC. 24 J.C. LONG ET AL. regions are now emerging (Yu et al., 2002; Fischer et al., Long and colleagues showed that partitioning diversity 2006; Wall et al., 2008). These studies tend to utilize into within and between groups components is sensitive small samples of individuals that are limited in their ge- to a host of a priori assumptions (Urbanek et al., 1996; ographic coverage. Nonetheless, these studies have pro- Long and Kittles, 2003). First, the expected diversity is vided provocative results. the same within all populations sampled. Second, the Yu and colleagues collected DNA sequences comprising expected diversity between any pair of populations 25,000 nucleotides for each member in a sample of 30 within a region is the same, regardless of the region. individuals (Yu et al., 2002). These 25,000 nucleotides Third, the expected diversity between any pair of popu- represent 50 autosomal loci each composed of 500 con- lations in different regions is the same, regardless of the tiguous base pairs. Ten of these individuals were Afri- pair of regions. When these assumptions are violated, can, 10 Asian, and 10 European. The investigators the total diversity is underestimated, the component of selected individuals from each continent from different diversity within groups is over-estimated, and the com- local groups residing in widely spaced regions, but only ponent of diversity between groups is underestimated. a single person represented each local group. This sam- Long and Kittles found that some human groups are far pling scheme extricates the between region component of more diverged than would be implied by standard com- nucleotide diversity but it confounds the diversity within ponents of genetic diversity, whereas other groups are populations with that between populations within the much less diverged (Long and Kittles, 2003). same region. The unexpected result from this study is The present study revisits the question of genetic di- that nucleotide diversity is greater between two African versity within and between populations. We provide new DNA sequences than between an African DNA sequence data from direct DNA sequencing of 63 noncoding loci. and a European DNA sequence, or an African DNA The total sequence length summed over all loci is 38,534 sequence and an Asian DNA sequence. Thus, in compar- base pairs. We analyze a total sample of 32 people, ing the African sample to the European sample or the which despite its small size, has multiple individuals Asian sample, the estimated between groups diversity from eight local populations and multiple local popula- component is negative. tions from Africa, Europe, and Asia. We also analyze a Fischer and colleagues (Fischer et al., 2006) analyzed large set of STR data for 46 populations from Africa, DNA sequences comprising 22,401 nucleotides collected Europe, and Asia. These STR data are from the CEPH by Voight and colleagues (Voight et al., 2005) for each diversity panel (Rosenberg et al., 2002), with the addi- member in a sample of 45 individuals. These 22,401 nu- tion of a sample from the Gujarati of India (Rosenberg cleotides represent 26 autosomal loci each composed of et al., 2006). Our strategy is as follows. First, for our 860 contiguous base pairs. This sample includes 15 DNA sequence data, we estimate components of diversity individuals from each of three human populations: at the same levels of hierarchical population structure Hausa, Italian, and Han Chinese. This sampling scheme that Lewontin did (Lewontin, 1972). Second, we use an provides a valid estimate of nucleotide diversity within expanded hierarchical arrangement of populations to see populations, but it confounds the diversity for popula- i) if this arrangement achieves a significantly better fit tions within geographic regions with the diversity to the data than does Lewontin’s arrangement, and ii) to between geographic regions. These researchers found see whether this arrangement alters Lewontin’s conclu- that the diversity between populations (including both sions about the apportionment of diversity within and components) ranged from 9 to 15%, depending on the between human populations. Third, we repeat the first pair of populations being compared. The interesting fea- two steps of the analysis using the STR loci. The impor- ture of this study is that Fischer and colleagues went on tant question is—Are the patterns of nucleotide diversity to sequence the homologous loci in multiple samples that we observe for DNA sequences in eight populations from two species of great apes.