Deborah A. Bolnick

Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans

American Beauty Modern Native American ancestry traces back to an East Asian migration across Beringia. However, some Native American skeletons from the late Pleistocene show phenotypic characteristics more similar to other, more geographically distant, human populations. Chatters et al. (p. 750) describe a skeleton with a Paleoamerican phenotype from the eastern Yucatan, dating to approximately 12 to 13 thousand years ago, with a relatively common extant Native American mitochondrial DNA haplotype. The Paleoamerican phenotype may thus have evolved independently among Native American populations. The differences between Paleoamericans and Native Americans likely resulted from local evolution. Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

Ancient DNA perspectives on American colonization and population history.

Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.

Opsin gene polymorphism predicts trichromacy in a cathemeral lemur

Recent research has identified polymorphic trichromacy in three diurnal strepsirrhines: Coquerels sifaka (Propithecus coquereli), black and white ruffed lemurs (Varecia variegata), and red ruffed lemurs (V. rubra). Current hypotheses suggest that the transitions to diurnality experienced by Propithecus and Varecia were necessary precursors to their independent acquisitions of trichromacy. Accordingly, cathemeral lemurs are thought to lack the M/L opsin gene polymorphism necessary for trichromacy. In this study, the M/L opsin gene was sequenced in ten cathemeral blue‐eyed black lemurs (Eulemur macaco flavifrons). This analysis identified a polymorphism identical to that of other trichromatic strepsirrhines at the critical amino acid position 285 in exon 5 of the M/L opsin gene. Thus, polymorphic trichromacy is likely present in at least one cathemeral Eulemur species, suggesting that strict diurnality is not necessary for trichromacy. The presence of trichromacy in E. m. flavifrons suggests that a re‐evaluation of current hypotheses regarding the evolution of strepsirrhine trichromacy may be necessary. Although the M/L opsin polymorphism may have been independently acquired three times in the lemurid–indriid clade, the distribution of opsin alleles in lemurids and indriids may also be consistent with a common origin of trichromacy in the last common ancestor of either the lemurids or the lemurid–indriid clade. Am. J. Primatol. 71:86–90, 2009.

Problematic Use of Greenberg's Linguistic Classification of the Americas in Studies of Native American Genetic Variation

To the Editor: In recent years, there has been a burgeoning interest in comparisons of genetic and linguistic variation across human populations. This synthetic approach can be a powerful tool for reconstructing human prehistory, but only when the patterns of genetic and linguistic variation are accurately represented (Szathmary 1993). If one or both patterns are inaccurate, the resulting conclusions about human prehistory or gene-language correlations may be incorrect. Here, we present evidence that comparisons of genetic and linguistic variation in the Americas are problematic when they are based on Greenberg’s (1987) classification of Native American languages, for these very reasons. Greenberg (1987) argued that all Native American languages, except those of the “Na-Dene” and Eskimo-Aleut groups, are similar and can be classified into a single linguistic unit, which he called “Amerind.” His tripartite classification (Amerind, Na-Dene, and Eskimo-Aleut) was based on the method of multilateral comparison, which examines many languages simultaneously to detect similarities in a small number of basic words and grammatical elements (Greenberg 1987). Greenberg (1987) also suggested that his three language groupings represent three separate migrations to the Americas, and Greenberg et al. (1986) interpreted their synthesis of the linguistic, dental, and genetic evidence as supportive of this three-migration hypothesis. Over the past 18 years, this three-migration model has become entrenched in the genetics literature as the hypothesis against which new genetic data are tested (e.g., Torroni et al. 1993; Merriwether et al. 1995; Zegura et al. 2004), and Greenberg’s linguistic classification has been the primary scheme used in studies comparing genetic and linguistic variation in the Americas. Of 100 studies of Native American genetic variation published between 1987 and 2004, 61 cite Greenberg (1987) or Greenberg et al. (1986), and at least 19 others were influenced by his tripartite classification (15 studies use the Amerind, Na-Dene, and Eskimo-Aleut groupings, and 4 others use the similar language groupings of Greenberg’s student M. Ruhlen.) Whereas Greenberg’s classification has been widely and uncritically used by human geneticists, it has been rejected by virtually all historical linguists who study Native American languages. There are many errors in the data on which his classification is based (Goddard 1987; Adelaar 1989; Berman 1992; Kimball 1992; Poser 1992), and Greenberg’s criteria for determining linguistic relationships are widely regarded as invalid. His method of multilateral comparison assembled only superficial similarities between languages, and Greenberg did not distinguish similarities due to common ancestry (i.e., homology) from those due to other factors (which other linguists do). Linguistic similarities can also be due to factors such as chance, borrowing from neighboring languages, and onomatopoeia, so proposals of remote linguistic relationships are only plausible when these other possible explanations have been eliminated (Matisoff 1990; Mithun 1990; Goddard and Campbell 1994; Campbell 1997; Ringe 2000). Greenberg made no attempt to eliminate such explanations, and the putative long-range similarities he amassed appear to be mostly chance resemblances and the result of misanalysis—he compared many languages simultaneously (which increases the probability of finding chance resemblances), examined arbitrary segments of words, equated words with very different meanings (e.g., excrement, night, and grass), failed to analyze the structure of some words and falsely analyzed that of others, neglected regular sound correspondences between languages, and misinterpreted well-established findings (Chafe 1987; Bright 1988; Campbell 1988, 1997; Golla 1988; Goddard 1990; Rankin 1992; McMahon and McMahon 1995; Nichols and Peterson 1996). Consequently, empirical studies have shown that “the method of multilateral comparison fails every test; its results are utterly unreliable. Multilateral comparison is worse than useless: it is positively misleading, since the patterns of ‘evidence’ that it adduces in support of proposed linguistic relationships are in many cases mathematically indistinguishable from random patterns of chance resemblances” (Ringe 1994, p. 28; cf. Ringe 2002). Because of these problems, Greenberg’s methodology has proven incapable of distinguishing plausible proposals of linguistic relationships from implausible ones, such as Finnish-Amerind (Campbell 1988). Thus, specialists in Native American linguistics insist that Greenberg’s methodology was so flawed that it completely invalidates his conclusions about the unity of Amerind, and Greenberg himself estimated that 80%–90% of linguists agreed with this assessment (Lewin 1988). Given this, the use of Greenberg’s (1987) classification can confound attempts to understand the relationship between genetic and linguistic variation in the Americas. Many studies of Native American genetic variation continue to use this classification (e.g., Bortolini et al. 2002, 2003; Fernandez-Cobo et al. 2002; Lell et al. 2002; Gomez-Casado et al. 2003; Zegura et al. 2004). However, Hunley and Long (2004) recently showed that there is a poor fit between Greenberg’s classification and the patterns of Native American mtDNA variation. On the basis of their findings, we believe that Greenberg’s groupings should no longer be used in analyses of mtDNA variation. To further evaluate how the use of this classification influences our understanding of the relationship between genetic and linguistic variation in the Americas, we examined how well different linguistic classifications “explain” the patterns of Native American Y-chromosome variation. Data were compiled on the Y-chromosome haplogroups of 523 Native Americans, representing 36 populations (table 1). We compared hierarchical analyses of molecular variance (AMOVAs), using Greenberg’s (1987) classification and a more conservative one (Campbell 1997) that is widely accepted by specialists in historical linguistics of Native American languages (Golla 2000; Hill and Hill 2000). The AMOVAs were based on population frequencies of the haplogroups known to be pre–European contact Native American lineages (Q-M19, Q-M3*, Q-M242*, and C-M130). All calculations were performed by Arlequin 2.000 (Schneider et al. 2000). Table 1 Populations and Language Classifications Used in AMOVAs The AMOVAs show that differences among Greenberg’s three groups could account for some genetic variance (ΦCT=0.319; P=.027), but the more generally accepted linguistic classification (as given in Campbell [1997]) of the same populations (17 groups) explainsa greater proportion of the total genetic variance (ΦCT=0.448; P<.001). The magnitude of ΦCT increases 40.4% when the accepted language classification is used, which indicates that it is important to consider language classifications other than that of Greenberg (1987) when evaluating the relationship between genes and language in the Americas. Other factors, such as geography, have likely influenced patterns of genetic variation more than language, but accepted language groupings should, nonetheless, be used when exploring these relationships. Thus, in future studies comparing genetic and linguistic variation in the Americas, we recommend use of the consensus linguistic classification, as given in Campbell (1997), Goddard (1996), and Mithun (1999), rather than Greenberg’s tripartite classification (Greenberg et al. 1986; Greenberg 1987). In addition, since there is no legitimate reason to believe that “Amerind” is a unified group (linguistic or otherwise), it has been essentially abandoned in linguistics and should not be used in genetic analyses. Finally, because synthetic studies provide such important insights into human prehistory, we advocate continued collaboration between geneticists and linguists (and other anthropologists) to ensure accurate comparisons of genetic, linguistic, and cultural variation.

The Illusive Gold Standard in Genetic Ancestry Testing

New regulations on disclosure, authority, and responsibility would shape how genetic ancestry tests are used. Genetic ancestry testing is being applied in areas as diverse as forensics, genealogical research, immigration control, and biomedical research (1–3). Use of ancestry as a potential risk factor for disease is entrenched in clinical decision-making (4), so it is not surprising that techniques to determine genetic ancestry are increasingly deployed to identify genetic variants associated with disease and drug response (5). Recently, direct-to-consumer (DTC) personal genomics companies have used ancestry information to calculate individual risk profiles for a range of diseases and traits.

Nocturnal Light Environments Influence Color Vision and Signatures of Selection on the OPN1SW Opsin Gene in Nocturnal Lemurs

Although loss of short-wavelength-sensitive (SWS) cones and dichromatic color vision in mammals has traditionally been linked to a nocturnal lifestyle, recent studies have identified variation in selective pressure for the maintenance of the OPN1SW opsin gene (and thus, potentially dichromacy) among nocturnal mammalian lineages. These studies hypothesize that purifying selection to retain SWS cones may be associated with a selective advantage for nocturnal color vision under certain ecological conditions. In this study, we explore the effect of nocturnal light environment on OPN1SW opsin gene evolution in a diverse sample of nocturnal lemurs (106 individuals, 19 species, and 5 genera). Using both phylogenetic and population genetic approaches, we test whether species from closed canopy rainforests, which are impoverished in short-wavelength light, have experienced relaxed selection compared with species from open canopy forests. We identify clear signatures of differential selection on OPN1SW by habitat type. Our results suggest that open canopy species generally experience strong purifying selection to maintain SWS cones. In contrast, closed canopy species experience weaker purifying selection or a relaxation of selection on OPN1SW. We also found evidence of nonfunctional OPN1SW genes in all Phaner species and in Cheirogaleus medius, implying at least three independent losses of SWS cones in cheirogaleids. Our results suggest that the evolution of color vision in nocturnal lemurs has been influenced by nocturnal light environment.

Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA.

Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis.

Migration and social structure among the hopewell: evidence from ancient DNA

For more than a century, archaeologists have studied the cultural and skeletal remains of the prehistoric Native Americans known as the “Hopewell Moundbuilders.” While many aspects of the Hopewell phenomenon are now well understood, questions still remain about the genetic makeup, burial practices, and social structure of Hopewell communities. To help answer these questions, we extracted mitochondrial DNA (mtDNA) from the skeletal remains of 39 individuals buried at the Pete Klunk Mound Group in Illinois. The pattern of mtDNA variation at this site suggests that matrilineal relationships did not strongly influence burial practices. Because different forms of mortuary activity were not associated with distinct genetic lineages, this study provides no evidence of a maternally inherited or ascribed status system in this society. The genetic data collected here also help clarify another aspect of Illinois Hopewell social structure by suggesting a matrilocal system of post-marital residence. Finally, when these data were considered in conjunction with mtDNA data previously collected from the Hopewell Mound Group in Ohio (Mills 2003), they demonstrated that migration and gene flow did accompany the cultural exchange between Hopewell communities in the Illinois and Ohio Valleys.

Clines Without Classes: How to Make Sense of Human Variation

This article examines Shiao, Bode, Beyer, and Selvig’s (2012) arguments in their article “The Genomic Challenge to the Social Construction of Race” and finds that their claims are based on fundamentally flawed interpretations of current genetic research. We discuss current genomic and genetic knowledge about human biological variation to demonstrate why and how Shiao et al.’s recommendations for future sociological studies and social policy, based on their inadequate understanding of genomic methods and evidence, are similarly flawed and will lead sociology astray.

The genetic impact of aztec imperialism: Ancient mitochondrial DNA evidence from Xaltocan, Mexico

In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the sites conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocans demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the sites conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan.