Kari Britt Schroeder

A private allele ubiquitous in the Americas

The three-wave migration hypothesis of Greenberg et al. has permeated the genetic literature on the peopling of the Americas. Greenberg et al. proposed that Na-Dene, Aleut-Eskimo and Amerind are language phyla which represent separate migrations from Asia to the Americas. We show that a unique allele at autosomal microsatellite locus D9S1120 is present in all sampled North and South American populations, including the Na-Dene and Aleut-Eskimo, and in related Western Beringian groups, at an average frequency of 31.7%. This allele was not observed in any sampled putative Asian source populations or in other worldwide populations. Neither selection nor admixture explains the distribution of this regionally specific marker. The simplest explanation for the ubiquity of this allele across the Americas is that the same founding population contributed a large fraction of ancestry to all modern Native American populations.

Evaluating the Farming/Language Dispersal Hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica

The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adop-tion of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA vari-ation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances (r = 0.33–0.384; P < 0.02), whereas mtDNA diversity correlates significantly with only geographic distance (r = 0.619; P = 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273–3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.

Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history.

In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.

A Maximum-Likelihood Method to Correct for Allelic Dropout in Microsatellite Data with No Replicate Genotypes

Allelic dropout is a commonly observed source of missing data in microsatellite genotypes, in which one or both allelic copies at a locus fail to be amplified by the polymerase chain reaction. Especially for samples with poor DNA quality, this problem causes a downward bias in estimates of observed heterozygosity and an upward bias in estimates of inbreeding, owing to mistaken classifications of heterozygotes as homozygotes when one of the two copies drops out. One general approach for avoiding allelic dropout involves repeated genotyping of homozygous loci to minimize the effects of experimental error. Existing computational alternatives often require replicate genotyping as well. These approaches, however, are costly and are suitable only when enough DNA is available for repeated genotyping. In this study, we propose a maximum-likelihood approach together with an expectation-maximization algorithm to jointly estimate allelic dropout rates and allele frequencies when only one set of nonreplicated genotypes is available. Our method considers estimates of allelic dropout caused by both sample-specific factors and locus-specific factors, and it allows for deviation from Hardy–Weinberg equilibrium owing to inbreeding. Using the estimated parameters, we correct the bias in the estimation of observed heterozygosity through the use of multiple imputations of alleles in cases where dropout might have occurred. With simulated data, we show that our method can (1) effectively reproduce patterns of missing data and heterozygosity observed in real data; (2) correctly estimate model parameters, including sample-specific dropout rates, locus-specific dropout rates, and the inbreeding coefficient; and (3) successfully correct the downward bias in estimating the observed heterozygosity. We find that our method is fairly robust to violations of model assumptions caused by population structure and by genotyping errors from sources other than allelic dropout. Because the data sets imputed under our model can be investigated in additional subsequent analyses, our method will be useful for preparing data for applications in diverse contexts in population genetics and molecular ecology.

Being there: A brief visit to a neighbourhood induces the social attitudes of that neighbourhood

There are differences between human groups in social behaviours and the attitudes that underlie them, such as trust. However, the psychological mechanisms that produce and reproduce this variation are not well understood. In particular, it is not clear whether assimilation to the social culture of a group requires lengthy socialization within that group, or can be more rapidly and reversibly evoked by exposure to the group’s environment and the behaviour of its members. Here, we report the results of a two-part study in two neighbourhoods of a British city, one economically deprived with relatively high crime, and the other affluent and lower in crime. In the first part of the study, we surveyed residents and found that the residents of the deprived neighbourhood had lower levels of social trust and higher levels of paranoia than the residents of the affluent neighbourhood. In the second part, we experimentally transported student volunteers who resided in neither neighbourhood to one or the other, and had them walk around delivering questionnaires to houses. We surveyed their trust and paranoia, and found significant differences according to which neighbourhood they had been sent to. The differences in the visitors mirrored the differences seen in the residents, with visitors to the deprived neighbourhood reporting lower social trust and higher paranoia than visitors to the affluent one. The magnitudes of the neighbourhood differences in the visitors, who only spent up to 45 min in the locations, were nearly as great as the magnitudes of those amongst the residents. We discuss the relevance of our findings to differential psychology, neighbourhood effects on social outcomes, and models of cultural evolution.

Variants at serotonin transporter and 2A receptor genes predict cooperative behavior differentially according to presence of punishment

Punishment of free-riding has been implicated in the evolution of cooperation in humans, and yet mechanisms for punishment avoidance remain largely uninvestigated. Individual variation in these mechanisms may stem from variation in the serotonergic system, which modulates processing of aversive stimuli. Functional serotonin gene variants have been associated with variation in the processing of aversive stimuli and widely studied as risk factors for psychiatric disorders. We show that variants at the serotonin transporter gene (SLC6A4) and serotonin 2A receptor gene (HTR2A) predict contributions to the public good in economic games, dependent upon whether contribution behavior can be punished. Participants with a variant at the serotonin transporter gene contribute more, leading to group-level differences in cooperation, but this effect dissipates in the presence of punishment. When contribution behavior can be punished, those with a variant at the serotonin 2A receptor gene contribute more than those without it. This variant also predicts a more stressful experience of the games. The diversity of institutions (including norms) that govern cooperation and punishment may create selective pressures for punishment avoidance that change rapidly across time and space. Variant-specific epigenetic regulation of these genes, as well as population-level variation in the frequencies of these variants, may facilitate adaptation to local norms of cooperation and punishment.

Local norms of cheating and the cultural evolution of crime and punishment: a study of two urban neighborhoods

The prevalence of antisocial behavior varies across time and place. The likelihood of committing such behavior is affected by, and also affects, the local social environment. To further our understanding of this dynamic process, we conducted two studies of antisocial behavior, punishment, and social norms. These studies took place in two neighborhoods in Newcastle Upon Tyne, England. According to a previous study, Neighborhood A enjoys relatively low frequencies of antisocial behavior and crime and high levels of social capital. In contrast, Neighborhood B is characterized by relatively high frequencies of antisocial behavior and crime and low levels of social capital. In Study 1, we used an economic game to assess neighborhood differences in theft, third-party punishment (3PP) of theft, and expectation of 3PP. Participants also reported their perceived neighborhood frequency of cooperative norm violation (“cheating”). Participants in Neighborhood B thought that their neighbors commonly cheat but did not condone cheating. They stole more money from their neighbors in the game, and were less punitive of those who did, than the residents of Neighborhood A. Perceived cheating was positively associated with theft, negatively associated with the expectation of 3PP, and central to the neighborhood difference. Lower trust in one’s neighbors and a greater subjective value of the monetary cost of punishment contributed to the reduced punishment observed in Neighborhood B. In Study 2, we examined the causality of cooperative norm violation on expectation of 3PP with a norms manipulation. Residents in Neighborhood B who were informed that cheating is locally uncommon were more expectant of 3PP. In sum, our results provide support for three potentially simultaneous positive feedback mechanisms by which the perception that others are behaving antisocially can lead to further antisocial behavior: (1) motivation to avoid being suckered, (2) decreased punishment of antisocial behavior, and (3) decreased expectation of punishment of antisocial behavior. Consideration of these mechanisms and of norm psychology will help us to understand how neighborhoods can descend into an antisocial culture and get stuck there.

Uses and limitations of genetic data relating to athapaskan migrations: A reply to seymour

We appreciate a number of the points that Seymour (2009) makes in her article, ‘‘Comments on genetic data relating to Athapaskan migrations: Implications of the Malhi et al. study for the Apache and Navajo.’’ As molecular anthropologists, we are aware that treating individuals sampled from linguistic or cultural groups as representatives of biological populations is an imperfect approximation to sampling biological populations. Moreover, as Seymour points out, it is dangerous to assume that a limited sampling from a subgroup is representative of the group as a whole, and we should have been more cautious about making inferences regarding all of Southern Athapaskan prehistory from a limited sample of the Navajo and Apache. We also agree with Seymour that, undoubtedly, our research would have benefited from closer interactions with archaeologists and/or Native Americans in the Southwest or Subarctic. Collecting genetic samples from Native American communities to investigate population prehistory can be a formidable challenge, because of the history of coloniza