Milk is a major food of global economic importance and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption and we identify individuals consuming cattle, sheep and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15^th century CE.

The genetic trait of lactase persistence (LP) is associated with at least five independent functional single nucleotide variants in a regulatory region about 14 kb upstream of the lactase gene [−13910*T (rs4988235), −13907*G (rs41525747), −13915*G (rs41380347), −14009*G (rs869051967) and −14010*C (rs145946881)]. These alleles have been inferred to have spread recently and present-day frequencies have been attributed to positive selection for the ability of adult humans to digest lactose without risk of symptoms of lactose intolerance. One of the inferential approaches used to estimate the level of past selection has been to determine the extent of haplotype homozygosity (EHH) of the sequence surrounding the SNP of interest. We report here new data on the frequencies of the known LP alleles in the ‘Old World’ and their haplotype lineages. We examine and confirm EHH of each of the LP alleles in relation to their distinct lineages, but also show marked EHH for one of the older haplotypes that does not carry any of the five LP alleles. The region of EHH of this (B) haplotype exactly coincides with a region of suppressed recombination that is detectable in families as well as in population data, and the results show how such suppression may have exaggerated haplotype-based measures of past selection.

The genetic trait of lactase persistence is attributable to allelic variants in an enhancer region upstream of the lactase gene, LCT. To date, five different functional alleles, −13910*T, −13907*G, −13915*G, −14009*G and −14010*C, have been identified. The co-occurrence of several of these alleles in Ethiopian lactose digesters leads to a pattern of sequence diversity characteristic of a ‘soft selective sweep’. Here we hypothesise that throughout Africa, where multiple functional alleles co-exist, the enhancer diversity will be greater in groups who are traditional milk drinkers than in non-milk drinkers, as the result of this sort of parallel selection. Samples from 23 distinct groups from 10 different countries were examined. Each group was classified ‘Yes ‘or ‘No’ for milk-drinking, and ethnicity, language spoken and geographic location were recorded. Predicted lactase persistence frequency and enhancer diversity were, as hypothesised, higher in the milk drinkers than the non-milk-drinkers, but this was almost entirely accounted for by the Afro-Asiatic language speaking peoples of east Africa. The other groups, including the ‘Nilo-Saharan language speaking’ milk-drinkers, show lower frequencies of LP and lower diversity, and there was a north-east to south-west decline in overall diversity. Amongst the Afro-Asiatic (Cushitic) language speaking Oromo, however, the geographic cline was not evident and the southern pastoralist Borana showed much higher LP frequency and enhancer diversity than the other groups. Together these results reflect the effects of parallel selection, the stochastic processes of the occurrence and spread of the mutations, and time depth of milk drinking tradition.

The Articulation of Genomics, Mestizaje, and Indigenous Identities in Chile: A Case Study of the Social Implications of Genomic Research in Light of Current Research Practices

Background: Despite its enormous health and social burden, there are limited published studies describing the epidemiology of violent deaths in Chile. We described violent mortality rate trends in Chile between 2001 and 2018, its current spatial distribution and ecological level correlates. Methods: A population-based study using publicly accessible data. We calculated age-adjusted mortality rates per 100,000 persons for sex, age, intention, and mechanism of death. Next, we used linear regression to estimate time trends for sex and intention. We then employed hierarchical Poisson analyses to model the spatial distribution across 345 municipalities and the influence of six ecological level variables. Results: The average rate of violent death in Chile between 2001 and 2018 was 15.9 per 100,000 people, with the majority (70.3%) of these attributed to suicide. Suffocation was the most common mechanism of death for suicide (82.3%) and cut/pierce for homicide (43.1%), followed by firearm (33.2%). Violent deaths are trending downward in Chile across all categories except suicides by women, which have remained stable. Poverty rates and urban population were positively associated with violent mortality rates. Conclusions: Although violence-related deaths seem to be decreasing, disparities across gender, age group, and geographic location may have continuing effects on mortality rates.

The genetic trait of lactase persistence (LP) evolved as an adaptation to milking pastoralism in the Old World and is a well‐known example of positive natural selection in humans. However, the specific mechanisms conferring this selective advantage are unknown. To understand the relationship between milk drinking, LP, growth, reproduction, and survival, communities of the Coquimbo Region in Chile, with recent adoption of milking agropastoralism, were used as a model population.DNA samples and data on stature, reproduction, and diet were collected from 451 participants. Lactose tolerance tests were done on 41 of them. The European −13,910*T(rs4988235) was the only LP causative variant found, showing strong association (99.6%) with LP phenotype.Models of associations of inferred LP status and milk consumption, with fertility, mortality, height, and weight were adjusted with measures of ancestry and relatedness to control for population structure. Although we found no statistically significant effect of LP on fertility, a significant effect (P = 0.002) was observed of LP on body mass index (BMI) in males and of BMI on fertility (P = 0.003). These results fail to support a causal relationship between LP and fertility yet suggest the idea of a nutritional advantage of LP. Furthermore, the proportion of European ancestry around the genetic region of −13,910*Tis significantly higher (P = 0.008) than the proportion of European ancestry genome‐wide, providing evidence of recent positive selection since European–Amerindian admixture. This signature was absent in nonpastoralist Latin American populations, supporting the hypothesis of specific adaptation to milking agropastoralism in the Coquimbo communities.