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For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United States. We show that nine individuals buried in an elite crypt at Pueblo Bonito, the largest structure in the canyon, have identical mitochondrial genomes. Analyses of nuclear genome data from six samples with the highest DNA preservation demonstrate mother–daughter and grandmother–grandson relationships, evidence for a multigenerational matrilineal descent group. Together, these results demonstrate the persistence of an elite matriline in Chaco for ∼330 years. In ancient cultures without a writing system, it is difficult to infer the basis of status and rank. Here the authors analyse ancient DNA from nine presumed elite individuals buried successively over a 300-year period at Chaco Canyon, and show evidence of matrilineal relationships.

Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of “lifestyle” diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be “mismatched” and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit “genotype by environment” (GxE) interactions, with different health effects in “ancestral” versus “modern” environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the “matched” to “mismatched” spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.

The genusCucurbita(squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops’ progenitor species are scarce or unknown in the wild. We hypothesize that Holocene ecological shifts and megafaunal extinctions severely impacted wildCucurbita,whereas their domestic counterparts adapted to changing conditions via symbiosis with human cultivators. First, we used high-throughput sequencing to analyze complete plastid genomes of 91 totalCucurbitasamples, comprising ancient (n= 19), modern wild (n= 30), andmodern domestic (n= 42) taxa. This analysis demonstrates independent domestication in eastern North America, evidence of a previously unknown pathway to domestication in northeastern Mexico, and broad archaeological distributions of taxa currently unknown in the wild. Further, sequence similarity between distant wild populations suggests recent fragmentation. Collectively, these results point to wild-type declines coinciding with widespread domestication. Second, we hypothesize that the disappearance of large herbivores struck a critical ecological blow against wildCucurbita,and we take initial steps to consider this hypothesis through crossmammal analyses of bitter taste receptor gene repertoires. Directly, megafauna consumedCucurbitafruits and dispersed their seeds; wildCucurbitawere likely left without mutualistic dispersal partners in the Holocene because they are unpalatable to smaller surviving mammals with more bitter taste receptor genes. Indirectly, megafauna maintained mosaic-like landscapes ideal forCucurbita,and vegetative changes following the megafaunal extinctions likely crowded out their disturbed-ground niche. Thus, anthropogenic landscapes provided favorable growth habitats and willing dispersal partners in the wake of ecological upheaval.

Understanding the process of genetic adaptation in response to human-mediated ecological change will help elucidate the eco-evolutionary impacts of human activity. In the 1930s red imported fire ants ( Solenopsis invicta ) were accidently introduced to the Southeastern USA, where today they are both venomous predators and toxic prey to native eastern fence lizards ( Sceloporus undulatus ). Here, we investigate potential lizard adaptation to invasive fire ants by generating whole-genome sequences from 420 lizards across three populations: one with long exposure to fire ants, and two unexposed populations. Signatures of positive selection exclusive to the exposed population overlap immune system, growth factor pathway, and morphological development genes. Among invaded lizards, longer limbs (used to remove stinging ants) are associated with increased survival. We identify alleles associated with longer limbs that are highly differentiated from the unexposed populations, a pattern counter to the pre-invasion latitudinal cline for limb lengths based on museum specimens. While we cannot rule out other environmental differences between populations driving these patterns, these results do constitute plausible genetic adaptations in lizards invaded by fire ants. Red imported fire ants were accidently introduced to North America in the 1930s, since then imposing novel selective pressures on native ecosystems. This study identifies genomic signatures of recent adaptation in native eastern fence lizards potentially linked to exposure to these ants.

Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch 1 , 2 , 3 . This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis 4 . We found that copy number of the salivary amylase gene ( AMY1 ) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number–variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

Different human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example, hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The “pygmy” phenotype (small adult body size), characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent versus population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes of two pairs of populations: Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda and Andamanese rainforest hunter-gatherers and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the rainforest hunter-gatherers across the set of genes with “growth factor binding” functions (P < 0.001). Unexpectedly, for the rainforest groups, we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g., “cardiac muscle tissue development”; P = 0.001). We hypothesize that the growth hormone subresponsiveness likely underlying the adult small body-size phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations, we did not observe similar patterns of positive selection on sets of genes associated with growth or cardiac development, indicating our results most likely reflect a history of convergent adaptation to the similar ecology of rainforests rather than a more general evolutionary pattern.

Key Points Ancient DNA provides transformative insight into the history of human adaptation via the ability to directly track genetic variant frequency changes across space and time. Analyses of human, archaic hominin, and domesticated plant and animal ancient genomic data sets can each inform our understanding of past human evolution and behaviour. The number of published ancient genomic data sets is growing substantially each year, contributing expanded precision and power to evolutionary analyses based on these data. Human ancient genome data have already helped characterize the histories of biological adaptations to northern latitudes and cold climates, agriculture-associated dietary shifts, and a changing infectious disease landscape. After migrating out of Africa, ancient human populations acquired genetic variants conferring fitness advantages in Eurasian environments through adaptive introgression with archaic hominin populations who had already been inhabiting this region for hundreds of thousands of years. Ancient genome data reveal some substantial time lags between documented environmental or cultural changes and the appearance and spread of genetic variants associated with human biological adaptations, with possible implications for intervening human health and/or potential compensatory cultural behaviours. Ancient genomes can inform our understanding of the history of human adaptation through the direct tracking of changes in genetic variant frequency across different geographical locations and time periods. The authors review recent ancient DNA analyses of human, archaic hominin, pathogen, and domesticated animal and plant genomes, as well as the insights gained regarding past human evolution and behaviour. The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.

Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for UK Biobank individuals (~194,000 females and ~167,000 males) to identify a total of 114,199 single nucleotide polymorphisms (SNPs) significantly associated with at least one of the studied phenotypes in females, males, or both sexes (P<5x10 -8 ). From these loci we then identified 3,016 SNPs (2.6%) with significant differences in the strength of association between the female- and male-specific GWAS results at a low false-discovery rate (FDR<0.001). Genes with known roles in sexual differentiation are significantly enriched for co-localization with one or more of these SNPs versus SNPs associated with the phenotypes generally but not with sex differences (2.73-fold enrichment; permutation test; P = 0.0041). We also confirmed that the identified variants are disproportionately associated with greater phenotype effect sizes in the sex with the stronger association value. We then used the singleton density score statistic, which quantifies recent (within the last ~3,000 years; post-agriculture adoption in Britain) changes in the frequencies of alleles underlying polygenic traits, to identify a signature of recent positive selection on alleles associated with greater body fat percentage in females (permutation test; P = 0.0038; FDR = 0.0380), directionally opposite to that predicted by the sex differences reduction hypothesis. Otherwise, we found no evidence of positive selection for sex difference-associated alleles for any other trait. Overall, our results challenge the longstanding hypothesis that sex differences adaptively decreased following subsistence transitions from hunting and gathering to agriculture.

The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (F ST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and F ST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or F ST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior.

Researchers are divided about the relative importance of people versus climate in triggering the Late Holocene extinctions of the endemic large-bodied fauna on the island of Madagascar. Specifically, a dramatic and synchronous decline in arboreal pollen and increase in grass pollen ca 1000 yr ago has been alternatively interpreted as evidence for aridification, increased human activity, or both. As aridification and anthropogenic deforestation can have similar effects on vegetation, resolving which of these factors (if either) led to the demise of the megafauna on Madagascar has remained a challenge. We use stable nitrogen isotope (δ15N) values from radiocarbon-dated subfossil vertebrates to disentangle the relative importance of natural and human-induced changes. If increasing aridity were responsible for megafaunal decline, then we would expect an island-wide increase in δ15N values culminating in the highest values at the time of proposed maximum drought at ca 1000 yr ago. Alternatively, if climate were relatively stable and anthropogenic habitat alteration explains the palynological signal, then we would anticipate little or no change in habitat moisture, and no systematic, directional change in δ15N values over time. After accounting for the confounding influences of diet, geographic region, and coastal proximity, we find no change in δ15N values over the past 10 000 yr, and no support for a period of marked, geographically widespread aridification culminating 900–950 yr ago. Instead, increases in grasses at around that time may signal a transition in human land use to a more dedicated agro-pastoralist lifestyle, when megafaunal populations were already in decline. Land use changes ca 1000 yr ago would have simply accelerated the inevitable loss of Madagascar’s megafauna.