Dairying, diseases and the evolution of lactase persistence in Europe.

In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions2,3. Here we provide detailed distributions of milk exploitation across Europe over the past 9,000 years using around 7,000 pottery fat residues from more than 550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Notably, LP selection varying with levels of prehistoric milk exploitation is no better at explaining LP allele frequency trajectories than uniform selection since the Neolithic period. In the UK Biobank4,5 cohort of 500,000 contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests that other reasons for the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available but, under conditions of famine and/or increased pathogen exposure, this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitation-proxies for these drivers-provide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.

Ornamental plant domestication by aesthetics-driven human cultural niche construction.

Unlike plants that were domesticated to secure food, the domestication and breeding of ornamental plants are driven by aesthetic values. Here, we examine the major elements of the extended evolutionary synthesis (EES) theory that bridges the gap between the biology of ornamental plant domestication and the sociocultural motivations behind it. We propose that it involves specific elements of cumulative cultural evolution (CCE), plant gene-human culture coevolution (PGHCC), and niche construction (NC). Moreover, ornamental plant domestication represents an aesthetics-driven dimension of human niche construction that coevolved with socioeconomic changes and the adoption of new scientific technologies. Initially functioning as symbolic and aesthetic assets, ornamental plants became globally marketed material commodities as a result of the co-dependence of human CCE and prestige-competition motivations.

Archaeology, demography and life history theory together can help us explain past and present population patterns.

Population matters. Demographic patterns are both a cause and a consequence of human behaviour in other important domains, such as subsistence, cooperation, politics and culture. Demographers interested in contemporary and recent historical populations have rich data at their fingertips; the importance of demography means many interested parties have gathered demographic data, much of which is now readily available for all to explore. Those interested in the demography of the distant past are not so fortunate, given the lack of written records. Nevertheless, the emergence in recent years of a new interest in the demography of ancient populations has seen the development of a range of new methods for piecing together archaeological, skeletal and DNA evidence to reconstruct past population patterns. These efforts have found evidence in support of the view that the relatively low long-term population growth rates of prehistoric human populations, albeit ultimately conditioned by carrying capacities, may have been owing to 'boom-bust' cycles at the regional level; rapid population growth, followed by population decline. In fact, this archaeological research may have come to the same conclusion as some contemporary demographers: that demography can be remarkably hard to predict, at least in the short term. It also fits with evidence from biology that primates, and particularly humans, may be adapted to environmental variability, leading to associated demographic stochasticity. This evidence of the fluctuating nature of human demographic patterns may be of considerable significance in understanding our species' evolution, and of understanding what our species future demographic trajectories might be. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.

Food Income and the Evolution of Forager Mobility.

Forager mobility tends to be high, although ethnographic studies indicate ecological factors such as resource abundance and reliability, population density and effective temperature influence the cost-to-benefit assessment of movement decisions. We investigate the evolution of mobility using an agent-based and spatially explicit cultural evolutionary model that considers the feedback between foragers and their environment. We introduce Outcomes Clustering, an approach to categorizing simulated system states arising from complex stochastic processes shaped by multiple interacting parameters. We find that decreased mobility evolves under conditions of high resource replenishment and low resource depletion, with a concomitant trend of increased population density and, counter-intuitively, decreased food incomes. Conversely, increased mobility co-occurs with lower population densities and higher food incomes. We replicate the well-known relationships between mobility, population density, and resource quality, while predicting reduced food income, and consequently the reduction in health status observed in early sedentary populations without the need to invoke factors such as reduced diet quality or increased pathogen loads.

Holocene fluctuations in human population demonstrate repeated links to food production and climate.

We consider the long-term relationship between human demography, food production, and Holocene climate via an archaeological radiocarbon date series of unprecedented sampling density and detail. There is striking consistency in the inferred human population dynamics across different regions of Britain and Ireland during the middle and later Holocene. Major cross-regional population downturns in population coincide with episodes of more abrupt change in North Atlantic climate and witness societal responses in food procurement as visible in directly dated plants and animals, often with moves toward hardier cereals, increased pastoralism, and/or gathered resources. For the Neolithic, this evidence questions existing models of wholly endogenous demographic boom-bust. For the wider Holocene, it demonstrates that climate-related disruptions have been quasi-periodic drivers of societal and subsistence change.

Revealing patterns of cultural transmission from frequency data: equilibrium and non-equilibrium assumptions.

A long tradition of cultural evolutionary studies has developed a rich repertoire of mathematical models of social learning. Early studies have laid the foundation of more recent endeavours to infer patterns of cultural transmission from observed frequencies of a variety of cultural data, from decorative motifs on potsherds to baby names and musical preferences. While this wide range of applications provides an opportunity for the development of generalisable analytical workflows, archaeological data present new questions and challenges that require further methodological and theoretical discussion. Here we examine the decorative motifs of Neolithic pottery from an archaeological assemblage in Western Germany, and argue that the widely used (and relatively undiscussed) assumption that observed frequencies are the result of a system in equilibrium conditions is unwarranted, and can lead to incorrect conclusions. We analyse our data with a simulation-based inferential framework that can overcome some of the intrinsic limitations in archaeological data, as well as handle both equilibrium conditions and instances where the mode of cultural transmission is time-variant. Results suggest that none of the models examined can produce the observed pattern under equilibrium conditions, and suggest. instead temporal shifts in the patterns of cultural transmission.

European Neolithic societies showed early warning signals of population collapse.

Ecosystems on the verge of major reorganization-regime shift-may exhibit declining resilience, which can be detected using a collection of generic statistical tests known as early warning signals (EWSs). This study explores whether EWSs anticipated human population collapse during the European Neolithic. It analyzes recent reconstructions of European Neolithic (8-4 kya) population trends that reveal regime shifts from a period of rapid growth following the introduction of agriculture to a period of instability and collapse. We find statistical support for EWSs in advance of population collapse. Seven of nine regional datasets exhibit increasing autocorrelation and variance leading up to collapse, suggesting that these societies began to recover from perturbation more slowly as resilience declined. We derive EWS statistics from a prehistoric population proxy based on summed archaeological radiocarbon date probability densities. We use simulation to validate our methods and show that sampling biases, atmospheric effects, radiocarbon calibration error, and taphonomic processes are unlikely to explain the observed EWS patterns. The implications of these results for understanding the dynamics of Neolithic ecosystems are discussed, and we present a general framework for analyzing societal regime shifts using EWS at large spatial and temporal scales. We suggest that our findings are consistent with an adaptive cycling model that highlights both the vulnerability and resilience of early European populations. We close by discussing the implications of the detection of EWS in human systems for archaeology and sustainability science.

Early Neolithic genomes from the eastern Fertile Crescent.

We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.

Early farmers from across Europe directly descended from Neolithic Aegeans.

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Size Reduction in Early European Domestic Cattle Relates to Intensification of Neolithic Herding Strategies.

Our analysis of over 28,000 osteometric measurements from fossil remains dating between c. 5600 and 1500 BCE reveals a substantial reduction in body mass of 33% in Neolithic central European domestic cattle. We investigate various plausible explanations for this phenotypic adaptation, dismissing climatic change as a causal factor, and further rejecting the hypothesis that it was caused by an increase in the proportion of smaller adult females in the population. Instead we find some support for the hypothesis that the size decrease was driven by a demographic shift towards smaller newborns from sub-adult breeding as a result of intensifying meat production strategies during the Neolithic.

A generative inference framework for analysing patterns of cultural change in sparse population data with evidence for fashion trends in LBK culture.

Cultural change can be quantified by temporal changes in frequency of different cultural artefacts and it is a central question to identify what underlying cultural transmission processes could have caused the observed frequency changes. Observed changes, however, often describe the dynamics in samples of the population of artefacts, whereas transmission processes act on the whole population. Here we develop a modelling framework aimed at addressing this inference problem. To do so, we firstly generate population structures from which the observed sample could have been drawn randomly and then determine theoretical samples at a later time t2 produced under the assumption that changes in frequencies are caused by a specific transmission process. Thereby we also account for the potential effect of time-averaging processes in the generation of the observed sample. Subsequent statistical comparisons (e.g. using Bayesian inference) of the theoretical and observed samples at t2 can establish which processes could have produced the observed frequency data. In this way, we infer underlying transmission processes directly from available data without any equilibrium assumption. We apply this framework to a dataset describing pottery from settlements of some of the first farmers in Europe (the LBK culture) and conclude that the observed frequency dynamic of different types of decorated pottery is consistent with age-dependent selection, a preference for 'young' pottery types which is potentially indicative of fashion trends.

Transition to farming more likely for small, conservative groups with property rights, but increased productivity is not essential.

Theories for the origins of agriculture are still debated, with a range of different explanations offered. Computational models can be used to test these theories and explore new hypotheses; Bowles and Choi [Bowles S, Choi J-K (2013) Proc Natl Acad Sci USA 110(22):8830-8835] have developed one such model. Their model shows the coevolution of farming and farming-friendly property rights, and by including climate variability, replicates the timings for the emergence of these events seen in the archaeological record. Because the processes modeled occurred a long time ago, it can be difficult to justify exact parameter values; hence, we propose a fitting to idealized outcomes (FIO) method to explore the model's parameter space in more detail. We have replicated the model of Bowles and Choi, and used the FIO method to identify complexities and interactions of the model previously unidentified. Our results indicate that the key parameters for the emergence of farming are group structuring, group size, conservatism, and farming-friendly property rights (lending further support to Bowles and Choi's original proposal). We also find that although advantageous, it is not essential that farming productivity be greater than foraging productivity for farming to emerge. In addition, we highlight how model behaviors can be missed when gauging parameter sensitivity via a fix-all-but-one variation approach.

The neolithic demographic transition in Europe: correlation with juvenility index supports interpretation of the summed calibrated radiocarbon date probability distribution (SCDPD) as a valid demographic proxy.

Analysis of the proportion of immature skeletons recovered from European prehistoric cemeteries has shown that the transition to agriculture after 9000 BP triggered a long-term increase in human fertility. Here we compare the largest analysis of European cemeteries to date with an independent line of evidence, the summed calibrated date probability distribution of radiocarbon dates (SCDPD) from archaeological sites. Our cemetery reanalysis confirms increased growth rates after the introduction of agriculture; the radiocarbon analysis also shows this pattern, and a significant correlation between both lines of evidence confirms the demographic validity of SCDPDs. We analyze the areal extent of Neolithic enclosures and demographic data from ethnographically known farming and foraging societies and we estimate differences in population levels at individual sites. We find little effect on the overall shape and precision of the SCDPD and we observe a small increase in the correlation with the cemetery trends. The SCDPD analysis supports the hypothesis that the transition to agriculture dramatically increased demographic growth, but it was followed within centuries by a general pattern of collapse even after accounting for higher settlement densities during the Neolithic. The study supports the unique contribution of SCDPDs as a valid demographic proxy for the demographic patterns associated with early agriculture.

Regional population collapse followed initial agriculture booms in mid-Holocene Europe.

Following its initial arrival in SE Europe 8,500 years ago agriculture spread throughout the continent, changing food production and consumption patterns and increasing population densities. Here we show that, in contrast to the steady population growth usually assumed, the introduction of agriculture into Europe was followed by a boom-and-bust pattern in the density of regional populations. We demonstrate that summed calibrated radiocarbon date distributions and simulation can be used to test the significance of these demographic booms and busts in the context of uncertainty in the radiocarbon date calibration curve and archaeological sampling. We report these results for Central and Northwest Europe between 8,000 and 4,000 cal. BP and investigate the relationship between these patterns and climate. However, we find no evidence to support a relationship. Our results thus suggest that the demographic patterns may have arisen from endogenous causes, although this remains speculative.

A non-equilibrium neutral model for analysing cultural change.

Neutral evolution is a frequently used model to analyse changes in frequencies of cultural variants over time. Variants are chosen to be copied according to their relative frequency and new variants are introduced by a process of random mutation. Here we present a non-equilibrium neutral model which accounts for temporally varying population sizes and mutation rates and makes it possible to analyse the cultural system under consideration at any point in time. This framework gives an indication whether observed changes in the frequency distributions of a set of cultural variants between two time points are consistent with the random copying hypothesis. We find that the likelihood of the existence of the observed assemblage at the end of the considered time period (expressed by the probability of the observed number of cultural variants present in the population during the whole period under neutral evolution) is a powerful indicator of departures from neutrality. Further, we study the effects of frequency-dependent selection on the evolutionary trajectories and present a case study of change in the decoration of pottery in early Neolithic Central Europe. Based on the framework developed we show that neutral evolution is not an adequate description of the observed changes in frequency.

Descent with modification and the archaeological record.

Recent years have seen major advances in our understanding of the way in which cultural transmission takes place and the factors that affect it. The theoretical foundations of those advances have been built by postulating the existence of a variety of different processes and deriving their consequences mathematically or by simulation. The operation of these processes in the real world can be studied through experiment and naturalistic observation. In contrast, archaeologists have an 'inverse problem'. For them the object of study is the residues of different behaviours represented by the archaeological record and the problem is to infer the microscale processes that produced them, a vital task for cultural evolution since this is the only direct record of past cultural patterns. The situation is analogous to that faced by population geneticists scanning large number of genes and looking for evidence of selection as opposed to drift, but more complicated for many reasons, not least the enormous variety of different forces that affect cultural transmission. This paper reviews the progress that has been made in inferring processes from patterns and the role of demography in those processes, together with the problems that have arisen.