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’.     

Reconstructing the dynamics of ancient human populations from radiocarbon dates: 10 000 years of population growth in Australia

Measuring trends in the size of prehistoric populations is fundamental to our understanding of the demography of ancient people and their responses to environmental change. Archaeologists commonly use the temporal distribution of radiocarbon dates to reconstruct population trends, but this can give a false picture of population growth because of the loss of evidence from older sites. We demonstrate a method for quantifying this bias, and we use it to test for population growth through the Holocene of Australia. We used model simulations to show how turnover of site occupation across an archaeological landscape, interacting with erasure of evidence at abandoned sites, can create an increase in apparent site occupation towards the present when occupation density is actually constant. By estimating the probabilities of abandonment and erasure from archaeological data, we then used the model to show that this effect does not account for the observed increase in occupation through the Holocene in Australia. This is best explained by population growth, which was low for the first part of the Holocene but accelerated about 5000 years ago. Our results provide new evidence for the dynamism of non-agricultural populations through the Holocene.     

Population history and natural selection shape patterns of genetic variation in 132 genes

Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes. Although the signature that natural selection imparts on DNA sequence variation is difficult to disentangle from the effects of neutral processes such as population demographic history, selective and demographic forces can be distinguished by analyzing multiple loci dispersed throughout the genome. We studied the molecular evolution of 132 genes by comprehensively resequencing them in 24 African-Americans and 23 European-Americans. We developed a rigorous computational approach for taking into account multiple hypothesis tests and demographic history and found that while many apparent selective events can instead be explained by demography, there is also strong evidence for positive or balancing selection at eight genes in the European-American population, but none in the African-American population. Our results suggest that the migration of modern humans out of Africa into new environments was accompanied by genetic adaptations to emergent selective forces. In addition, a region containing four contiguous genes on Chromosome 7 showed striking evidence of a recent selective sweep in European-Americans. More generally, our results have important implications for mapping genes underlying complex human diseases.     

Possible congenital hemolytic anemia in prehistoric coastal inhabitants of Israel.

The spread of thalassemia among prehistoric populations of the Mediterranean Basin has been linked to the increased risk to early agriculturalists posed by the Plasmodium falciparum parasite. The diagnosis of the disease in human skeletal remains, however, has usually been based on a single pathological criterion, porotic hyperostosis. This paper reports on what we believe to be the earliest case of thalassemia yet identified in the prehistoric record. Our diagnosis of the disease in an individual from the submerged Prepottery Neolithic B village of Atlit-Yam off the Israeli coast is based on a pathological humerus demonstrating a pattern of deformation characteristic of clinical thalassemia. The implications of these findings for our understanding of human societies undergoing the transition from foraging to agriculture in the Near East are discussed.     

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.     

Evolution in stage-structured populations

For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande's theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price's theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations.     

海岱地区大汶口文化时期人口死亡年龄的统计分布特征

人口死亡年龄是揭示一个族群健康状况和社会经济条件的重要指标。本文根据海岱地区大汶口文化时期九个墓地人骨遗存的发掘报告,运用定量统计的方法检验了人口死亡年龄分布特征。发现该区大汶口文化时期人口的死亡年龄分布近似服从正态分布。最后探讨了造成人口低死亡年龄的可能原因,并给出了这一概率分布的数学意义以及在史前人口学中的应用前景。     

Cultural evolution and prehistoric demography

One prominent feature of human culture is that different populations have different tools, technologies and cultural artefacts, and these unique toolkits can also differ in size and complexity. Over the past few decades, researchers in the fields of prehistoric demography and cultural evolution have addressed a number of questions regarding variation in toolkit size and complexity across prehistoric and modern populations. Several factors have been proposed as possible explanations for this variation: in particular, the mobility of a population, the resources it uses, the volatility of its environment and the number of individuals in the population. Using a variety of methods, including empirical and ethnographic research, computational models and laboratory-based experiments, researchers have found disparate results regarding each hypothesis. These discordant findings have led to debate over the factors that most significantly influence toolkit size and composition. For instance, several computational, empirical and laboratory studies of food-producing populations have found a positive correlation between the number of individuals in a population and toolkit size, whereas similar studies of hunter–gatherer populations have found little evidence of such a link. In this paper, we conduct a comprehensive review of the literature in this field of study and propose corollaries and interdisciplinary approaches with the goal of reconciling dissimilar findings into a more comprehensive view of cultural toolkit variation.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.     

Migration in Archeology: The Baby and the Bathwater

Migration has been largely ignored by archeologists for the last two decades. Yet prehistoric demography and population studies are accepted as central concerns, and neither of these can be studied profitably without an understanding of migration. Recent books by Rouse and Renfrew have resurrected migration as a subject of serious analysis. It is proposed here that systems-oriented archeologists, in rejecting migration, have thrown out the baby with the bathwater. Traditional archeological approaches to migration fall short because a methodology for examining prehistoric migration must be dependent upon an understanding of the general structure of migration as a patterned human behavior. Aspects of such a structure are suggested and an application to a particular case in Eastern Europe is described.     

Human Migration Patterns in Yemen and Implications for Reconstructing Prehistoric Population Movements

Population migration has played an important role in human evolutionary history and in the patterning of human genetic variation. A deeper and empirically-based understanding of human migration dynamics is needed in order to interpret genetic and archaeological evidence and to accurately reconstruct the prehistoric processes that comprise human evolutionary history. Current empirical estimates of migration include either short time frames (i.e. within one generation) or partial knowledge about migration, such as proportion of migrants or distance of migration. An analysis of migration that includes both proportion of migrants and distance, and direction over multiple generations would better inform prehistoric reconstructions. To evaluate human migration, we use GPS coordinates from the place of residence of the Yemeni individuals sampled in our study, their birthplaces and their parents'' and grandparents'' birthplaces to calculate the proportion of migrants, as well as the distance and direction of migration events between each generation. We test for differences in these values between the generations and identify factors that influence the probability of migration. Our results show that the proportion and distance of migration between females and males is similar within generations. In contrast, the proportion and distance of migration is significantly lower in the grandparents'' generation, most likely reflecting the decreasing effect of technology. Based on our results, we calculate the proportion of migration events (0.102) and mean and median distances of migration (96 km and 26 km) for the grandparent''s generation to represent early times in human evolution. These estimates can serve to set parameter values of demographic models in model-based methods of prehistoric reconstruction, such as approximate Bayesian computation. Our study provides the first empirically-based estimates of human migration over multiple generations in a developing country and these estimates are intended to enable more precise reconstruction of the demographic processes that characterized human evolution.     

Demographic uniformitarianism: the theoretical basis of prehistoric demographic research and its cross-disciplinary challenges

A principle of demographic uniformitarianism underpins all research into prehistoric demography (palaeodemography). This principle—which argues for continuity in the evolved mechanisms underlying modern human demographic processes and their response to environmental stimuli between past and present—provides the cross-disciplinary basis for palaeodemographic reconstruction and analysis. Prompted by the recent growth and interest in the field of prehistoric demography, this paper reviews the principle of demographic uniformitarianism, evaluates how it relates to two key debates in palaeodemographic research and seeks to delimit its range of applicability to past human and hominin populations.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.     

Habitat saturation and the spatial evolutionary ecology of altruism

Under which ecological conditions should individuals help their neighbours? We investigate the effect of habitat saturation on the evolution of helping behaviours in a spatially structured population. We combine the formalisms of population genetics and spatial moment equations to tease out the effects of various physiological (direct benefits and costs of helping) and ecological parameters (such as the density of empty sites) on the selection gradient on helping. Our analysis highlights the crucial importance of demography for the evolution of helping behaviours. It shows that habitat saturation can have contrasting effects, depending on the form of competition (direct vs. indirect competition) and on the conditionality of helping. In our attempt to bridge the gap between spatial ecology and population genetics, we derive an expression for relatedness that takes into account both habitat saturation and the spatial structure of genetic variation. This analysis helps clarify discrepancies in the results obtained by previous theoretical studies. It also provides a theoretical framework taking into account the interplay between demography and kin selection, in which new biological questions can be explored.     

Summed Probability Distribution of 14C Dates Suggests Regional Divergences in the Population Dynamics of the Jomon Period in Eastern Japan

Recent advances in the use of summed probability distribution (SPD) of calibrated ¹⁴C dates have opened new possibilities for studying prehistoric demography. The degree of correlation between climate change and population dynamics can now be accurately quantified, and divergences in the demographic history of distinct geographic areas can be statistically assessed. Here we contribute to this research agenda by reconstructing the prehistoric population change of Jomon hunter-gatherers between 7,000 and 3,000 cal BP. We collected 1,433 ¹⁴C dates from three different regions in Eastern Japan (Kanto, Aomori and Hokkaido) and established that the observed fluctuations in the SPDs were statistically significant. We also introduced a new non-parametric permutation test for comparing multiple sets of SPDs that highlights point of divergences in the population history of different geographic regions. Our analyses indicate a general rise-and-fall pattern shared by the three regions but also some key regional differences during the 6^th millennium cal BP. The results confirm some of the patterns suggested by previous archaeological studies based on house and site counts but offer statistical significance and an absolute chronological framework that will enable future studies aiming to establish potential correlation with climatic changes.     

Modern human origins and prehistoric demography of Europe in light of the present-day genetic diversity

Dynamic advance in DNA sequencing methods and progress in formal population genetics analyses made it possible to infer aspects of human evolution from the DNA diversity distribution and frequency in contemporary populations. While providing some general background concerning the origins of modern human, this paper focuses on the dynamics of prehistoric population in Europe. The relevance of the present-day genetic diversity studies in elucidating prehistoric events is presented in the context of archeological and paleoanthropological evidence. The questions of the Neanderthal admixture as well as of the relative contribution of different waves of prehistoric migrations to the gene pool of modern Europeans are discussed.     

LDJump: Estimating variable recombination rates from population genetic data

As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits demography to be taken into account. It uses several summary statistics within a regression model fitted on suitable scenarios. Our proposed method is accurate, computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate. An application to human genome data suggests a good congruence between our estimated and experimentally identified hotspots. Our method is implemented in the R ‐package LDJump, which is freely available at https://github.com/PhHermann/LDJump .     

Signature of recent historical events in the European Y-chromosomal STR haplotype distribution

Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.L. Roewer and P.J.P. Croucher contributed equally to this paper.This revised version was published online in February 2005 with corrections to the addresses of the authors of the Forensic Y-Chromosome Research Group.     

Population density and size facilitate interactive capacity and the rise of the state

Radiocarbon summed probability distribution (SPD) methods promise to illuminate the role of demography in shaping prehistoric social processes, but theories linking population indices to social organization are still uncommon. Here, we develop Power Theory, a formal model of political centralization that casts population density and size as key variables modulating the interactive capacity of political agents to construct power over others. To evaluate this argument, we generated an SPD from 755 radiocarbon dates for 10 000–1000 BP from Central, North Central and North Coast Peru, a period when Peruvian political form developed from ‘quasi-egalitarianism’ to state levels of political centralization. These data are congruent with theoretical expectations of the model but also point to an artefactual distortion previously unremarked in SPD research.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.     

Inference with selection,varying population size,and evolving population structure: application of ABC to a forward–backward coalescent process with interactions

Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed a priori known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interactions and asexual reproduction. We develop an inferential procedure for ecological, demographic, and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated data from a toy model, and to real data by analyzing the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia human populations in order to test whether different social organizations show significantly different fertilities.Subject terms: Genetic variation, Phylogenetics, Ecological genetics     

新石器时代关中地区人类生业模式演变的生物考古学证据

农业的起源与发展,改变了人类食物资源的获取方式。作为史前文化发展的中心,关中地区史前人类生业模式演变规律与影响因素的探索,将为北方地区农业的起源、发展与传播,文化交流对农业发展的影响,人类对环境变迁的适应等热点问题研究提供重要依据。本文对关中地区史前不同文化、不同遗址人与动物骨骼的稳定同位素以及动植物遗存进行了综合分析。结果显示,受文化的发展与交流、区域地理环境的差异、气候的演变等因素影响,关中地区史前先民生业模式呈现时空差异。老官台文化先民的生业模式中旱作农业与狩猎采集并重。仰韶文化早期,旱作农业成为先民生业模式的主体,但不同区域发展水平不同;另外,家畜饲养的发展速度要滞后于农作物。仰韶文化中、晚期至龙山文化早期,水稻与小麦先后传入,形成以粟、黍旱作农业为主,兼营水稻、大豆等的多元化农业结构;水稻对仰韶文化中期先民的食谱产生影响,而同时期家畜饲养主要依赖于粟黍类农作物。龙山文化,黍、粟农业比重下降,水稻含量相对增加,并对先民与家畜的食谱产生影响;肉食获取方式以饲养活动为主,渔猎活动为辅。     

The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes

The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.