Major Demographic Events Research Articles

100 ancient genomes show repeated population turnovers in Neolithic Denmark

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

The Impact of Recent Demography on Functional Genetic Variation in North African Human Groups.

The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing is particularly relevant to determine the effects of these demographic events on current-day North Africans' genomes, since it allows to focus on those parts of the genome that are more likely to have direct biomedical consequences. Whole-exome sequencing can also be used to assess the effect of recent demography in functional genetic variation and the efficacy of natural selection, a long-lasting debate. In the present work, we use newly generated whole-exome sequencing and genome-wide array genotypes to investigate the effect of demography in functional variation in 7 North African populations, considering both cultural and demographic differences and with a special focus on Amazigh (plur. Imazighen) groups. We detect genetic differences among populations related to their degree of isolation and the presence of bottlenecks in their recent history. We find differences in the functional part of the genome that suggest a relaxation of purifying selection in the more isolated groups, allowing for an increase of putatively damaging variation. Our results also show a shift in mutational load coinciding with major demographic events in the region and reveal differences within and between cultural and geographic groups.

The loss of biodiversity in Madagascar is contemporaneous with major demographic events

Only 400km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large-bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.

Long-term demographic trends and spatio-temporal distribution of past human activity in Central Europe: Comparison of archaeological and palaeoecological proxies

Estimating past population dynamics has become a major research topic for archaeology, which uses several proxies for studying past demography. The Czech Republic represents a unique region with abundant digital archaeological and palynological datasets comprising tens of thousands of records covering the whole Holocene. We used these datasets to quantify long-term demographic trends and to delimit past human activity in space and time. Our results, based on large data from both disciplines, are one of the first quantitative results covering the whole Czech Republic. Through summed probability distributions of radiocarbon dates and spatio-temporal modelling of human activity based on archaeological sites, we identified four major demographic events and processes between 10,000 BCE and 1000 CE – the beginning of the Neolithic at 5400 BCE, the Eneolithic/Bronze Age transition in the 3rd millennium BCE, Bronze Age expansion after 1500 BCE, and mediaeval expansion after 500 CE. We identified two settlement cores in the lowlands, with additional inner and outer peripheries with different demographic histories. Our study clearly shows that prehistoric and early historic population dynamics were not a homogenised process and were regionalized according to local environmental and social conditions. The comparison of archaeological results with pollen-based vegetation proxies also showed regional aspects in human-vegetation interactions. Agro-pastoral communities dwelling in the lowlands mostly influenced the openness of the landscape, used for fields and pastures, whereas contemporary communities with a similar economic mode residing in a different region are more visible in pollen records through species and structural changes in woodlands. The agro-pastoral subsistence strategy did not start everywhere with the onset of the Neolithic: in some regions it failed after several centuries, in others, the foraging lifestyle persisted significantly longer, and farming became a major economic strategy much later. Our study shows that archaeological site-based and 14C-based demographic proxies cannot be utilized for all periods and regions due to several limitations. Only the combination of different quantitative and qualitative archaeological proxies for population does reveal important details.

Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China.

Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species. Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG). Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during glacial periods and range expansion during interglacial periods. Our study corroborates the importance of combining multiple lines of evidence when reconstructing Quaternary population evolutionary histories.

The interplay of demography and selection during maize domestication and expansion

BackgroundThe history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes.ResultsWe investigate these processes using high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize, and four wild teosinte individuals (Zea mays ssp. parviglumis). Genome-wide demographic analyses reveal that maize experienced pronounced declines in effective population size due to both a protracted domestication bottleneck and serial founder effects during post-domestication spread, while parviglumis in the Balsas River Valley experienced population growth. The domestication bottleneck and subsequent spread led to an increase in deleterious alleles in the domesticate compared to the wild progenitor. This cost is particularly pronounced in Andean maize, which has experienced a more dramatic founder event compared to other maize populations. Additionally, we detect introgression from the wild teosinte Zea mays ssp. mexicana into maize in the highlands of Mexico, Guatemala, and the southwestern USA, which reduces the prevalence of deleterious alleles likely due to the higher long-term effective population size of teosinte.ConclusionsThese findings underscore the strong interaction between historical demography and the efficiency of selection and illustrate how domesticated species are particularly useful for understanding these processes. The landscape of deleterious alleles and therefore evolutionary potential is clearly influenced by recent demography, a factor that could bear importantly on many species that have experienced recent demographic shifts.

Genetic reconstructions of invasion history.

A diverse array of molecular markers and constantly evolving analytical approaches have been employed to reconstruct the invasion histories of the most notorious invasions. Detailed information on the source(s) of introduction, invasion route, type of vectors, number of independent introductions and pathways of secondary spread has been corroborated for a large number of biological invasions. In this review, I present the promises and limitations of current techniques while discussing future directions. Broad phylogeographic surveys of native and introduced populations have traced back invasion routes with surprising precision. These approaches often further clarify species boundaries and reveal complex patterns of genetic relationships with noninvasive relatives. Moreover, fine-scale analyses of population genetics or genomics allow deep inferences on the colonization dynamics across invaded ranges and can reveal the extent of gene flow among populations across various geographical scales, major demographic events such as genetic bottlenecks as well as other important evolutionary events such as hybridization with native taxa, inbreeding and selective sweeps. Genetic data have been often corroborated successfully with historical, geographical and ecological data to enable a comprehensive reconstruction of the invasion process. The advent of next-generation sequencing, along with the availability of extensive databases of repository sequences generated by barcoding projects opens the opportunity to broadly monitor biodiversity, to identify early invasions and to quantify failed invasions that would otherwise remain inconspicuous to the human eye.

COMPILATION AND ANALYSIS OF PRE-COLUMBIAN SETTLEMENT DATA IN THE BASIN OF MEXICO

AbstractA key component of archaeological research in the Basin of Mexico was a series of systematic regional surveys conducted between 1960 and 1975. This essay discusses efforts to finalize settlement data generated by those surveys, and preliminary analyses of the resulting dataset that include geographic information system applications to examine patterns of settlement over time. The paper begins by reviewing the surveys and the information they produced for more than 3,900 sites. Analyses of demographics, settlement hierarchies, and environmental patterning reveal periods of slow population increase and decrease that indicate no major demographic events, but noteworthy shifts in settlement types and environmental focus. Analyses of spatial patterning reveal evidence of considerable geographic shifts in settlement over time, probable widespread reliance on irrigation throughout much of the pre-Columbian basin, likely major shifts in adaptation to the central lake system in the region, and intraregional migration as a key demographic process in settlement patterning. Amid growing understanding of pre-Columbian settlement patterns in the Basin of Mexico, this paper also defines key research problems involving demographic mobility, the role of water control in adaptation and sociocultural evolution, and implications of changing environmental emphasis in settlement patterning.

Demographic perspectives on the transition to adulthood: An introduction

This special issue of Advances in Life Course Research is dedicated to a demographic perspective on the transition to adulthood. In our view, there are at least two compelling reasons to do so. First, the current conceptualization of the transition to adulthood as mainly a subjective process in which young men and women gradually gain autonomy and responsibility, is at best one-sided. It is our contention that traditional markers – and ‘new’ markers like unmarried cohabitation – still constitute very important events in young people’s life course that significantly influence their future life chances and outcomes. Second, the field of major demographic events during the transition to adulthood itself offers so many substantive and methodological challenges that it is worthwhile to examine at least a number of them. In the remainder of this introductory article, we have three aims. First, we will try to substantiate our claim that studying demographic markers in young adulthood is still an important goal for life course studies. Second, we will discuss some of the substantive and methodological challenges that research in this area is facing. And third, we will discuss the contribution of the substantive articles in this special issue to these challenges.

Genetic spatial structure in a butterfly metapopulation correlates better with past than present demographic structure

The Glanville fritillary butterfly (Melitaea cinxia) has been studied in the Aland Islands in Finland since 1991, where it occurs as a classic metapopulation in a large network of 4000 dry meadows. Much ecological work has been conducted on this species, but population genetic studies have been hampered by paucity of suitable genetic markers. Here, using single nucleotide polymorphisms and microsatellites developed for the Glanville fritillary, we examine the correspondence between the demographic and genetic spatial structures. Given the dynamic nature of the metapopulation, the current genetic spatial structure may bear a signal of past changes in population sizes and past patterns of gene flow rather than reflect the current demographic structure or landscape structure. We analyse this question with demographic data for 10 years, using the Rand index to assess the similarity between the genetic, demographic, and landscape spatial structures. Our results show that the current genetic spatial structure is better explained by the past rather than by the current demographic spatial structure or by the spatial configuration of the habitat in the landscape. Furthermore, current genetic diversity is significantly explained by past metapopulation sizes. The time lag between major demographic events and change in the genetic spatial structure and diversity has implications for the study of spatial dynamics.

Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes?--Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity.

BackgroundCircum-Antarctic waters harbour a rare example of a marine species flock – the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survived Pleistocene climatic fluctuations characterised by repeated advances of continental glaciers as far as the shelf break that probably resulted in a loss of habitat for benthic organisms. Pelagic ecosystems, on the other hand, might have flourished during glacial maxima due to the northward expansion of Antarctic polar waters. In order to better understand the role of ecological traits in Quaternary climatic fluctuations, we performed demographic analyses of populations of four fish species from the tribe Trematominae, including both fully benthic and pelagic species using the mitochondrial cytochrome b gene and an intron from the nuclear S7 gene.ResultsNuclear and cytoplasmic markers showed differences in the rate and time of population expansions as well as the likely population structure. Neutrality tests suggest that such discordance comes from different coalescence dynamics of each marker, rather than from selective pressure. Demographic analyses based on intraspecific DNA diversity suggest a recent population expansion in both benthic species, dated by the cyt b locus to the last glacial cycle, whereas the population structure of pelagic feeders either did not deviate from a constant-size model or indicated that the onset of the major population expansion of these species by far predated those of the benthic species. Similar patterns were apparent even when comparing previously published data on other Southern Ocean organisms, but we observed considerable heterogeneity within both groups with regard to the onset of major demographic events and rates.ConclusionOur data suggest benthic and pelagic species reacted differently to the Pleistocene ice-sheet expansions that probably significantly reduced the suitable habitat for benthic species. However, the asynchronous timing of major demographic events observed in different species within both "ecological guilds", imply that the species examined here may have different population and evolutionary histories, and that more species should be analysed in order to more precisely assess the role of life history in the response of organisms to climatic changes.

Pensions in an ageing society: a symposium

Two major demographic events, the progressive fall in fertility and greaterlongevity, are changing the structure of the world population, although atvarious rates in different regions (UN, 2005). What has been called by demogra-phers the demographic transition should be welcomed insofar as it is likely tobring about a much needed stabilization of the world population that, nonetheless,is expected to increase by one third by the end of this century, from the currentlevel of 6.5 billion. Moreover, the greater control women have over fecundityand the fall in child mortality rates—factors that help to explain the decline infertility—and the expectation of a longer old-age are significant achievements.These achievements come at a price, however: i.e. population ageing—since bydefinition, populations with low fertility (the dominant factor) and with long lifeexpectancy (a subsidiary factor) are, on average, older than populations withhigh fertility and short life expectancy.While the trend depicted above is global, the variety of regional situations isstriking. The demographic transition is at an advanced stage in the more developedcountries, where it started two centuries ago; the post-World War II baby boom doesnot contradict the secular patterns. In a few years, the demographic transition willbring about dramatic consequences in some countries, namely the European Medi-terranean countries and Japan, but also in Germany, where the native population isexpected to fall, and where, despite substantial immigration, the ageing processwill scale upwards.

Cambodia: Reconstructing the Demographic Stab of the Past and Forecasting the Demographic Scar of the Future

Cambodia went through 5 years of violent internal conflicts (1970–1975), including the spread of the American–Vietnamese war into the country, followed by four more years of brutal and chaotic Khmer Rouge government (1975–1979). The result was almost 2 million deaths. This article attempts to contribute to the reconstruction of the demographic history of Cambodia. This is done in three ways. First, by analysing scars in the pyramids corresponding to the recent past, present and future; second, by estimating major demographic events during the 1970s, especially excess deaths; and third, by comparing the size and composition of a simulated normal population with the real population.