Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes.

f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.

Four decades of measuring stillbirths and neonatal deaths in Demographic and Health Surveys: historical review.

BACKGROUND: Worldwide, an estimated 5.1 million stillbirths and neonatal deaths occur annually, 98% in low- and middle-income countries. Limited coverage of civil and vital registration systems necessitates reliance on women's retrospective reporting in household surveys for data on these deaths. The predominant platform, Demographic and Health Surveys (DHS), has evolved over the last 35 years and differs by country, yet no previous study has described these differences and the effects of these changes on stillbirth and neonatal death measurement. METHODS: We undertook a review of DHS model questionnaires, protocols and methodological reports from DHS-I to DHS-VII, focusing on the collection of information on stillbirth and neonatal deaths describing differences in approaches, questionnaires and geographic reach up to December 9, 2019. We analysed the resultant data, applied previously used data quality criteria including ratios of stillbirth rate (SBR) to neonatal mortality rate (NMR) and early NMR (ENMR) to NMR, comparing by country, over time and by DHS module. RESULTS: DHS has conducted >320 surveys in 90 countries since 1984. Two types of maternity history have been used: full birth history (FBH) and full pregnancy history (FPH). A FBH collecting information only on live births has been included in all model questionnaires to date, with data on stillbirths collected through a reproductive calendar (DHS II-VI) or using additional questions on non-live births (DHS-VII). FPH collecting information on all pregnancies including live births, miscarriages, abortions and stillbirths has been used in 17 countries. We found no evidence of variation in stillbirth data quality assessed by SBR:NMR over time for FBH surveys with reproductive calendar, some variation for surveys with FBH in DHS-VII and most variation among the surveys conducted with a FPH. ENMR:NMR ratio increased over time, which may reflect changes in data quality or real epidemiological change. CONCLUSION: DHS remains the major data source for pregnancy outcomes worldwide. Although the DHS model questionnaire has evolved over the last three and half decades, more robust evidence is required concerning optimal methods to obtain accurate data on stillbirths and neonatal deaths through household surveys and also to develop and test standardised data quality criteria.

Applications of Bayesian Skyline Plots and Approximate Bayesian Computation for Human Demography.

Bayesian methods have been adopted by anthropologists for their utility in resolving complex questions about human history based on genetic data. The main advantages of Bayesian methods include simple model comparison, presenting results as a summary of probability distributions, and the explicit inclusion of prior information into analyses. In the field of anthropological genetics, for example, implementing Bayesian skyline plots and approximate Bayesian computation is becoming ubiquitous as means to analyze genetic data for the purpose of demographic or historic inference. Correspondingly, there is a critical need for better understanding of the underlying assumptions, proper applications, and limitations of these two methods by the larger anthropological community. Here we review Bayesian skyline plots and approximate Bayesian computation as applied to human demography and provide examples of the application of these methods to anthropological research questions. We also review the two core components of Bayesian demographic analysis: the coalescent and Bayesian inference. Our goal is to describe their basic mechanics in an attempt to demystify them.

A Cohort Perspective on the Demography of Grandparenthood: Past, Present, and Future Changes in Race and Sex Disparities in the United States.

How has the demography of grandparenthood changed over the last century? How have racial inequalities in grandparenthood changed, and how are they expected to change in the future? Massive improvements in mortality, increasing childlessness, and fertility postponement have profoundly altered the likelihood that people become grandparents as well as the timing and length of grandparenthood for those that do. The demography of grandparenthood is important to understand for those taking a multigenerational perspective of stratification and racial inequality because these processes define the onset and duration of intergenerational relationships in ways that constrain the forms and levels of intergenerational transfers that can occur within them. In this article, we discuss four measures of the demography of grandparenthood and use simulated data to estimate the broad contours of historical changes in the demography of grandparenthood in the United States for the 1880-1960 birth cohorts. Then we examine race and sex differences in grandparenthood in the past and present, which reveal declining inequality in the demography of grandparenthood and a projection of increasing group convergence in the coming decades.

Clinical prediction and the idea of a population.

Using an analysis of the British Medical Journal over the past 170 years, this article describes how changes in the idea of a population have informed new technologies of medical prediction. These approaches have largely replaced older ideas of clinical prognosis based on understanding the natural histories of the underlying pathologies. The 19th-century idea of a population, which provided a denominator for medical events such as births and deaths, was constrained in its predictive power by its method of enumerating individual bodies. During the 20th century, populations were increasingly constructed through inferential techniques based on patient groups and samples seen to possess variable characteristics. The emergence of these new virtual populations created the conditions for the emergence of predictive algorithms that are used to foretell our medical futures.

Distribution of living Cupressaceae reflects the breakup of Pangea.

Most extant genus-level radiations in gymnosperms are of Oligocene age or younger, reflecting widespread extinction during climate cooling at the Oligocene/Miocene boundary [∼23 million years ago (Ma)]. Recent biogeographic studies have revealed many instances of long-distance dispersal in gymnosperms as well as in angiosperms. Acting together, extinction and long-distance dispersal are likely to erase historical biogeographic signals. Notwithstanding this problem, we show that phylogenetic relationships in the gymnosperm family Cupressaceae (162 species, 32 genera) exhibit patterns expected from the Jurassic/Cretaceous breakup of Pangea. A phylogeny was generated for 122 representatives covering all genera, using up to 10,000 nucleotides of plastid, mitochondrial, and nuclear sequence per species. Relying on 16 fossil calibration points and three molecular dating methods, we show that Cupressaceae originated during the Triassic, when Pangea was intact. Vicariance between the two subfamilies, the Laurasian Cupressoideae and the Gondwanan Callitroideae, occurred around 153 Ma (124-183 Ma), when Gondwana and Laurasia were separating. Three further intercontinental disjunctions involving the Northern and Southern Hemisphere are coincidental with or immediately followed the breakup of Pangea.

Historical effects on beta diversity and community assembly in Amazonian trees.

We present a unique perspective on the role of historical processes in community assembly by synthesizing analyses of species turnover among communities with environmental data and independent, population genetic-derived estimates of among-community dispersal. We sampled floodplain and terra firme communities of the diverse tree genus Inga (Fabaceae) across a 250-km transect in Amazonian Peru and found patterns of distance-decay in compositional similarity in both habitat types. However, conventional analyses of distance-decay masked a zone of increased species turnover present in the middle of the transect. We estimated past seed dispersal among the same communities by examining geographic plastid DNA variation for eight widespread Inga species and uncovered a population genetic break in the majority of species that is geographically coincident with the zone of increased species turnover. Analyses of these and 12 additional Inga species shared between two communities located on opposite sides of the zone showed that the populations experienced divergence 42,000-612,000 y ago. Our results suggest that the observed distance decay is the result not of environmental gradients or dispersal limitation coupled with ecological drift--as conventionally interpreted under neutral ecological theory--but rather of secondary contact between historically separated communities. Thus, even at this small spatial scale, historical processes seem to significantly impact species' distributions and community assembly. Other documented zones of increased species turnover found in the western Amazon basin or elsewhere may be related to similar historical processes.

Evolutionary demography of agricultural expansion in preindustrial northern Finland.

A shift from nomadic foraging to sedentary agriculture was a major turning point in human evolutionary history, increasing our population size and eventually leading to the development of modern societies. We however lack understanding of the changes in life histories that contributed to the increased population growth rate of agriculturalists, because comparable individual-based reproductive records of sympatric populations of agriculturalists and foragers are rarely found. Here, we compared key life-history traits and population growth rate using comprehensive data from the seventieth to nineteenth century Northern Finland: indigenous Sami were nomadic hunter-fishers and reindeer herders, whereas sympatric agricultural Finns relied predominantly on animal husbandry. We found that agriculture-based families had higher lifetime fecundity, faster birth spacing and lower maternal mortality. Furthermore, agricultural Finns had 6.2% higher annual population growth rate than traditional Sami, which was accounted by differences between the subsistence modes in age-specific fecundity but not in mortality. Our results provide, to our knowledge, the most detailed demonstration yet of the demographic changes and evolutionary benefits that resulted from agricultural revolution.

Pagan-Christian change in northeastern Hungary in the 10th-13th centuries AD--a palaeodemographic aspect.

In the present paper the authors compared skeletal populations (2421 individuals) excavated from four cemeteries, namely Hajdúdorog-Gyúlás (10th century AD), Hajdidorog-Temetöhegy (11th century AD), Hajdúdorog-Katidülö (12th-13th century AD) and Hajdúdorog-Szálldáföld (12th-13th century AD) from a micro-region of Northern Hajdúság (located in the northern part of the Great Hungarian Plain in Hungary in the Carpathian Basin) based on demographic data. The cemeteries were dated to the age of the Hungarian conquest and the Arpadian age and provided representative data for anthropological research. Previous studies based on craniological and archaeological investigations have already suggested that there was discontinuity in the population history between the 10th and the 11th centuries AD and continuity between the 11th and 12th centuries AD in this region. This hypothesis could be partially supported by demographic investigations because conclusive evidence was found that there must have been a change in the population at the turn of the 10th and 11th centuries AD, and there was certain continuity between the 11th and 12-13th centuries AD. The authors suppose that there were two crises in the examined period: the first crisis set in at the transition from the pagan era (10th century AD) to the Christian era (from the beginning of the 11th century AD, with population resettlements within the Carpathian Basin), the second might have been more moderate and meant burying the dead of the populations lacking a church in the churchyards of villages which had a church. At that time one graveyard around a church may have been used by several village populations.

Disciplining ethnicity: social sorting intersects with political demography in Israel's pre-state period.

This article presents an analysis of the professional and political activities of the demographer Roberto Bachi prior to Israel's establishment as a state in 1948. The article describes his involvement in two interconnected major areas: first, his advocacy of pro-natal policies, connected to a nation-building strategy by the Jewish population to achieve numerical dominance over Arab Palestinians in areas to be incorporated in the Jewish state, and second, the development of Jewish ethnic distinctions, particularly the 'Mizrahi type', to track differences in birthrates and changing cultural features within the Jewish population. The article also revises the historical record by showing the importance of this ethnic classification in the years prior to the large waves of Jewish immigration from Arab countries. Without the reworking of the popular category 'Mizrahi' into a scientifically systematized category by a demographer who would become the head of the state's Central Bureau of Statistics upon its founding in 1948, this binary social epistemology could not be as strong and legitimate as it actually was. Two factors account for Bachi's success. First was his ability to provide a new way of understanding the present in terms of the future. His numerical predictions on the Jewish and Arab demographic development made statistics and demography an indispensable technology for public policy and social planning. Second was his role as a boundary actor--a unique mediating position between political and scientific spheres. The Israeli case study exemplifies similar dynamics found in other countries during periods of structuring the modern state, namely, processes in which experts of infrastructural knowledge such as statistics and demography saw themselves as responsible for the national progress and its social modernity.

Epidemiology's 350th Anniversary: 1662-2012.

Between 1600 and 1700, sudden, profound, and multifarious changes occurred in philosophy, science, medicine, politics, and society. In an extremely convulsed century, these profound and convergent upheavals produced the equivalent of a cultural big bang, which opened a new domain of knowledge acquisition based on population thinking and group comparisons. In 1662, when John Graunt applied-for the first time-the new approach to the analysis of causes of death in London, he gave epidemiology a singular date of birth. This was exactly 350 years ago.

Going local with ancient DNA: A review of human histories from regional perspectives.

Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.

The research of W.E. Mayer (1953-2012): a spectrum of immune systems.

Over a period of some 20 years, Werner Eugen Mayer played a significant role in establishing a framework for molecular studies of Mhc genes in multiple vertebrates. His work largely concerned gene isolation, sequencing, and related bioinformatic analyses both for the Mhc and for immune system genes of about 200 species, ranging from apes, monkeys, rodents, and marsupials, through to birds, bony fishes, and lampreys. In addition to his exploration of diverse Mhc genes, Werner is remembered for playing a critical role in the development of two important insights into the evolution of immune systems. His was among the first published DNA sequence-based descriptions of trans-species evolution of Mhc alleles, including the first description of the long-lived polymorphisms shared by humans and chimpanzees. This research opened the way for using Mhc polymorphisms in demographic analyses. The second important insight in which he played a prominent role involved the characterization of immune cells and their expressed genes in the lamprey, a jawless vertebrate. His findings helped to indicate the considerable degree to which extant immune mechanisms were co-opted in the creation of the adaptive immune system of jawed vertebrates.

Using ecological niche modelling to predict spatial and temporal distribution patterns in Chinese gibbons: lessons from the present and the past.

Ecological niche modelling (ENM) is used to predict species' tolerance to changing environmental conditions. Understanding changes in the spatial distribution of species across time is essential in order to develop effective conservation strategies. Here we map the past and present distribution of gibbons across China, a country experiencing extensive anthropogenic habitat destruction and ongoing biodiversity loss. The distribution of gibbons across three time intervals is described based on fossil, historical and modern-day data, and ENM, implemented using DIVA-GIS, is used to predict how modern-day gibbon distributions might respond to future climate change. Predictions based on modern-day data alone fail to reveal patterns of environmental tolerance and geographical distribution shown by gibbons in the relatively recent historical period, emphasizing the need to incorporate past as well as present data in conservation analyses.

Immigrants' health in Europe: a cross-classified multilevel approach to examine origin country, destination country, and community effects.

In this study, we examined origin, destination, and community effects on first- and second-generation immigrants' health in Europe. We used information from the European Social Surveys (2002­2008) on 19,210 immigrants from 123 countries of origin, living in 31 European countries. Cross-classified multilevel regression analyses reveal that political suppression in the origin country and living in countries with large numbers of immigrant peers have a detrimental influence on immigrants' health. Originating from predominantly Islamic countries and good average health among natives in the destination country appear to be beneficial. Additionally, the results point toward health selection mechanisms into migration.

Adolescent mortality at Winchester College, 1393-1540: new evidence for medieval mortality and methodological considerations for historical demography.

This article presents new data on mortality in the late medieval period, and suggests methodologies for analysing incomplete datasets. Using data collated from the records of Winchester College this study follows the lives of 2,692 individuals, and analyses adolescent mortality in the sample group for the period 1393-1540. This study of mortality among 10-18 year olds is the first of its kind to produce data for a sample of adolescents in late medieval England, and thereby contributes significant new data to our understanding of late medieval mortality. These data are placed within the context of that obtained for other medieval population samples, most notably with studies of medieval monastic groups.

[Demographic and epidemiological quantification in Balearic hygienism, 1850-1930]. / La cuantificación demográfica y epidemiológica en el higienismo balear, 1850-1930.

At the end of the 19th century, social medicine promoted the use of quantification as a means to evaluate the health status of populations. In Majorca, hygienists such as the physicians Enric Fajarnés, Bernat Riera, Antoni Mayol and Emili Darder and the civil engineer Eusebi Estada sought a better understanding of health status by considering the population growth, the demographic and epidemiological profile and the influence of weather on mortality. These calculations showed that the Balearic population had a good health status in comparison to the population of mainland Spain, although less so in the international context. These results were explained by the benevolence of the insular climate, a factor that would also guarantee the success of the public health reforms proposed.

Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia.

Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations - Yaghnobis and Tajiks - with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.