Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition.

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

Parental relatedness through time revealed by runs of homozygosity in ancient DNA.

Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.

Sex ratio at birth in Vietnam among six subnational regions during 1980-2050, estimation and probabilistic projection using a Bayesian hierarchical time series model with 2.9 million birth records.

The sex ratio at birth (SRB, i.e., the ratio of male to female births) in Vietnam has been imbalanced since the 2000s. Previous studies have revealed a rapid increase in the SRB over the past 15 years and the presence of important variations across regions. More recent studies suggested that the nation's SRB may have plateaued during the 2010s. Given the lack of exhaustive birth registration data in Vietnam, it is necessary to estimate and project levels and trends in the regional SRBs in Vietnam based on a reproducible statistical approach. We compiled an extensive database on regional Vietnam SRBs based on all publicly available surveys and censuses and used a Bayesian hierarchical time series mixture model to estimate and project SRB in Vietnam by region from 1980 to 2050. The Bayesian model incorporates the uncertainties from the observations and year-by-year natural fluctuation. It includes a binary parameter to detect the existence of sex ratio transitions among Vietnamese regions. Furthermore, we model the SRB imbalance using a trapezoid function to capture the increase, stagnation, and decrease of the sex ratio transition by Vietnamese regions. The model results show that four out of six Vietnamese regions, namely, Northern Midlands and Mountain Areas, Northern Central and Central Coastal Areas, Red River Delta, and South East, have existing sex imbalances at birth. The rise in SRB in the Red River Delta was the fastest, as it took only 12 years and was more pronounced, with the SRB reaching the local maximum of 1.146 with a 95% credible interval (1.129, 1.163) in 2013. The model projections suggest that the current decade will record a sustained decline in sex imbalances at birth, and the SRB should be back to the national SRB baseline level of 1.06 in all regions by the mid-2030s.

First modern human settlement recorded in the Iberian hinterland occurred during Heinrich Stadial 2 within harsh environmental conditions.

As the south-westernmost region of Europe, the Iberian Peninsula stands as a key area for understanding the process of modern human dispersal into Eurasia. However, the precise timing, ecological setting and cultural context of this process remains controversial concerning its spatiotemporal distribution within the different regions of the peninsula. While traditional models assumed that the whole Iberian hinterland was avoided by modern humans due to ecological factors until the retreat of the Last Glacial Maximum, recent research has demonstrated that hunter-gatherers entered the Iberian interior at least during Solutrean times. We provide a multi-proxy geoarchaeological, chronometric and paleoecological study on human-environment interactions based on the key site of Peña Capón (Guadalajara, Spain). Results show (1) that this site hosts the oldest modern human presence recorded to date in central Iberia, associated to pre-Solutrean cultural traditions around 26,000 years ago, and (2) that this presence occurred during Heinrich Stadial 2 within harsh environmental conditions. These findings demonstrate that this area of the Iberian hinterland was recurrently occupied regardless of climate and environmental variability, thus challenging the widely accepted hypothesis that ecological risk hampered the human settlement of the Iberian interior highlands since the first arrival of modern humans to Southwest Europe.

Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences.

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

Widespread reforestation before European influence on Amazonia.

An estimated 90 to 95% of Indigenous people in Amazonia died after European contact. This population collapse is postulated to have caused decreases in atmospheric carbon dioxide concentrations at around 1610 CE, as a result of a wave of land abandonment in the wake of disease, slavery, and warfare, whereby the attendant reversion to forest substantially increased terrestrial carbon sequestration. On the basis of 39 Amazonian fossil pollen records, we show that there was no synchronous reforestation event associated with such an atmospheric carbon dioxide response after European arrival in Amazonia. Instead, we find that, at most sites, land abandonment and forest regrowth began about 300 to 600 years before European arrival. Pre-European pandemics, social strife, or environmental change may have contributed to these early site abandonments and ecological shifts.

Genetic and demographic history define a conservation strategy for earth's most endangered pinniped, the Mediterranean monk seal Monachus monachus.

The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species' unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.

A genetic history of the pre-contact Caribbean.

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.

Directly modelling population dynamics in the South American Arid Diagonal using 14C dates.

Large anthropogenic 14C datasets are widely used to generate summed probability distributions (SPDs) as a proxy for past human population levels. However, SPDs are a poor proxy when datasets are small, bearing little relationship to true population dynamics. Instead, more robust inferences can be achieved by directly modelling the population and assessing the model likelihood given the data. We introduce the R package ADMUR which uses a continuous piecewise linear (CPL) model of population change, calculates the model likelihood given a 14C dataset, estimates credible intervals using Markov chain Monte Carlo, applies a goodness-of-fit test, and uses the Schwarz Criterion to compare CPL models. We demonstrate the efficacy of this method using toy data, showing that spurious dynamics are avoided when sample sizes are small, and true population dynamics are recovered as sample sizes increase. Finally, we use an improved 14C dataset for the South American Arid Diagonal to compare CPL modelling to current simulation methods, and identify three Holocene phases when population trajectory estimates changed from rapid initial growth of 4.15% per generation to a decline of 0.05% per generation between 10 821 and 7055 yr BP, then gently grew at 0.58% per generation until 2500 yr BP. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.

Population dynamics in pre-Inca human groups from the Osmore Valley, the Azapa Valley and the coast of the South Central Andes.

The present study applies a dental morphological perspective to the understanding of the complex pre-contact population history of the South Central Andes, through the detection of the underlying dynamics, and the assessment of the biological ties among groups. It presents an analysis of 1591 individuals from 66 sites that date from the Archaic to the Late Intermediate phases from Bolivia, Chile and Peru. The results suggest this area is characterized by significant movement of people and cultures and, at the same time, by long standing population continuity, and highlight the need for wider perspectives capable of taking into account both the different micro-regional realities and the region in its entirety.

Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru.

Many native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jívaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.

A fine-scale multi-step approach to understand fish recruitment variability.

Recruitment is one of the dominant processes regulating fish population productivity. It is, however, notoriously difficult to predict, as it is the result of a complex multi-step process. Various fine-scale drivers might act on the pathway from adult population characteristics to spawning behaviour and egg production, and then to recruitment. Here, we provide a holistic analysis of the Northwest Atlantic mackerel recruitment process from 1982 to 2017 and exemplify why broad-scale recruitment-environment relationships could become unstable over time. Various demographic and environmental drivers had a synergetic effect on recruitment, but larval survival through a spatio-temporal match with prey was shown to be the key process. Recruitment was also mediated by maternal effects and a parent-offspring fitness trade-off due to the different feeding regimes of adults and larvae. A mismatch curtails the effects of high larval prey densities, so that despite the abundance of food in recent years, recruitment was relatively low and the pre-existing relationship with overall prey abundance broke down. Our results reaffirm major recruitment hypotheses and demonstrate the importance of fine-scale processes along the recruitment pathway, helping to improve recruitment predictions and potentially fisheries management.

Thomas Robert Malthus, naturalist of the mind.

In 1798, Thomas Robert Malthus's infamous An Essay on the Principle of Population was published. The publication of the Essay is best remembered for Malthus's principle - that population multiplies geometrically as opposed to subsistence increasing arithmetically. What is not well known, however, is that Malthus's Essay also offered a sophisticated - and heterodox - theory of mind. Despite a recent revival in Malthusian scholarship, Malthus's theory of mind has been largely forgotten. The present study attempts to address this neglected area within the literature, by evaluating Malthus's contribution to the naturalization of the soul. I first situate Malthus's theory of mind within the Essay's broader naturalization project, examining Malthus's role as naturalist; his views on humans as animals; and the Essay's cosmology. This is followed by an exploration of the making and reception of the Essay, illustrating how readers widely interpreted Malthus's theory of mind as a theory of naturalization. Finally, I reconstruct Malthus's naturalized system of mind, discussing the mechanisms and dynamics involved in the operation of a materialist mind. In sum, I argue for the centrality of Malthus's Essay in the larger naturalization movement, specifically as it pertains to the soul.

Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic.

Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.

The role of ecological niche evolution on diversification patterns of birds distinctly distributed between the Amazonia and Atlantic rainforests.

The Amazonian and Atlantic Forest share several organisms that are currently isolated but were continuously distributed during the Quaternary period. As both biomes are under different climatic regimes, paleoclimatic events may have modulated species' niches due to a lack of gene flow and imposing divergent selection pressure. Here, we assessed patterns of ecological niche overlap in 37 species of birds with disjunct ranges between the Amazonian and Brazilian Atlantic Forests. We performed niche overlap analysis and ecological niche modeling using four machine-learning algorithms to evaluate whether species' ecological niches evolved or remained conserved after the past South American biogeographic events. We found a low niche overlap among the same species populations in the two biomes. However, niche similarity tests showed that, for half of the species, the overlap was higher than the ones generated by our null models. These results lead us to conclude that niche conservatism was not enough to avoid ecological differentiation among species even though detected in many species. In sum, our results support the role of climatic changes in late-Pleistocene-that isolated Amazon and the Atlantic Forest-as a driving force of ecological differences among the same species populations and potential mechanism of current diversification in both regions.

Correlation between δ18Ow and δ18Οen for estimating human mobility and paleomobility patterns.

In this study a methodology for identifying the geographic origin of unidentified persons, their residence and moving patterns while providing information on lifestyle, diet and socio-economic status by combining stable isotopic data, with the biological information (isotopic composition of the skeleton), is presented. This is accomplished by comparing the oxygen isotopic composition of the spring water that individuals were drinking, during their living period, with the oxygen isotopic composition of their tooth enamel bioapatite. Spring water and teeth samples were collected from individuals from three different areas of Greece: North Greece, Central Greece and South Greece and isotopic analysis of δ13C and δ18O of tooth enamel bioapatite and δ18O of spring water were conducted. For these three areas the isotopic methodology is a promising tool for discriminating the provenance. Furthermore, as a case study, this methodology is applied to two archeological sites of Greece (Medieval-Thebes and Roman-Edessa) in order to determine paleomobility patterns.

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.

Revisiting mid-twentieth-century fertility shifts from a global perspective.

In the developed world, the historic process of fertility decline was interrupted by an unexpected period of increasing fertility called the baby boom. Recent studies suggest that a similar trend change in fertility may have occurred in many less developed nations at approximately the same time. Using cohort fertility data for 26 less developed countries from around the world taken from the Integrated Public Use Microdata Series, International (IPUMS-I), this paper aims to ascertain the extent to which these trend changes occurred in a large sample of countries around the world. It offers convincing proof of the existence of an upward shift in fertility among cohorts born during the 1930s, which was common to many countries in the less developed world. Despite many similarities with the baby boom, there are also differences stemming, mostly, from its timing with respect to the demographic transition.

Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE.

The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who, over a period of 3,500 years, brought food production to the furthest corners of the continent. However, this wave of expansion was far from homogeneous, and climatic factors may have driven a marked slowdown observed at higher latitudes. Here, we test this hypothesis by assembling a large database of archaeological dates of first arrival of farming to quantify the expansion dynamics. We identify four axes of expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups.