Human Population History Research Articles

Genetic diversity of North African populations in the 17q21 genomic region.

The demographic history of human populations in North Africa has been characterized by complex migration processes that have determined the current genetic structure of these populations. We examined the autosomal markers of eight sampled populations in northern Africa (Tunisia and Libya) to explore their genetic structure and to place them in a global context. We genotyped a set of 30 autosomal single-nucleotide polymorphisms (SNPs) extending 9.5Mb and encompassing the 17q21 inversion region. Our data include 403 individuals from Tunisia and Libya. To put our populations in the global context, we analyzed our data in comparison with other populations, including those of the 1000 Genomes Project. To evaluate the data, we conducted genetic diversity, principal component, STRUCTURE, and haplotype analyses. The analysis of genetic composition revealed the genetic heterogeneity of North African populations. The principal component and STRUCTURE analyses converged and revealed the intermediate position of North Africans between Europeans and Asians. Haplotypic analysis demonstrated that the normal (H1) and inverted (H2) polymorphisms in the chromosome 17q21 region occur in North Africa at frequencies similar to those found in European and Southwest Asian populations. The results highlight the complex demographic history of North Africa, reflecting the influence of genetic flow from Europe and the Near East that dates to the prehistoric period. These gene flows added to demographic factors (inbreeding, endogamy), natural factors (topography, Sahara), and cultural factors that play a role in the emergence of the diverse and heterogeneous genetic structures of North African populations. This study contributes to a better understanding of the complex structure of North African populations.

MtDNA “nomenclutter” and its consequences on the interpretation of genetic data

Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., “macro-haplogroups”) vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers' understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This “clutter” leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as “macro-haplogroups”, “meso-haplogroups”, and “micro-haplogroups”. Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster, and then implemented into haplogroup callers such as HaploGrep3. This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies.

Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes.

Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.

Urban colonization of invasive species on islands: Mus musculus and Rattus rattus genetics of establishment on Cozumel Island

Humans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouse Mus musculus and the black rat Rattus rattus on Cozumel Island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our genetic findings suggest that introduction of individuals of different geographic sources to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Notably, we found that the genetic structure of the house mouse sampled within the city of San Miguel Cozumel is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance to prevent these invasive species to disperse further.

Distinct positions of genetic and oral histories: Perspectives from India

Over the past decade, genomic data has contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great’s army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.

Settlement Chronology and Subsistence Patterns in Cabo Pulmo, Baja California Sur, Mexico

ABSTRACT Cabo Pulmo National Park (CPNP), within the East Cape of Baja California Sur, Mexico, is the location of a highly productive rocky reef ecosystem that was likely attractive to people throughout the Holocene. AMS radiocarbon dates from sites along the coast and faunal data from two excavated sites, D20 and D27, indicate people were present in the region by at least 7120–6755 cal b.p. (D34), but evidence of persistent occupation and possibly higher population densities postdates 2110–1945 cal b.p. (D27, Unit 1). The most prominent sites with intact stratified archaeological deposits appear to be focused adjacent to prominent rocky points, where assemblages include a variety of marine mollusks, fish, birds, terrestrial and marine mammals, and sea turtle remains. At both D20 and D27, there is evidence people targeted small fishes including sardines, likely with nets. This study highlights the strong archaeological potential in CPNP to address questions about human coastal adaptations and population history during the Holocene, emphasizing the importance of protecting cultural resources in an area at risk from growing tourism and residential development.

The Trivers-Willard Effect for Educational Investment: Evidence from an African Sample

The Trivers-Willard hypothesis (TWH) states that individuals in good condition favor offspring of the sex that has a higher variance in reproductive value. Empirical studies with historical human populations suggest that the TWH might explain biased birth-ratios as well as biased parental investment in male or female offspring. However, empirical tests of the TWH in modern human populations are less conclusive.In this study, we investigate whether parental investment in education might be skewed according to the TWH in an African sample (N = 314) that includes students from 8 different countries. The data show that male students who rate their family’s wealth high tend to report more parental involvement in their own education, whereas the opposite is true for female students. This pattern is in accordance with the TWH for parental investment. The results support the validity of evolutionary explanations of behavioral bias in the context of parental investment in offspring education.

International Conference on Reconstructing the Human Population Histories of South Asia Using Archaeology and Genetics

International Conference on Reconstructing the Human Population Histories of South Asia Using Archaeology and Genetics

Prevalence and distribution of ossification of the ligamenta flava in a 16th–18th century skeletal population sample from Poland

ObjectiveThis study aimed to determine the prevalence of the ossification of the ligamenta flava (OLF) among skeletal remains from Poland. Materials and methods124 skeletons aged 25 years and older were analyzed. The presence and size of OLF were observed macroscopically. OLF was recorded at the cranial and caudal attachment sites of each vertebra. The following factors were analyzed: age at death, sex, and presence of other spondyloarthropathies. ResultsThe crude prevalence of OLF in the analyzed series was 68.55 %. OLF was located most frequently in the lower thoracic spine. A statistically significant relationship was observed between the presence of OLF and age at death. OLF coincided with degenerative spondyloarthropathies of the thoracolumbar spine. ConclusionsThe results of this study indicate that OLF was not a rare condition in past populations of European ancestry. Analysis of OLF prevalence in skeletal materials can contribute to reconstruction of the conditions and lifestyles of past people. SignificanceThis study shed new light on the prevalence of OLF and provides information on the variability of OLF in past European populations. The evaluation of the prevalence of OLF represents an important contribution to the field of paleopathology in understanding disease changes in prehistoric and historic human populations. LimitationsThe analyzed material came from unknown populations without demographic data. Sex and age at death were assessed using standard anthropological methods. Suggestions for further researchIt is important to understand the influence of sociocultural factors and physical activity patterns on the development of OLF.

Marsh archive reveals human population history and future implications for estuarine health in Long Island Sound

Coastal marshes are efficient ecosystems providing a multitude of benefits for invertebrates, birds, fish and humans alike. Yet despite these benefits, wetlands are threatened by anthropogenic inputs such as human wastewater which contain high levels of nitrogen (N). Increased nitrogen loads cause eutrophication and hypoxia in estuaries leading to further degradation of these valuable ecosystems that are already stressed by sea level rise and climate change. Policies to protect wetlands via wastewater treatments are reactive rather than proactive and a growing body of research shows that characteristics associated with population health and economic activity can be identified in wastewater. Analysis of a 2-m salt marsh sediment core reveals δN15 signatures indicative of human population rise and connects human impact to ecosystem health. Using key X-ray fluorescence (XRF), pollen, sediment and nitrogen signatures along the core, a robust chronology was produced dating back to 1700. This result was coupled with population data to observe the relationship between δN15 levels and population over three centuries. There is a statistically significant positive correlation between δN15 and population. Other external factors such as federal government policies (regulating clean water) show a clear reduction in this association but the use of synthetic nitrogen fertilizer masks the strength of this relationship. Further research to refine the relationship between population and δN15 could be beneficial in predicting nitrogen loads as human population grows, which in turn would create a proactive system to protect our coastal ecosystems.

Non-native plant species richness and influence of greenhouses and human populations in the conterminous United States

BackgroundOne issue in invasive plant ecology is identification of the factors related to the invasion process that increase number of non-native species. When invasion by non-native species increases, so does the probability that some non-native species will become harmful, or classified as invasive species, which disrupt natural ecosystems with attendant economic and social costs. I quantified patterns of how non-native species richness varied with vegetation types and human populations. To evaluate the relative importance of different predictor variables for invasion pathways in the conterminous United States, I modeled non-native plant species richness by county compared to current and historical human populations; greenhouses and nurseries; railroads, pipelines, transmission lines, and oil and gas wells; and land covers of impervious surface, development intensity categories, agriculture, and vegetation types. I also modeled these variables within vegetation types, excluding vegetation variables.ResultsTo summarize patterns, non-native plant species richness increased from 72 to 200 with increasing human population density classes. Forests and forest land use mosaics had the greatest mean number of non-native plant species, ranging from 121 to 166, whereas grasslands and grassland mosaics had the least number of non-native plant species, about 70. For modeling variable importance, all combined variables had R2 values of 56% (random forests regressor) and 54% (cubist regressor) for predictions of withheld observations of non-native plant species richness, with greenhouse density and percent forestlands as most influential variables. Single variables of greenhouses (R2 = 29%), historical and current human populations (R2 = 27% and 23%), impervious surface (25%), and medium intensity development (23%) were most associated with non-native plant species richness. For vegetation types, greenhouse and historical human population densities were influential variables particularly in forestlands, shrublands, and wetlands.ConclusionsBased on these models, human population measures and horticultural locations of greenhouses and plant nurseries may have stronger relationships than measures of land use disturbance and transport with non-native plant species richness.

Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations.

The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.

A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska

Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.

Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise

Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene transformed the Southeast Asian coastal landscape, but the impact on human demography remains unclear. Here, we create a paleogeographic map, focusing on sea-level changes during the period spanning the LGM to the present-day and infer the human population history in Southeast and South Asia using 763 high-coverage whole-genome sequencing datasets from 59 ethnic groups. We show that sea-level rise, in particular meltwater pulses 1 A (MWP1A, ~14,500–14,000 years ago) and 1B (MWP1B, ~11,500–11,000 years ago), reduced land area by over 50% since the LGM, resulting in segregation of local human populations. Following periods of rapid sea-level rises, population pressure drove the migration of Malaysian Negritos into South Asia. Integrated paleogeographic and population genomic analysis demonstrates the earliest documented instance of forced human migration driven by sea-level rise.

Genomic Insights into the Population History of the Resande or Swedish Travelers.

The Resande are a minority ethnic group in Sweden, who were characterized by an itinerant way of life, and they have been suggested to originate from the mixture between Swedish and Romani populations. Because the population history of the Resande has been scarcely studied, we analyzed genome-wide genotype array data from unrelated Resande individuals in order to shed light on their origins and demographic history for the first time from a genetic perspective. Our results confirm the Romani-related ancestry of this population and suggest an admixture event between a Romani-like population and a general Swedish-like population that occurred approximately between the mid-18th and mid-19th centuries, two centuries after the arrival of the first historically reported Romani families in Sweden. This inferred date suggests that the Romani group involved in the admixture is related to the pre-18th-century arrivals of Romani in Scandinavia. In addition, a reduction in the population size is detected previous to the admixture event, suggesting a subtle signal of isolation. The present work constitutes a step forward toward a better representation of ethnic minorities and underrepresented groups in population genetic analyses. In order to know in more detail the complete history of human populations, it is time to focus on studying populations that have not been previously considered for a general scenario and that can provide valuable information to fill in the gaps that still remain uncovered.

Inferring linguistic transmission between generations at the scale of individuals

Abstract Historical linguistics strongly benefited from recent methodological advances inspired by phylogenetics. Nevertheless, no available method uses contemporaneous within-population linguistic diversity to reconstruct the history of human populations. Here, we developed an approach inspired from population genetics to perform historical linguistic inferences from linguistic data sampled at the individual scale, within a population. We built four within-population demographic models of linguistic transmission over generations, each differing by the number of teachers involved during the language acquisition and the relative roles of the teachers. We then compared the simulated data obtained with these models with real contemporaneous linguistic data sampled from Tajik speakers from Central Asia, an area known for its large within-population linguistic diversity, using approximate Bayesian computation methods. Under this statistical framework, we were able to select the models that best explained the data, and infer the best-fitting parameters under the selected models. The selected model assumes that the lexicon of individuals is the result of a vertical transmission by two teachers, with a specific lexicon for each teacher. This demonstrates the feasibility of using contemporaneous within-population linguistic diversity to infer historical features of human cultural evolution.

Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia.

As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.

Holocene deforestation history of NE Belgium: An evaluation of pollen- and population-based approaches for reconstructing land cover

Several methods to reconstruct past land cover are available which can be roughly divided into approaches based on pollen data and approaches based on (estimates of) historical human population. In this study, the REVEALS model and non-metric multidimensional scaling (NMDS) are applied to pollen sequences obtained from multiple alluvial floodplains located in the sandy and loamy regions of northeastern Belgium, thereby obtaining the first regional (semi-)quantitative estimates of Holocene landscape openness for this area. These estimates are subsequently compared to the two most widely-used scenarios for anthropogenic land cover change (ALCC): KK10 and HYDE.In contrast with the two population-based ALCC scenarios, the pollen-based reconstructions are well in agreement and indicate considerable variability in past land cover, not only between the two regions but even between the individual catchments. This agreement implies that NMDS could serve as an alternative approach to provide insight in large amounts of pollen data in case not all required model parameters are available to run the REVEALS model. Moreover, NMDS can provide a better understanding of which taxa are related to a particular type of landscape. Taking into account such insights in the interpretation of the REVEALS model output might help to pinpoint the onset of significant human impact on the landscape more precisely. Given that alluvial sites often experienced early anthropogenic impact, including pollen data obtained from alluvial sites could not only improve the spatial coverage and accuracy of current pollen-based land cover reconstructions but could also improve our understanding of human transformation of the landscape, which can in turn contribute to an improvement of the ALCC scenarios.

Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago.

The Philippines, with the recent discovery of an archaic hominin in Luzon and an extensive ethnolinguistic diversity of more than 100 Indigenous peoples, is crucial to understanding human evolution and population history in Island Southeast Asia. Advances in DNA sequencing technologies enable the rapid generation of genomic data to robustly address questions about origins, relatedness, and population movements. With the increased genetic sampling in the country, especially by international scientists, it is vital to revisit ethical rules and guidelines relevant to conducting research among Indigenous peoples. Our team led fieldwork expeditions between 2019 and February 2020 in Zamboanga and the Sulu Archipelago, a chain of islands connecting the Mindanao and Borneo landmasses. The trips concluded with a collection of 2,149 DNA samples from 104 field sites. We present our fieldwork experience among the mostly sea-oriented Sama-Bajaw and Tausug-speaking communities and propose recommendations to address the ethical challenges of conducting such research. This work contributes toward building an enabling research environment in the Philippines that respects the rights and autonomy of Indigenous peoples, who are the rightful owners of their DNA and all genetic information contained therein.

Cumulative effects of long-term anthropogenic impacts on resident fish communities in subarctic fishing harbours

Ecosystems perceived to have sustained historical human pressure from multiple stressors are often considered to be degraded. Diversity and abundance of marine macroflora and macrofauna were observed at 17 harbour sites in Newfoundland (Canada) over four consecutive years (2008–2011), to determine cumulative effects of long-term anthropogenic impacts on coastal marine biota in small fishing harbours. A Principal Component Analysis was applied to evaluate the relative effects of physical harbour characteristics (harbour shape, size, and orientation), and those directly associated with anthropogenic influence (current and historical human population size, human landscape “footprint”, and operating capacity of the local fishing industry), on marine vegetation, fish, and invertebrate macrofauna. The first three principal components explained 77% of the cumulative variance of the physical harbour and anthropogenic variables. PC1 was dominated by variables associated with human use, and site depth; PC2 was associated with physical site orientation and the cumulative wharf length; and PC3 was associated with long-term use and harbour area. The densities of cod (Gadus spp.) and crab species increased significantly along the gradient of human impact metrics, while winter flounder (Pseudopleuronectes americanus), cunner (Tautogolaborus adspersus) and shorthorn sculpin (Myoxocephalus scorpius) decreased. Sessile fauna diversity and density, and flora percent cover correlated with long-term use and harbour area. Species densities changed in response to cumulative effects of long term human settlement near harbours, but prominent species were ubiquitous in these coastal ecosystems.