Out of Africa by spontaneous migration waves

The Microbiota and Evolution of Obesity

Obesity is a major global concern and is generally attributed to a combination of genetic and environmental factors. Several hypotheses have been proposed to explain the evolutionary origins of obesity epidemic, including thrifty and drifty genotypes, and changes in thermogenesis. Here, we put forward the hypothesis of metaflammation, which proposes that due to intense selection pressures exerted by environmental pathogens, specific genes that help develop a robust defense mechanism against infectious diseases have had evolutionary advantages and that this may contribute to obesity in modern times due to connections between the immune and energy storage systems. Indeed, incorporating the genetic variations of gut microbiota into the complex genetic framework of obesity makes it more polygenic than previously believed. Thus, uncovering the evolutionary origins of obesity requires a multifaceted approach that considers the complexity of human history, the unique genetic makeup of different populations, and the influence of gut microbiome on host genetics.

Hyperandrogenism associated with polycystic ovary syndrome may have a protective effect against fracture risk in female athletes: A pilot study

OBJECTIVES

Polycystic ovary syndrome (PCOS), characterized by polycystic ovaries, anovulation, and hyperandrogenism, is believed to be an evolutionary mismatch disease. Past research has examined PCOS as a uniform disease, despite variation in phenotypes across diagnostic categories, but establishing an evolutionary mismatch requires a focus on individual traits. We suggest PCOS hyperandrogenism may have been beneficial in ancestral environments because it reduced fracture risk and associated morbidity and mortality due to increased bone mineral density (BMD). We test this hypothesis by assessing fracture frequency, a proxy for BMD, in highly active females with and without PCOS hyperandrogenism.

METHODS

Sixty-seven reproductive-aged women were surveyed and grouped as: high intensity interval training (HIIT; a proxy for metabolic and physical stress) athletes with hyperandrogenic PCOS (31.24%), HIIT athletes without PCOS (29.85%), and nonathletes with hyperandrogenic PCOS (38.81%). Fracture occurrence was compared between the groups using independent samples Kruskal-Wallis tests for non-normally distributed data, and multiple regression analysis was used to examine anthropometrics, lifestyle and reproductive factors, PCOS status, and exercise frequency on fracture occurrence.

RESULTS

Fracture occurrence was higher in non-PCOS athletes (3.8 ± 4.3) than PCOS-athletes (1.2 ± 1.4, p = .11) and PCOS-non-athletes (1.0 ± 1.4, p < .01). PCOS-athletes and nonathletes did not differ significantly in fracture occurrence (p = .33). These results were independent of factors associated with bone health.

CONCLUSIONS

These preliminary findings suggest females with PCOS-related hyperandrogenism may be less likely to experience bone fractures and provide an initial step to explaining why PCOS has persisted despite marked negative reproductive consequences in modern populations.

The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies

Large scale databases are critical for helping scientists decipher long-term patterns in human evolution. This paper describes the conception and development of such a research database and illustrates how big data can be harnessed to formulate new ideas about the past. The Role of Culture in Early Expansions of Humans (ROCEEH) is a transdisciplinary research center whose aim is to study the origins of culture and the multifaceted aspects of human expansions across Africa and Eurasia over the last three million years. To support its research, the ROCEEH team developed an online tool named the ROCEEH Out of Africa Database (ROAD) and implemented its web-based applications. ROAD integrates geographical data as well as archaeological, paleoanthropological, paleontological and paleobotanical content within a robust chronological framework. In fact, a unique feature of ROAD is its ability to dynamically link scientific data both spatially and temporally, thereby allowing its reuse in ways that were not originally conceived. The data stem from published sources spanning the last 150 years, including those generated by the research team. Descriptions of these data rely on the development of a standardized vocabulary and profit from online explanations of each table and attribute. By synthesizing legacy data, ROAD facilitates the reuse of heritage data in novel ways. Database queries yield structured information in a variety of interoperable formats. By visualizing data on maps, users can explore this vast dataset and develop their own theories. By downloading data, users can conduct further quantitative analyses, for example with Geographic Information Systems, modeling programs and artificial intelligence. In this paper, we demonstrate the innovative nature of ROAD and show how it helps scientists studying human evolution to access datasets from different fields, thereby connecting the social and natural sciences. Because it permits the reuse of "old" data in new ways, ROAD is now an indispensable tool for researchers of human evolution and paleogeography.

pmTR database: population matched (pm) germline allelic variants of T-cell receptor (TR) loci

The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information when studying the genetic basis of population-specific immune responses in disease and in vaccination. Therefore, we meticulously identified true germline alleles enriched with complete TR allele sequences and their frequencies across 26 different human populations, profiled by "1000 Genomes data". We identified 205 TRAV, 249 TRBV, 16 TRGV and 5 TRDV germline alleles supported by at least four haplotypes. The diversity of germline allelic variants in the TR loci is the highest in Africans, while the majority of the Non-African alleles are specific to the Asian populations, suggesting a diverse profile of TR germline alleles in different human populations. Interestingly, the alleles in the IMGT database are frequent and common across all five super-populations. We believe that this new set of germline TR sequences represents a valuable new resource which we have made available through the new population-matched TR (pmTR) database, accessible via https://pmtrig.lumc.nl/ .

Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations

Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be specific to human populations. The current immunogenetics resources gather the germline alleles, however, lack the population specificity of the alleles which poses limitations for disease-association studies related to immune responses in different human populations. Therefore, we systematically identified germline alleles from 26 different human populations around the world, profiled by "1000 Genomes" data. We identified 409 IGHV, 179 IGKV, and 199 IGLV germline alleles supported by at least seven haplotypes. The diversity of germline alleles is the highest in Africans. Remarkably, the variants in the identified novel alleles show strikingly conserved patterns, the same as found in other IG databases, suggesting over-time evolutionary selection processes. We could relate the genetic variants to population-specific immune responses, e.g. IGHV1-69 for flu in Africans. The population matched IG (pmIG) resource will enhance our understanding of the SHM-related B-cell receptor selection processes in (infectious) diseases and vaccination within and between different human populations.

Discovering the opposite shore: How did hominins cross sea straits?

Understanding hominin expansions requires the comprehension of movement processes at different scales. In many models of hominin expansion these processes are viewed as being determined by large-scale effects, such as changes in climate and vegetation spanning continents and thousands or even millions of years. However, these large-scale patterns of expansions also need to be considered as possibly resulting from the accumulation of small-scale decisions of individual hominins. Moving on a continental scale may for instance involve crossing a water barrier. We present a generalized agent-based model for simulating the crossing of a water barrier where the agents represent the hominin individuals. The model can be configured to represent a variety of movement modes across water. Here, we compare four different behavioral scenarios in conjunction with a set of water barrier configurations, in which agents move in water by either paddling, drifting, swimming or rafting. We introduce the crossing-success-rate (CSR) to quantify the performance in water crossing. Our study suggests that more focus should be directed towards the exploration of behavioral models for hominins, as directionality may be a more powerful factor for crossing a barrier than environmental opportunities alone. A prerequisite for this is to perceive the opposite shore. Furthermore, to provide a comprehensive understanding of hominin expansions, the CSR allows for the integration of results obtained from small-scale simulations into large-scale models for hominin expansion.

Genetic diversity of the Sudanese: insights on origin and implications for health

By virtue of their cultural, linguistic and genetic legacies, many populations from Sudan have deep histories in the region and retain high genetic diversities. Sudan’s location in north east Africa, a unique spot believed to act as a climatic refuge during periods of climate extremes, might have dictated that fate. Among the marked consequences of this diversity is the potential to provide information on the origin and structure of human populations within and outside the continent, as well as migration patterns towards various parts of the African continent, and out of Africa. The diverse Sudanese gene pool further has the potential to inform on genetic adaptations driven by culture and the environment resulting in unique and interesting traits, some of which are yet to be investigated. In addition, these genomes could offer clues to complex issues of causation amidst the challenge of new paradigms in biology underpinned by the genomic revolution.

The Proportion of APOE4 Carriers Among Non-Demented Individuals: A Pooled Analysis of 389,000 Community-Dwellers

BACKGROUND

The apolipoprotein E epsilon 4 (APOE4) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Its carriage percentage in non-demented population varies across geographic regions and ethnic groups.

OBJECTIVE

To estimate the proportion of APOE4 (2/4, 3/4, or 4/4) carriers in non-demented community-dwellers.

METHODS

PubMed, EMBASE, and China National Knowledge Infrastructure were searched from inception to April 20, 2020. Community-based studies that reported APOE polymorphisms with a sample of≥500 non-demented participants were included. Random-effects models were used to pool the results. Meta-regression and subgroup analyses were performed to test the source of heterogeneity and stratified effects. Age-standardized pooled proportion estimates (ASPPE) were calculated by direct standardization method.

RESULTS

A total of 121 studies were included, with a pooled sample of  389,000 community-dwellers from 38 countries. The global average proportion of APOE4 carriers was 23.9% (age-standardized proportion: 26.3%; 2.1% for APOE4/4, 20.6% for APOE3/4 and 2.3% for APOE2/4), and varied significantly with geographical regions (from 19.3% to 30.0%) and ethnic groups (from 19.1% to 37.5%). The proportion was highest in Africa, followed by Europe, North America, Oceania, and lowest in South America and Asia (p < 0.0001). With respect to ethnicity, it was highest in Africans, followed by Caucasians, and was lowest in Hispanics/Latinos and Chinese (p < 0.0001).

CONCLUSION

APOE4 carriers are common in communities, especially in Africans and Caucasians. Developing precision medicine strategies in this specific high-risk population is highly warranted in the future.

What have the revelations about Neanderthal DNA revealed about Homo sapiens?

Genetic studies have presented increasing indications about the complexity of the interactions between Homo sapiens, Neanderthals and Denisovans, during Pleistocene. The results indicate potential replacement or admixture of the groups of hominins that lived in the same region at different times. Recently, the time of separation among these hominins in relation to the Last Common Ancestor – LCA has been reasonably well established. Events of mixing with emphasis on the Neanderthal gene flow into H. sapiens outside Africa, Denisovans into H. sapiens ancestors in Oceania and continental Asia, Neanderthals into Denisovans, as well as the origin of some phenotypic features in specific populations such as the color of the skin, eyes, hair and predisposition to develop certain kinds of diseases have also been found. The current information supports the existence of both replacement and interbreeding events, and indicates the need to revise the two main explanatory models, the Multiregional and the Out-of-Africa hypotheses, about the origin and evolution of H. sapiens and its co-relatives. There is definitely no longer the possibility of justifying only one model over the other. This paper aims to provide a brief review and update on the debate around this issue, considering the advances brought about by the recent genetic as well as morphological traits analyses.

Climate variability in early expansions of Homo sapiens in light of the new record of micromammals in Misliya Cave, Israel

In this study, we provide the first taphonomic and taxonomic descriptions of the micromammals from Misliya Cave, where recently a Homo sapiens hemimaxilla has been reported. This finding significantly extends the time frame for the out-of-Africa presence of anatomically modern humans. It also provides an opportunity to reassess variation in early modern human population responses to climate change in the Levantine sequence. Information on species ranking and diversity estimations (Shannon functions) is obtained from quantitative data across 31 Levantine assemblages and investigated in a broad comparative frame using multivariate analyses. Recent models of human-climate interactions in the late Early-Middle Paleolithic of the southern Levant have drawn heavily on on-site associations of human fossils with remains of micromammals. However, there has been little, if any, attempt to examine the long-term picture of how paleocommunities of micromammals responded qualitatively and quantitatively to climatic oscillations of the region by altering their compositional complexity. Consequently, our understanding is vastly limited in regard to the paleoecosystem functions that linked past precipitation shifts to changes in primary producers and consumers or as to the background climatic conditions that allowed for the development of highly nonanalog ancient communities in the region. Although previous studies argued for a correspondence between alternations in H. sapiens and Neanderthal occupations of the Levant and faunal shifts in key biostratigraphic indicator taxa (such as Euro-Siberian Ellobius versus Saharo-Arabian Mastomys and Arvicanthis), our data indicate the likelihood that early H. sapiens populations (Misliya and Qafzeh hominins) persisted through high amplitudes of paleoecological and climatic oscillations. It is unlikely, given these results, that climate functioned as a significant filter of early modern human persistence and genetic interactions with Neanderthals in the Levant.