Human Evolutionary History Research Articles

Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens.

Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4×10−7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.

Higher Education in the Fourth Industrial Revolution Age

The fourth industrial revolution has made an important step in the history of human development and for higher education today under the context that the impact of the industrial revolution 4.0 has been preparing for great opportunities and challenges. Within range of this article, the author focuses on researching important impacts of the fourth industrial revolution in coming time: training activities of higher education institutions; curriculum content, teaching methods; start-up issues in training institutions; learning environment, methods, materials, equipment, demand and process of learners have many changes. On that basis, the author analyzes some orientations for the higher education development in Vietnam today in the context of the fourth industrial revolution.

Social Status and Its Relationship to Non-specific Stress at Late Iron Age Non Ban Jak, Northeast Thailand

The rise of social inequality is a key development in human history and is linked to deteriorating health. These associated health impacts are poorly understood for Iron Age (420 B.C.–A.D. 500) northeast Thailand. To clarify this issue we investigate whether social status differences influence non-specific stress at the site of Non Ban Jak (A.D. 300–800), which comprises two separate burial mounds. These mounds are thought to represent the neighborhoods of two distinct social groups at the site. Quantitative analyses were used to explore differences in grave goods among the adults of Non Ban Jak (N = 47). Long bone lengths, ages at death, and linear enamel hypoplasia (LEH) were examined to explore differences in non-specific stress on the basis of age, sex, burial mound, and mortuary phase. Results demonstrated that older adults of both sexes, males of all ages, and west mound individuals received greater grave good quantities and may therefore have been of higher social status. West mound individuals were taller and had a lower prevalence of LEH compared to those from the east mound. Although female LEH prevalence and mortality were reduced relative to males, decreasing stature over time and high neonatal mortality indicated greater female stress. Lower-status individuals may therefore have suffered increased stress relative to those of higher status. Artifactual and epigraphic evidence supports the suggestion of sex- and class-based status differences at Non Ban Jak, legitimized and perpetuated through the adoption of residential burial and new religious ideologies. การปรากฎขึ้นของความไม่เท่าเทียมทางสังคมเป็นพัฒนาการสำคัญอย่างหนึ่งในประวัติศาสตร์มนุษยชาติและเชื่อมโยงกับสุขภาพที่เสื่อมลง ความรู้ความเข้าใจเกี่ยวกับสุขภาวะที่เกี่ยวเนื่องกับความไม่เท่าเทียมทางสังคมในสมัยเหล็ก (ประมาณ ๒,๔๐๐ – ๑,๕๐๐ ปีมาแล้ว) ในภาคตะวันออกเฉียงเหนือนี้ยังมีน้อย ดังนั้น เพื่อสร้างความเข้าใจให้ชัดเจนในเรื่องนี้ เราจึงได้ศึกษาตรวจสอบว่าความแตกต่างด้านสถานะทางสังคมมีอิทธิพลต่อความตึงเครียดหรือไม่ ทั้งนี้ เราใช้หลักฐานทางโบราณคดีจากแหล่งโบราณคดีโนนบ้านจาก (กำหนดอายุระหว่าง ๒,๓๐๐ – ๑,๒๐๐ ปีมาแล้ว) ซึ่งมีเนินหลุมฝังศพ ๒ เนิน เราเชื่อว่าเนินดินหลุมฝังศพทั้งสองเนินนี้เป็นแหล่งฝังศพของกลุ่มคน ๒ กลุ่มที่เป็นเพื่อนบ้านกันหรือมีความใกล้ชิดทางสังคม เราใช้วิธีการวิเคราะห์เชิงปริมาณในการศึกษาตรวจสอบความแตกต่างของวัตถุอุทิศที่พบร่วมกับหลุมฝังศพของคนในวัยที่เป็นผู้ใหญ่ นอกจากนี้ เรายังวิเคราะห์ความยาวของกระดูกแขน-ขา อายุเมื่อตาย และการเสื่อมผุของเคลือบฟัน เพื่อตรวจสอบระดับความแตกต่างของความตึงเครียดตามเพศ อายุ/วัย กลุ่มสังคม และช่วงเวลา ผลการศึกษาพบว่าผู้ใหญ่วัยสูงอายุทั้งเพศหญิงและชาย ผู้ชายทุกวัย และกลุ่มคนจากเนินฝังศพด้านตะวันตกมีจำนวนวัตถุอุทิศมากกว่ากลุ่มคนจากเนินฝังศพทางตะวันออก และดังนั้นคนที่ถูกฝังในเนินดินฝังสพทางตะวันตกอาจจะมีสถานภาพสูงกว่าคนที่ถูกฝังในเนินดินหลุมฝังศพทางตะวันออก คนที่ถูกฝังในเนินดินหลุมฝังศพทางตะวันตกมีร่างกายที่สูงกว่าและมีการเสื่อมผุของเคลือบฟันน้อยกว่าคนที่ฝังที่เนินดินทางตะวันออก และแม้ว่าการเสื่อมผุของเคลือบฟันและอัตราการเสียชีวิตของผู้หญิงลดลงเมื่อเปรียบเทียบกับผู้ชาย แต่ผู้หญิงก็มีส่วนสูงเฉลี่ยลดลง และมีอัตราการเสียชีวิตของทารกในครรภ์สูงขึ้นตามช่วงเวลาซึ่งอาจจะแสดงว่าผู้หญิงมีชีวิตความตึงเครียด และคนที่มีสถานภาพทางสังคมต่ำก็มีความตึงเครียดมากกว่าคนที่มีสภาพทางสังคมที่สูงด้วย หลักฐานประเภทโบราณวัตถุและจารึกโบราณสนับสนุนว่าความแตกต่างทางสถานภาพทางสังคมและเพศที่แหล่งโบราณคดีโนนบ้านจากเกิดขึ้นและดำรงอยู่ดังจะสะท้อนให้เห็นจากการฝังศพในที่อยู่อาศัยและการเข้ามาของระบบความเชื่อทางศาสนาอันใหม่

Organization of restrictive quarantine measures to prevent especially dangerous infections

Especially dangerous infections (EDIs) belong to the conditionally labelled group of infectious diseases that pose an exceptional epidemic threat. They are highly contagious, rapidly spreading and capable of affecting wide sections of the population in the shortest possible time, they are characterized by the severity of clinical symptoms and high mortality rates. At the present stage, the term "especially dangerous infections" is used only in the territory of the countries of the former USSR, all over the world this concept is defined as "infectious diseases that pose an extreme threat to public health on an international scale." Over the entire history of human development, more people have died as a result of epidemics and pandemics than in all wars combined. The list of especially dangerous infections and measures to prevent their spread were fixed in the International Health Regulations (IHR), adopted at the 22nd session of the WHO's World Health Assembly on July 26, 1969. In 1970, at the 23rd session of the WHO's Assembly, typhus and relapsing fever were excluded from the list of quarantine infections. As amended in 1981, the list included only three diseases represented by plague, cholera and anthrax. However, now annual additions of new infections endemic to different parts of the earth to this list take place. To date, the World Health Organization (WHO) has already included more than 100 diseases in the list of especially dangerous infections.

Fauna and conservation in the context of formal education: a study of urban and rural students in the semi-arid region of Brazil

BackgroundIn addition to playing a key role in the dynamics of ecosystems, animal diversity, especially that of wild vertebrates, is intimately linked with human evolutionary history, which has resulted in diverse interactions that must be emphasized in formal education processes. We analyzed several methods of approaches used for biological education in order to teach about wild vertebrates and their conservation in urban and rural schools in the semi-arid region of Brazil.MethodsData were obtained via questionnaires applied to 990 students, of which 528 were urban and 462 rural, distributed among the seven grades/years that comprise the last two cycles of basic education in Brazil. The richness and diversity of the animals cited by the students were calculated, being the diversity using an adaptation of the equation for the Shannon-Weaver Index (H′). Data were analyzed using non-parametric descriptive statistics.ResultsMammals and birds had the greatest richness and diversity of animals cited as most-studied in science/biology classes, and also the most indicated as occurring in the studied region. Among mammals, large carnivores with a showy appearance and utilitarian value had the highest citation frequencies, while there was a tendency for limited recognition of faunistic diversity in the other groups mentioned. Almost 70% of the students stated that their schooling processes dealt with the conservation of wild animals; however, about 50% of the students in both urban and rural contexts did not express conceptual understanding about the conservation of nature.ConclusionsThe recognition of animal diversity, especially vertebrates, beyond just mammals and birds, as well as conceptual clarity about the conservation of nature, are fundamental factors for the development of critical awareness of fauna and its conservation, and where the processes of schooling have a preponderant role. Finally, the study contributes to the legitimization of Ethnobiology as an interdisciplinary field of knowledge, especially in its interface with education, in addition to pointing out the importance of optimizing efforts in approaches to biodiversity conservation in formal educational processes.

The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes.

Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago1. Here we examine the effect of this event using 14.4million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.

Genetic structure and forensic characteristics of the Kyrgyz population from Kizilsu Kirghiz autonomous prefecture based on autosomal DIPs.

Living in the heart of Eurasia, the Kyrgyz ethnic minority have a complex human evolutionary and migration history. However, the genetic architecture of the Kyrgyz population has not been fully explored. We studied 526 Kyrgyz samples from Kizilsu Kirghiz Autonomous Prefecture in Xinjiang using the Investigator® DIPplex kit. All loci followed Hardy-Weinberg equilibrium (HWE). The combined power of discrimination (CPD) and combined power of paternity exclusion (CPE) was 0.9999999999988 and 0.9936, respectively. Compared with 90 reference populations, five InDels (HLD99, HLD81, HLD64, HLD118, and HLD111) have the potential to distinguish the Kyrgyz/Uyghur/Kazak population from other East Asian populations. Our results suggested a close genetic relationship between the Kyrgyz population and the Uyghur/Kazak populations, followed by South Asian populations. This was in accordance with the inland migration hypothesis or modern human migration influenced by warfare. Overall, this system can be used as a powerful tool in forensic individual identification and as a complementary tool in paternity cases and biogeographic ancestry analyses.

Cultural and reproductive success and the causes of war: A Yanomamö perspective

Inter-group competition including warfare is posited to be a key force in human evolution ( Alexander, 1990 ; Choi & Bowles, 2007 ; Wrangham, 1999). Chagnon's research on the Yanomamö is seminal to understanding warfare in the types of societies characteristic of human evolutionary history. Chagnon's empirical analyses of the hypothesis that competition for status or cultural success is linked to reproduction ( Irons, 1979 ) and warfare attracted considerable controversy. Potential causal factors include “blood revenge”, mate competition, resource shortages or inequality, and peace-making institutions ( Boehm, 1984 ; Keeley's (1997) ; Meggitt, 1977; Wiessner and Pupu, 2012 ; Wrangham et al., 2006 ). Here we highlight Chagnon's contributions to the study of human warfare.

What Is "Normal" Infant Sleep? Why We Still Do Not Know.

The human need for sleep is universal and unquestioned; however, humans vary in their sleep needs according to age, individual differences, as well as cultural and social norms and practices. Therefore, what is "normal" in infant sleep and the development of sleep architecture in humans is highly dependent on biological and sociocultural variables as well as socially constructed assumptions about what infant sleep "should" look like. This paper uses a multidisciplinary approach to review papers from fields including pediatrics, anthropology, psychology, medicine, and sociology to understand "normal" infant sleep. Because human culture and behavioral practice changes much more quickly than evolved human biology, and because human evolutionary history occurred in the context of breastfeeding and cosleeping, new work in the field of infant sleep architecture development would benefit from a multidisciplinary approach. To come to a consensus about what is "normal" infant sleep, researchers must agree on underlying basic assumptions of infant sleep from which to ask question and interpret findings.

Human large-scale cooperation as a product of competition between cultural groups

A fundamental puzzle of human evolution is how we evolved to cooperate with genetically unrelated strangers in transient interactions. Group-level selection on culturally differentiated populations is one proposed explanation. We evaluate a central untested prediction of Cultural Group Selection theory, by assessing whether readiness to cooperate between individuals from different groups corresponds to the degree of cultural similarity between those groups. We documented the normative beliefs and cooperative dispositions of 759 individuals spanning nine clans nested within four pastoral ethnic groups of Kenya—the Turkana, Samburu, Rendille and Borana. We find that cooperation between groups is predicted by how culturally similar they are, suggesting that norms of cooperation in these societies have evolved under the influence of group-level selection on cultural variation. Such selection acting over human evolutionary history may explain why we cooperate readily with unrelated and unfamiliar individuals, and why humans’ unprecedented cooperative flexibility is nevertheless culturally parochial.

Is there a biological basis in the selection of medicinal plants in the human species? An initial approach based on chemosensory perception of taste

The ability to identify tastes associated with plant chemicals may have favored humans in identifying plant chemists with pharmacological activity throughout human evolutionary history. The genetic basis of taste perception influences people's varying sensitivity to perceive chemical stimuli of taste. This biological basis can play an important role in plant selection to compose local medical systems, given the argument in the ethnobiological literature that plant taste can influence their selection as a medicinal resource. Thus, we sought to investigate whether there is a biological basis in the selection of these resources. Our investigation was made through the survey of ethnobiological data on the knowledge of medicinal plants and sensitivity data on the perception of bitter taste in two local communities. We tested whether local experts and active tasters of medicinal plants are more sensitive to the perception of bitter taste than the rest of the population. Additionally, we evaluated whether people who are more sensitive to bitter taste cite more plants with taste and assign more therapeutic targets to them. We did not corroborate any of our assumptions. It is likely that the bitter taste threshold is not as relevant in the selection of medicinal plants as the processes of cultural transmission.

Copy number variation of CCL3L1 among three major ethnic groups in Malaysia

BackgroundC-C motif Chemokine Ligand 3 Like 1 (CCL3L1) is a multiallelic copy number variable, which plays a crucial role in immunoregulatory and hosts defense through the production of macrophage inflammatory protein (MIP)-1α. Variable range of the CCL3L1 copies from 0 to 14 copies have been documented in several different populations. However, there is still lack of report on the range of CCL3L1 copy number exclusively among Malaysians who are a multi-ethnic population. Thus, this study aims to extensively examine the distribution of CCL3L1 copy number in the three major populations from Malaysia namely Malay, Chinese and Indian. A diploid copy number of CCL3L1 for 393 Malaysians (Malay = 178, Indian = 90, and Chinese = 125) was quantified using Paralogue Ratio Tests (PRTs) and then validated with microsatellites analysis.ResultsTo our knowledge, this is the first report on the CCL3L1 copy number that has been attempted among Malaysians and the Chinese ethnic group exhibits a diverse pattern of CCL3L1 distribution copy number from the Malay and Indian (p < 0.0001). The CCL3L1 ranged from 0 to 8 copies for both the Malay and Indian ethnic groups while 0 to 10 copies for the Chinese ethnic. Consequently, the CCL3L1 copy number among major ethnic groups in the Malaysian population is found to be significantly varied when compared to the European population (p < 0.0001). The mean/median reported for the Malay, Chinese, Indian, and European are 2.759/2.869, 3.453/3.290, 2.437/1.970 and 2.001/1.940 respectively.ConclusionThis study reveals the existence of genetic variation of CCL3L1 in the Malaysian population, and suggests by examining genetic diversity on the ethnicity, and specific geographical region could help in reconstructing human evolutionary history and for the prediction of disease risk related to the CCL3L1 copy number.

АРХИТЕКТУРА СКВОЗЬ ПРИЗМУ КУЛЬТУРНОГО ПРОСТРАНСТВА

The need to establish links between cultural space and architecture, as a way of its existence throughout the history of mankind determines the relevance of the study. The purpose of the paper is to analyze interaction and connection between cultural space and architecture in history, as well as to identify forms and methods of this connection from origin to modern times. The author presents the analysis of cultural space in modern cultural science, identifies basic structural components of cultural space: representations, meanings and values expressed in semiotic models and in the picture of the world; social relations and communications embodied in the system of social roles and attitudes; and activities that permeate all of the elements above, linking them together. Architecture is perceived as one of the ways of cultural space existence, which includes not only a model of the world, vertical and horizontal orientation in space, but also a way to express value attitudes through fixing value dominants in certain parts of a building or spaces. The study is to show that architecture acts as a way of self-identification of culture, society, social groups, individual subjects by defining their place in geographical space, the existence of external and internal spaces as a semiotic expression of “friend/foe” position. The author examines the role of different types of architectural structures, allowing fixing social hierarchy and political power in the cultural space of different eras. As a result, a connection between cultural space and architecture is established, act as the ways of forming and functioning in society throughout the history of human development.

Anthropocene-related disease: The inevitable outcome of progressive niche modification?

While the Anthropocene is often discussed in terms of the health of the planet, there has been less attention paid to its impact on the health of humans. We argue that there is now sufficient evidence of broad and growing adverse effects on human health to consider Anthropocene-related diseases and their impact on public health as a category of conditions needing specific recognition and preventative action. Using the examples of climate change-related health challenges, non-communicable disease, antimicrobial resistance and the unique challenges of the digital environment, we discuss how the profound and pervasive environmental changes of the Anthropocene can affect our health, with broad effects on societal health. We frame this concept in terms of human evolutionary history and cultural evolution’s runaway characteristics, reflecting our drive for continual and cumulative innovation for reasons beyond simply survival and Darwinian fitness. As the causative agents are often remote from those populations most adversely affected, prevention and mitigation require collective societal and policy actions. Lay summary: There is increasing evidence that our uniquely evolved ability to modify our environments rapidly and at an accelerating pace is having impacts on our health, particularly non-communicable diseases and poor mental wellbeing. Reframing these public health challenges as Anthropocene-related diseases emphasizes the need for collective responsibility and systems approaches to prevention.

Status does not predict stress: Women in an egalitarian hunter-gatherer society.

It is widely believed that there is strong association between physiological stress and an individual's social status in their social hierarchy. This has been claimed for all humans cross-culturally, as well as in non-human animals living in social groups. However, the relationship between stress and social status has not been explored in any egalitarian hunter-gatherer society; it is also under investigated in exclusively female social groups. Most of human evolutionary history was spent in small, mobile foraging bands of hunter-gatherers with little economic differentiation - egalitarian societies. We analysed women's hair cortisol concentration along with two domains of women's social status (foraging reputation and popularity) in an egalitarian hunter-gatherer society, the Hadza. We hypothesized that higher social status would be associated with lower physiological indicators of stress in these women. Surprisingly, we did not find any association between either foraging reputation or popularity and hair cortisol concentration. The results of our study suggest that social status is not a consistent or powerful predictor of physiological stress levels in women in an egalitarian social structure. This challenges the notion that social status has the same basic physiological implications across all demographics and in all human societies.

Narrative space of former residences in old Beijing city amidst societal transformation

PurposeThe former residences of historical figures are typical landscape elements of historic districts, which are characterised by the styles of these residences and spiritual historical figures cultures. The purpose of this paper is to determine how the former residences respond once the historical figures living there have passed.Design/methodology/approachThe history of human culture and progression of urban construction – which are submerged in societal transformation – is recorded for old Beijing city. Narrative space theory is used and methods such as a content analysis, map overlay and the Geographic Information System are employed to analyse the selected 300 former residences of historical figures in old Beijing city.FindingsThe results are as follows: the political setting played a key role in the evolution process, three political narrative areas in the inner city and one cultural narrative area in the outer city form the narrative spatial structure of the former residences of historical figures, “government construction” and “resident construction” are the main reasons for the loss and destruction of narrative spaces and ordinary life is an important channel for showcasing the history of former residences. The narrative spaces of these residences carry double histories, namely, the development of human history and of city construction.Originality/valueDifferent from former studies that focus on the preservation of the single historical building, this study explores the integral logic of historic buildings in the whole city through narrative space theory to get a combination of culture and space.

Relationship of sanitation, water boiling, and mosquito nets to health biomarkers in a rural subsistence population.

Throughout human evolutionary history, parasites and pathogens were a major cause of mortality-modern urban life with public health infrastructure has changed disease exposure. We examine associations between boiling water, using latrines, mosquito net usage, and biomarkers among the Tsimane, a nonindustrial subsistence population with little public health infrastructure. We conducted cross sectional surveys on water, latrines, and bed nets among 507 heads of households (aged 18-92 years, median age 41 years). Regression models estimated associations between behaviors and health biomarkers (ie, white blood cell count [WBC], hemoglobin, eosinophil count, and erythrocyte sedimentation rate) adjusting for age, sex, body mass index, wealth, schooling, and distance to the nearby market town. Latrine use is associated with 6.5% lower WBC count (β = -679.6, P = .031, SE = 314.1), 17.4% lower eosinophil counts (β = -244.7, P = .023, SE = 107.2), and reduced odds of eosinophilia (adjusted OR = 0.40, P < .019, 95% CI = 0.18-0.86). Boiling water and mosquito net use are not significantly associated with any biomarkers measured. In a subsistence population currently undergoing epidemiological transition, we find that latrine use was associated with several objective measures of health. This suggests that relatively low cost and low maintenance public health interventions may wish to focus on latrine use, as there is unmet need and potential health benefits for those who use latrines. Additionally, while the cost is higher, public health organizations aimed at improving sanitation may be able to use minimally invasive field-collected biomarkers as a diagnostic to objectively test the efficacy of interventions with greater specificity than anthropometric measurements.

THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL.

Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.

Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.

Selective sweeps, the genetic footprint of positive selection, have been extensively studied in the past decades, with dozens of methods developed to identify swept regions. However, these methods suffer from both false positive and false negative reports, and the candidates identified with different methods are often inconsistent with each other. We propose that a biological cause of this problem can be population subdivision, and a technical cause can be incomplete, or inaccurate, modeling of the dynamic process associated with sweeps. Here we used simulations to show how these effects interact and potentially cause bias. In particular, we show that sweeps maybe misclassified as either hard or soft, when the true time stage of a sweep and that implied, or pre-supposed, by the model do not match. We call this “temporal misclassification”. Similarly, “spatial misclassification (softening)” can occur when hard sweeps, which are imported by migration into a new subpopulation, are falsely identified as soft. This can easily happen in case of local adaptation, i.e. when the sweeping allele is not under positive selection in the new subpopulation, and the underlying model assumes panmixis instead of substructure. The claim that most sweeps in the evolutionary history of humans were soft, may have to be reconsidered in the light of these findings.

Archaic hominin introgression into modern human genomes.

Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?