scholarly journals Genetic and climatic factors in the dispersal of Anatomically Modern Humans Out of Africa

2021 ◽  
Author(s):  
Raymond Tobler ◽  
Yassine Souilmi ◽  
Christian Huber ◽  
Nigel Bean ◽  
Chris Turney ◽  
...  
Keyword(s):  
Climatic Factors ◽  
Genetic Admixture ◽  
Human Populations ◽  
Genetic Adaptation ◽  
Modern Humans ◽  
Strong Selection ◽  
Skin Physiology ◽  
Anatomically Modern Humans ◽  
Out Of Africa ◽  
Genetic Signatures

Abstract The evolutionarily recent dispersal of Anatomically Modern Humans (AMH) out of Africa and across Eurasia provides an opportunity to study rapid genetic adaptation to multiple new environments. Genomic analyses of modern human populations have detected limited signals of strong selection such as hard sweeps, but genetic admixture between populations is capable of obscuring these patterns and is well known in recent human history, such as during the Bronze Age4. Here we show that ancient human genomic datasets contain multiple genetic signatures of strong selection including 57 hard sweeps, many with strong associations with cold adaptation. Similar genetic signatures of adaptation are also observed in adaptively-introgressed archaic hominin loci, as well as modern Arctic human groups. Consistent targets include the regulation of fat storage, skin physiology, cilia function and neural development; with multiple associations to modern western diseases. The spatiotemporal patterns of the hard sweeps allow reconstruction of early AMH population dispersals, and reveal a prolonged period of genetic adaptation (~80-50,000 years) following their initial out of Africa movement, before a rapid spread across Eurasia reaching as far as Australia.

scholarly journals An evolutionary medicine perspective on Neandertal extinction

2016 ◽  
Author(s):  
Alexis P. Sullivan ◽  
Marc de Manuel ◽  
Tomas Marques-Bonet ◽  
George H. Perry
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Pathogen Resistance ◽  
Modern Human ◽  
Innate Immune ◽  
Evolutionary Medicine ◽  
Genetic Admixture ◽  
Human Populations ◽  
Modern Humans ◽  
Anatomically Modern Humans

AbstractThe Eurasian sympatry of Neandertals and anatomically modern humans – beginning at least 45,000 years ago and lasting for more than 5,000 years – has long sparked anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the “differential pathogen resistance” extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture – and thus direct contact – between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (six chromosomes per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates – genes with the highest 1% genetic diversity genome-wide in non-human apes. In contrast, Neandertals had similar to higher levels of genetic diversity than humans in 13 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, this model does have limitations.

scholarly journals Revisiting the Out of Africa event with a novel Deep Learning approach

2020 ◽  
Author(s):  
Francesco Montinaro ◽  
Vasili Pankratov ◽  
Burak Yelmen ◽  
Luca Pagani ◽  
Mayukh Mondal
Keyword(s):  
Deep Learning ◽  
Sequential Monte Carlo ◽  
Whole Genome Sequence ◽  
Learning Approach ◽  
Whole Genome ◽  
Modern Humans ◽  
Anatomically Modern Humans ◽  
Out Of Africa ◽  
Approximate Bayesian ◽  
Back To Africa

AbstractAnatomically modern humans evolved around 300 thousand years ago in Africa1. Modern humans started to appear in the fossil record outside of Africa about 100 thousand years ago though other hominins existed throughout Eurasia much earlier2–4. Recently, several researchers argued in favour of a single out of Africa event for modern humans based on whole-genome sequences analyses5–7. However, the single out of Africa model is in contrast with some of the findings from fossil records, which supports two out of Africa8,9, and uniparental data, which proposes back to Africa movement10,11. Here, we used a novel deep learning approach coupled with Approximate Bayesian Computation and Sequential Monte Carlo to revisit these hypotheses from the whole genome sequence perspective. Our results support the back to Africa model over other alternatives. We estimated that there are two successive splits between Africa and out of African populations happening around 60-80 thousand years ago and separated by 12-13 thousand years. One of the populations resulting from the more recent split has to a large extent replaced the older West African population while the other one has founded the out of Africa populations.

The Archaeology of Archaic and Early ModernHomo Sapiens: An African Perspective

1993 ◽  
Vol 3 (1) ◽  
pp. 21-39 ◽  
Author(s):  
Philip Allsworth-Jones
Keyword(s):  
Near East ◽  
Middle Stone Age ◽  
Stone Age ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Anatomically Modern Humans ◽  
African Perspective ◽  
Out Of Africa

Whereas in Europe the transition from Middle to Upper Palaeolithic and the replacement of Neanderthal by anatomically modern humans appear to be synchronous events, in Africa this is not the case. Neanderthals as such were not present in Africa, and if the ‘Out of Africa’ model is correct, the ancestors of anatomically modern humans must have made their appearance in a Middle Stone Age context before 100,000 years ago. Subsequently, it seems that they coexisted with Neanderthals for up to 70,000 years in the Near East. If a direct biological correlation can be ruled out, the question arises: what was the impetus for an Upper Palaeolithic ‘revolution’ and why should it have taken place at all?

Late Pleistocene palaeolake in the interior of Oman: a potential key area for the dispersal of anatomically modern humans out-of-Africa?

2011 ◽  
Vol 27 (1) ◽  
pp. 13-16 ◽  
Author(s):  
Thomas M. Rosenberg ◽  
Frank Preusser ◽  
Ingo Blechschmidt ◽  
Dominik Fleitmann ◽  
Reto Jagher ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Modern Humans ◽  
Anatomically Modern Humans ◽  
Out Of Africa

scholarly journals The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia

Hereditas ◽  
2021 ◽  
Vol 158 (1) ◽  
Author(s):  
Úlfur Árnason
Keyword(s):  
Nuclear Dna ◽  
Maternal Inheritance ◽  
Homo Sapiens ◽  
Human Populations ◽  
Before Present ◽  
Modern Humans ◽  
Origin Of Modern Humans ◽  
The Common ◽  
Out Of Africa ◽  
Mtdna Introgression

Abstract Background The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH. Results In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs. The comparison showed full phylogenetic coherence between these two separate sets of data. The results were consistent with potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH at the same time as they lent no support to the OOAH. Conclusions The conformity between the mtDNA and Y-DNA phylogenies of Hss is consistent with the understanding that Eurasia was the donor and not the receiver in human evolution. The evolutionary problems related to OOAH became similarly exposed by the mtDNA introgression that took place from Hss into Neanderthals ≈ 500,000 YBP, a circumstance that demonstrated the early coexistence of the two lineages in Eurasia.

scholarly journals Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago

2017 ◽  
Author(s):  
Vicente M. Cabrera ◽  
Patricia Marrero ◽  
Khaled K. Abu-Amero ◽  
Jose M. Larruga
Keyword(s):  
Y Chromosome ◽  
Fossil Record ◽  
Climatic Conditions ◽  
African Origin ◽  
Modern Humans ◽  
Frequency Distributions ◽  
Human Movements ◽  
Anatomically Modern Humans ◽  
Out Of Africa ◽  
Southern Route

ABSTRACTBackgroundAfter three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya.ResultsThe coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.ConclusionsThese results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.

scholarly journals Out of Africa by spontaneous migration waves

2018 ◽  
Author(s):  
Paul D. Bons ◽  
Catherine C. Bauer ◽  
Hervé Bocherens ◽  
Tamara de Riese ◽  
Dorothée G. Drucker ◽  
...  
Keyword(s):  
Assortative Mating ◽  
Current Model ◽  
Source Region ◽  
Regional Differentiation ◽  
Power Law Distribution ◽  
Modern Humans ◽  
Large Wave ◽  
Anatomically Modern Humans ◽  
Out Of Africa ◽  
And Migration

AbstractHominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered “spontaneous”, as the current model excludes environmental or other factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.

Luminescence dating Hajar Mountain alluvial fan systems, northern Oman 

2021 ◽  
Author(s):  
Sam Woor ◽  
Julie Durcan ◽  
Ash Parton ◽  
David Thomas
Keyword(s):  
Late Quaternary ◽  
Alluvial Fan ◽  
Luminescence Dating ◽  
Modern Humans ◽  
Temporal Complexity ◽  
Human Dispersal ◽  
Palaeoenvironmental Change ◽  
Anatomically Modern Humans ◽  
Out Of Africa ◽  
Scale Data

<p>The alluvial/fluvial fan systems of northern Oman act as sensitive geoproxy records of Late Quaternary palaeohydrology and past landscape evolution, offering records of palaeoenvironmental change which cannot be reconstructed from nearby speleothem records alone (Parton et al., 2013). These systems also provide evidence for the important link between the changing abundance of freshwater in the Arabian interior and the dispersal of anatomically modern humans (AMHs) out of Africa (Rosenberg et al., 2012). Limited previous luminescence dating analyses have reported fan activation west of the Hajar during insolation maxima and monsoon intensification throughout the Late Quaternary (Parton et al., 2015). However, there are currently no studies to date which present chronologies for the fan systems to the east of the Hajar Mountains.</p><p>We present the first luminescence based chronology for the fan systems to the east of the Hajar Mountains, providing landform scale data on fan behaviour, including spatial-temporal complexity and variability. This facilitates comparison of the temporal response of fans east and west of the mountains, including differential responses to external forcing. Ages will also be compared with regional palaeoenvironmental and palaeoclimatic records, to inform landscape reconstructions in northern Oman during the late Quaternary.</p><p><strong>References</strong></p><p>Rosenberg, T.M., Preusser, F., Blechschmidt, I., Fleitmann, D., Jagher, R. and Matter, A., 2012. Late Pleistocene palaeolake in the interior of Oman: a potential key area for the dispersal of anatomically modern humans out‐of‐Africa?. Journal of Quaternary Science, 27(1), pp.13-16.</p><p>Parton, A., Farrant, A.R., Leng, M.J., Schwenninger, J.L., Rose, J.I., Uerpmann, H.P. and Parker, A.G., 2013. An early MIS 3 pluvial phase in Southeast Arabia: climatic and archaeological implications. Quaternary International, 300, pp.62-74.</p><p>Parton, A., Farrant, A.R., Leng, M.J., Telfer, M.W., Groucutt, H.S., Petraglia, M.D. and Parker, A.G., 2015. Alluvial fan records from southeast Arabia reveal multiple windows for human dispersal. Geology, 43(4), pp.295-298.</p><p> </p>

African and Asian perspectives on the origins of modern humans

1992 ◽  
Vol 337 (1280) ◽  
pp. 201-215 ◽  
Keyword(s):  
Cultural Differences ◽  
Far East ◽  
Human Populations ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Fossil Hominids ◽  
The Far East ◽  
Anatomically Modern Humans ◽  
The One ◽  
Noah's Ark

The ways in which the cultural evidence - in its chronological context - can be used to imply behavioural patterning and to identify possible causes of change are discussed. Improved reliability in dating methods, suites of dates from different regional localities, and new, firmly dated fossil hominids from crucial regions such as northeast Africa, the Levant, India and China, are essential for clarification of the origin and spread of the modern genepool. Hominid ancestry in Africa is reviewed, as well as the claims for an independent origin in Asia. The cultural differences and changes within Africa, West and South Asia and the Far East in the later Middle and early Upper Pleistocene are examined and compared, and some behavioural implications are suggested, taking account of the evolutionary frameworks suggested by the ‘multiregional evolution’ and ‘Noah’s Ark’ hypotheses of human evolution. A possible explanation is proposed for the cultural differences between Africa, West Asia and India on the one hand, and southeast Asia and the Far East on the other. The apparent hiatus between the appearance of the first anatomically modern humans, ca . 100 ka ago, and the appearance of the Upper Palaeolithic and other contemporaneous technological and behavioural changes around 40 ka ago, is discussed. It is suggested that the anatomical changes occurred first, and that neurological changes permitted the development of fully syntactic language some 50 ka later. The intellectual and behavioural revolution, best demonstrated by the ‘Upper Palaeolithic’ of Eurasia, seems to have been dependent on this linguistic development - within the modern genepool - and triggered the rapid migration of human populations throughout the Old World.

scholarly journals Impact of non-LTR retrotransposons in the differentiation and evolution of Anatomically Modern Humans

2017 ◽  
Author(s):  
Etienne Guichard ◽  
Valentina Peona ◽  
Guidantonio Malagoli-Tagliazucchi ◽  
Lucia Abitante ◽  
Evelyn Jagoda ◽  
...  
Keyword(s):  
Human Populations ◽  
Human Lineage ◽  
Ltr Retrotransposons ◽  
Modern Humans ◽  
Functional Variants ◽  
Expression Of Genes ◽  
Splicing Variants ◽  
Anatomically Modern Humans ◽  
And Migration ◽  
Species Specific

ABSTRACTTransposable Elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) extensively shaped the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Briefly, we first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. Notably, these insertions targeted genes more frequently than randomly expected and are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes targeted by human-specific N-LTRr insertions seems to reflect phenotypic changes that occurred during human evolution. Furthermore, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we also identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, which show traces of positive selection and are now fixed in all present-day human populations. In sum, our results strongly suggest that N-LTRr impacted our differentiation as a species and have been a constant source of genomic variability all throughout the evolution of the human lineage.

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