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 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.

scholarly journals Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

2015 ◽  
Author(s):  
PingHsun Hsieh ◽  
Krishna R Veeramah ◽  
Joseph Lachance ◽  
Sarah A Tishkoff ◽  
Jeffrey D Wall ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Muscle Development ◽  
Demographic History ◽  
Single Pulse ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Anatomically Modern Humans ◽  
History Of ◽  
African Pygmies

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist

2020 ◽  
Author(s):  
Erik R Funk ◽  
Garth M Spellman ◽  
Kevin Winker ◽  
Jack J Withrow ◽  
Kristen C Ruegg ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genome Sequence ◽  
Population Genetic ◽  
Approximate Bayesian Computation ◽  
Sequence Data ◽  
Species Group ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Approximate Bayesian

Abstract Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.]

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>

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