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.

scholarly journals Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans

2017 ◽  
Author(s):  
Matthias Steinrücken ◽  
Jeffrey P. Spence ◽  
John A. Kamm ◽  
Emilia Wieczorek ◽  
Yun S. Song
Keyword(s):  
Genetic Material ◽  
Genetic Load ◽  
Modern Human ◽  
Human Populations ◽  
Effective Population ◽  
Weak Selection ◽  
Modern Humans ◽  
High Coverage ◽  
Model Based ◽  
And Migration

AbstractGenetic evidence has revealed that the ancestors of modern human populations outside of Africa and their hominin sister groups, notably the Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence-tracts along modern-day human genomes provides insight into the ancient structure and migration patterns of these archaic populations. Furthermore, it facilitates studying the selective processes that lead to the accumulation or depletion of introgressed genetic variation. Recent studies have developed methods to localize these introgressed regions, reporting long regions that are depleted of Neanderthal introgression and enriched in genes, suggesting negative selection against the Neanderthal variants. On the other hand, enriched Neanderthal ancestry in hair- and skin-related genes suggests that some introgressed variants facilitated adaptation to new environments. Here, we present a model-based method called diCal-admix and apply it to detect tracts of Neanderthal introgression in modern humans. We demonstrate its efficiency and accuracy through extensive simulations. We use our method to detect introgressed regions in modern human individuals from the 1000 Genomes Project, using a high coverage genome from a Neanderthal individual from the Altai mountains as reference. Our introgression detection results and findings concerning their functional implications are largely concordant with previous studies, and are consistent with weak selection against Neanderthal ancestry. We find some evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals, resulting from small effective population size, rather than Dobzhansky-Müller incompatibilities. Finally, we investigate the role of the X-chromosome in the divergence between Neanderthals and modern humans.

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.

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

Mobile DNA ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Etienne Guichard ◽  
Valentina Peona ◽  
Guidantonio Malagoli Tagliazucchi ◽  
Lucia Abitante ◽  
Evelyn Jagoda ◽  
...  
Keyword(s):  
Ltr Retrotransposons ◽  
Modern Humans ◽  
Anatomically Modern Humans

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 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 Stochastic models support rapid peopling of Late Pleistocene Sahul

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Corey J. A. Bradshaw ◽  
Kasih Norman ◽  
Sean Ulm ◽  
Alan N. Williams ◽  
Chris Clarkson ◽  
...  
Keyword(s):  
Stochastic Models ◽  
Ecological Model ◽  
New Guinea ◽  
Emergent Properties ◽  
Modern Humans ◽  
Global Migration ◽  
Early Settlement ◽  
Anatomically Modern Humans ◽  
Settlement Event ◽  
Initial Entry

AbstractThe peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model’s emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156–208 human generations (4368–5599 years) and at a plausible rate of 0.71–0.92 km year−1. More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000–90,000 years ago, and the peopling of Eurasia in as little as 12,000–15,000 years via inland routes.

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