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 Oxytocin and vasotocin receptor variation sheds light into the evolution of human prosociality

2018 ◽  
Author(s):  
Constantina Theofanopoulou ◽  
Alejandro Andirkó ◽  
Cedric Boeckx ◽  
Erich D. Jarvis
Keyword(s):  
Balancing Selection ◽  
Modern Human ◽  
Primate Species ◽  
Human Populations ◽  
Modern Humans ◽  
Social Traits ◽  
Pathogenicity Prediction ◽  
Vasopressin Receptors ◽  
Specific Variation ◽  
Major Allele

AbstractModern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopressin receptors (VTR1A/AVPR1A and AVPR1B/VTR1B). Here, we compared the full genomic sequences of these receptors between modern humans, archaic humans, and 12 non-human primate species, and identified sites that show heterozygous variation in modern humans and archaic humans distinct from variation in other primates, and that have associated literature. We performed variant clustering, pathogenicity prediction, regulation, linkage disequilibrium frequency and selection analyses on data in different modern-human populations. We found five sites with modern human specific variation, where the modern human allele is the major allele in the global population (OTR: rs1042778, rs237885, rs6770632; VTR1A: rs10877969; VTR1B: rs33985287). Among them, the OTR-rs6770632 was predicted to be the most functional. We found two sites where alleles (OTR: rs59190448 and rs237888)1 present only in modern humans and archaic humans are under positive selection in modern humans, with rs237888 predicted to be a highly functional site. We identified three sites of convergent evolution between modern humans and bonobos (OTR: rs2228485 and rs237897; VTR1A: rs1042615), with OTR-rs2228485 ranking very highly in terms of functionality and being under balancing selection in modern humans. Our findings shed light on evolutionary questions of modern human and hominid prosociality, as well as on similarities in the social behavior between modern humans and bonobos.

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.

Review Feature: A review of The Mind in the Cave: Consciousness and the Origins of Art by David Lewis-Williams. London: Thames & Hudson, 2002. ISBN 0-500-05117-8 hardback £18.95 & US$29.95; 320 pp., 66 figs., 29 colour plates

2003 ◽  
Vol 13 (2) ◽  
pp. 263-279 ◽  
Author(s):  
David Lewis-Williams ◽  
E. Thomas Lawson ◽  
Knut Helskog ◽  
David S. Whitley ◽  
Paul Mellars
Keyword(s):  
Rock Art ◽  
David Lewis ◽  
Modern Human ◽  
Hominid Evolution ◽  
Modern Humans ◽  
Radiocarbon Dates ◽  
Anatomically Modern Humans ◽  
The Mind ◽  
Cave Art ◽  
West European

David Lewis-Williams is well-known in rock-art circles as the author of a series of articles drawing on ethnographic material and shamanism (notably connected with the San rock art of southern Africa) to gain new insights into the Palaeolithic cave art of western Europe. Some 15 years ago, with Thomas Dowson, he proposed that Palaeolithic art owed its inspiration at least in part to trance experiences (altered states of consciousness) associated with shamanistic practices. Since that article appeared, the shamanistic hypothesis has both been widely adopted and developed in the study of different rock-art traditions, and has become the subject of lively and sometimes heated controversy. In the present volume, Lewis-Williams takes the argument further, and combines the shamanistic hypothesis with an interpretation of the development of human consciousness. He thus enters another contentious area of archaeological debate, seeking to understand west European cave art in the context of (and as a marker of) the new intellectual capacities of anatomically modern humans. Radiocarbon dates for the earliest west European cave art now place it contemporary with the demise of the Neanderthals around 30,000 years ago, and cave art, along with carved or decorated portable items, appears to announce the arrival and denote the success of modern humans in this region. Lewis-Williams argues that such cave art would have been beyond the capabilities of Neanderthals, and that this kind of artistic ability is unique to anatomically modern humans. Furthermore, he concludes that the development of the new ability cannot have been the product of hundreds of thousands of years of gradual hominid evolution, but must have arisen much more abruptly, within the novel neurological structure of anatomically modern humans. The Mind in the Cave is thus the product of two hypotheses, both of them contentious — the shamanistic interpretation of west European Upper Palaeolithic cave art, and the cognitive separation of modern humans and Neanderthals. But is it as simple as that? Was cave art the hallmark of a new cognitive ability and social consciousness that were beyond the reach of previous hominids? And is shamanism an outgrowth of the hard-wired structure of the modern human brain? We begin this Review Feature with a brief summary by David Lewis-Williams of the book's principal arguments. There follows a series of comments addressing both the meaning of the west European cave art, and its wider relevance for the understanding of the Neanderthal/modern human transition.

scholarly journals The early Aurignacian dispersal of modern humans into westernmost Eurasia

2020 ◽  
Vol 117 (41) ◽  
pp. 25414-25422
Author(s):  
Jonathan A. Haws ◽  
Michael M. Benedetti ◽  
Sahra Talamo ◽  
Nuno Bicho ◽  
João Cascalheira ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
Modern Human ◽  
Human Populations ◽  
Southern Europe ◽  
Modern Humans ◽  
Present Evidence ◽  
Western Margin ◽  
Human Presence ◽  
Human Dispersal ◽  
Central Portugal

Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Sub Saharan Africa ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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 Archaic mitochondrial DNA inserts in modern day nuclear genomes

2019 ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes ◽  
Generation Sequencing

Abstract Background: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

scholarly journals Something old, something borrowed: Admixture and adaptation in human evolution

2018 ◽  
Author(s):  
Michael Dannemann ◽  
Fernando Racimo
Keyword(s):  
Human Evolution ◽  
Ancient Dna ◽  
Gene Pool ◽  
Recent Literature ◽  
Genetic Material ◽  
Modern Human ◽  
Human Populations ◽  
Modern Humans ◽  
Functional Assays ◽  
Over Time

Almost a decade ago, the sequencing of ancient DNA from archaic humans - Neanderthals and Denisovans - revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Were introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time.

scholarly journals Something old, something borrowed: Admixture and adaptation in human evolution

2018 ◽  
Author(s):  
Michael Dannemann ◽  
Fernando Racimo
Keyword(s):  
Human Evolution ◽  
Ancient Dna ◽  
Gene Pool ◽  
Recent Literature ◽  
Genetic Material ◽  
Modern Human ◽  
Human Populations ◽  
Modern Humans ◽  
Functional Assays ◽  
Over Time

Almost a decade ago, the sequencing of ancient DNA from archaic humans - Neanderthals and Denisovans - revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Were introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

2019 ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes ◽  
Generation Sequencing

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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