scholarly journals ABO genetic variation in Neanderthals and Denisovans

2020 ◽  
Author(s):  
Fernando A. Villanea ◽  
Emilia Huerta-Sanchez ◽  
P. Keolu Fox
Keyword(s):  
Balancing Selection ◽  
Low Frequency ◽  
Sequence Divergence ◽  
Modern Human ◽  
Blood Type ◽  
Modern Humans ◽  
Low Frequencies ◽  
Southeast Asians ◽  
Allele Variant ◽  
Genetic Landscape

1AbstractVariation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two derived Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two ancestral variant of the O1 allele, similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared to portions of the genome evolving neutrally.

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 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.

Clash of signs: Putting bilingualism back into language evolution

2020 ◽  
Author(s):  
Steven Samuel
Keyword(s):  
Language Evolution ◽  
Modern Human ◽  
Alarm Calls ◽  
Bilingual Children ◽  
Human Language ◽  
Typically Developing ◽  
Typically Developing Children ◽  
Modern Humans ◽  
The Real ◽  
Multiple Languages

Research and thinking into the cognitive aspects of language evolution has usually attempted to account for how the capacity for learning even one modern human language developed. Bilingualism has perhaps been thought of as something to think about only once the ‘real’ puzzle of monolingualism is solved, but this would assume in turn (and without evidence) that bilingualism evolved after monolingualism. All typically-developing children (and adults) are capable of learning multiple languages, and the majority of modern humans are at least bilingual. In this paper I ask whether by skipping bilingualism out of language evolution we have missed a trick. I propose that exposure to synonymous signs, such as food and alarm calls, are a necessary precondition for the abstracting away of sound from referent. In support of this possibility is evidence that modern day bilingual children are better at breaking this ‘word magic’ spell. More generally, language evolution should be viewed through the lens of bilingualism, as this is the end state we are attempting to explain.

scholarly journals Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽  
2021 ◽  
Vol 592 (7853) ◽  
pp. 253-257 ◽  
Author(s):  
Mateja Hajdinjak ◽  
Fabrizio Mafessoni ◽  
Laurits Skov ◽  
Benjamin Vernot ◽  
Alexander Hübner ◽  
...  
Keyword(s):  
Family History ◽  
East Asia ◽  
Late Pleistocene ◽  
Modern Human ◽  
Human Migration ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Genome Wide ◽  
Genome Wide Data

AbstractModern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

scholarly journals Earless toads sense low frequencies but miss the high notes

2017 ◽  
Vol 284 (1864) ◽  
pp. 20171670 ◽  
Author(s):  
Molly C. Womack ◽  
Jakob Christensen-Dalsgaard ◽  
Luis A. Coloma ◽  
Juan C. Chaparro ◽  
Kim L. Hoke
Keyword(s):  
High Frequency ◽  
Species Differences ◽  
Low Frequency ◽  
Auditory Brainstem ◽  
Low Frequencies ◽  
Hearing Sensitivity ◽  
Sensory Pathways ◽  
Airborne Sound ◽  
Vibrational Sensitivity ◽  
Species Specific

Sensory losses or reductions are frequently attributed to relaxed selection. However, anuran species have lost tympanic middle ears many times, despite anurans' use of acoustic communication and the benefit of middle ears for hearing airborne sound. Here we determine whether pre-existing alternative sensory pathways enable anurans lacking tympanic middle ears (termed earless anurans) to hear airborne sound as well as eared species or to better sense vibrations in the environment. We used auditory brainstem recordings to compare hearing and vibrational sensitivity among 10 species (six eared, four earless) within the Neotropical true toad family (Bufonidae). We found that species lacking middle ears are less sensitive to high-frequency sounds, however, low-frequency hearing and vibrational sensitivity are equivalent between eared and earless species. Furthermore, extratympanic hearing sensitivity varies among earless species, highlighting potential species differences in extratympanic hearing mechanisms. We argue that ancestral bufonids may have sufficient extratympanic hearing and vibrational sensitivity such that earless lineages tolerated the loss of high frequency hearing sensitivity by adopting species-specific behavioural strategies to detect conspecifics, predators and prey.

scholarly journals High Polymorphism at the Human Melanocortin 1 Receptor Locus

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1547-1557 ◽  
Author(s):  
Brinda K Rana ◽  
David Hewett-Emmett ◽  
Li Jin ◽  
Benny H-J Chang ◽  
Naymkhishing Sambuughin ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Nucleotide Diversity ◽  
Coat Color ◽  
Low Frequency ◽  
Melanocortin Receptor ◽  
Human Populations ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Southeast Asians ◽  
Color Changes

Abstract Variation in human skin/hair pigmentation is due to varied amounts of eumelanin (brown/black melanins) and phaeomelanin (red/yellow melanins) produced by the melanocytes. The melanocortin 1 receptor (MC1R) is a regulator of eu- and phaeomelanin production in the melanocytes, and MC1R mutations causing coat color changes are known in many mammals. We have sequenced the MC1R gene in 121 individuals sampled from world populations with an emphasis on Asian populations. We found variation at five nonsynonymous sites (resulting in the variants Arg67Gln, Asp84Glu, Val92Met, Arg151Cys, and Arg163Gln), but at only one synonymous site (A942G). Interestingly, the human consensus protein sequence is observed in all 25 African individuals studied, but at lower frequencies in the other populations examined, especially in East and Southeast Asians. The Arg163Gln variant is absent in the Africans studied, almost absent in Europeans, and at a low frequency (7%) in Indians, but is at an exceptionally high frequency (70%) in East and Southeast Asians. The MC1R gene in common and pygmy chimpanzees, gorilla, orangutan, and baboon was sequenced to study the evolution of MC1R. The ancestral human MC1R sequence is identical to the human consensus protein sequence, while MC1R varies considerably among higher primates. A comparison of the rates of substitution in genes in the melanocortin receptor family indicates that MC1R has evolved the fastest. In addition, the nucleotide diversity at the MC1R locus is shown to be several times higher than the average nucleotide diversity in human populations, possibly due to diversifying selection.

scholarly journals Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 863-872 ◽  
Author(s):  
Helmi Kuittinen ◽  
Montserrat Aguadé
Keyword(s):  
Nucleotide Diversity ◽  
Direct Relationship ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Neutral Theory ◽  
Low Frequency ◽  
The Other ◽  
Nucleotide Variation ◽  
Rapid Population Growth ◽  
History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

A waveform inversion technique for measuring elastic wave attenuation in cylindrical bars

Geophysics ◽  
1992 ◽  
Vol 57 (6) ◽  
pp. 854-859 ◽  
Author(s):  
Xiao Ming Tang
Keyword(s):  
Elastic Wave ◽  
Wave Attenuation ◽  
Waveform Inversion ◽  
Finite Size ◽  
Low Frequency ◽  
Frequency Range ◽  
Multiple Reflections ◽  
Low Frequencies ◽  
The Time Domain ◽  
Attenuation Values

A new technique for measuring elastic wave attenuation in the frequency range of 10–150 kHz consists of measuring low‐frequency waveforms using two cylindrical bars of the same material but of different lengths. The attenuation is obtained through two steps. In the first, the waveform measured within the shorter bar is propagated to the length of the longer bar, and the distortion of the waveform due to the dispersion effect of the cylindrical waveguide is compensated. The second step is the inversion for the attenuation or Q of the bar material by minimizing the difference between the waveform propagated from the shorter bar and the waveform measured within the longer bar. The waveform inversion is performed in the time domain, and the waveforms can be appropriately truncated to avoid multiple reflections due to the finite size of the (shorter) sample, allowing attenuation to be measured at long wavelengths or low frequencies. The frequency range in which this technique operates fills the gap between the resonant bar measurement (∼10 kHz) and ultrasonic measurement (∼100–1000 kHz). By using the technique, attenuation values in a PVC (a highly attenuative) material and in Sierra White granite were measured in the frequency range of 40–140 kHz. The obtained attenuation values for the two materials are found to be reliable and consistent.

Methods to isolate retrograde and prograde Rayleigh-wave signals

2019 ◽  
Vol 219 (2) ◽  
pp. 975-994 ◽  
Author(s):  
Gabriel Gribler ◽  
T Dylan Mikesell
Keyword(s):  
Rayleigh Wave ◽  
Time Domain ◽  
Fundamental Mode ◽  
Poisson Ratio ◽  
Low Frequency ◽  
Wave Dispersion ◽  
Low Frequencies ◽  
Retrograde Motion ◽  
Mode Identification ◽  
Time Frequency

SUMMARY Estimating shear wave velocity with depth from Rayleigh-wave dispersion data is limited by the accuracy of fundamental and higher mode identification and characterization. In many cases, the fundamental mode signal propagates exclusively in retrograde motion, while higher modes propagate in prograde motion. It has previously been shown that differences in particle motion can be identified with multicomponent recordings and used to separate prograde from retrograde signals. Here we explore the domain of existence of prograde motion of the fundamental mode, arising from a combination of two conditions: (1) a shallow, high-impedance contrast and (2) a high Poisson ratio material. We present solutions to isolate fundamental and higher mode signals using multicomponent recordings. Previously, a time-domain polarity mute was used with limited success due to the overlap in the time domain of fundamental and higher mode signals at low frequencies. We present several new approaches to overcome this low-frequency obstacle, all of which utilize the different particle motions of retrograde and prograde signals. First, the Hilbert transform is used to phase shift one component by 90° prior to summation or subtraction of the other component. This enhances either retrograde or prograde motion and can increase the mode amplitude. Secondly, we present a new time–frequency domain polarity mute to separate retrograde and prograde signals. We demonstrate these methods with synthetic and field data to highlight the improvements to dispersion images and the resulting dispersion curve extraction.

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.

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