scholarly journals Why should mitochondria define species?

2018 ◽  
Author(s):  
M.Y. Stoeckle ◽  
D.S. Thaler
Keyword(s):  
Animal Species ◽  
Population Expansion ◽  
Purifying Selection ◽  
Modern Human ◽  
Similar Process ◽  
Lineage Sorting ◽  
Modern Humans ◽  
Evolutionary Mechanisms ◽  
Domain Experts ◽  
Almost All

More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

scholarly journals Phospho-tuning immunity through Denisovan, modern human and mouse TNFAIP3 gene variants

2019 ◽  
Author(s):  
Nathan W. Zammit ◽  
Owen M. Siggs ◽  
Paul Gray ◽  
Keisuke Horikawa ◽  
Stephen R. Daley ◽  
...  
Keyword(s):  
Modern Human ◽  
Protease Domain ◽  
Modern Humans ◽  
Evolutionary Mechanisms ◽  
Tnfaip3 Gene ◽  
Trade Offs ◽  
Genomic Analyses ◽  
Anatomically Modern Humans ◽  
Microbial Tolerance ◽  
Human And Mouse

AbstractResisting or tolerating microbes are alternative strategies to survive infection, but little is known about the evolutionary mechanisms controlling this balance. Here, genomic analyses of anatomically modern humans, extinct Denisovan hominins, and mice revealed a series of missense variants in the immune response inhibitor A20 (encoded by TNFAIP3), substituting non-catalytic residues of the ubiquitin protease domain to diminish IκB-dependent phosphorylation and activation of A20. Two A20 variants with partial phosphorylation deficits appeared beneficial: one originating in Denisovans and introgressed in modern humans throughout Oceania, and another in a mouse strain resistant to Coxsackievirus. By contrast, a variant with 95% loss of phosphorylation caused spontaneous inflammatory disease in humans and mice. Analysis of the partial phosphorylation variant in mice revealed diminished tolerance of bacterial lipopolysaccharide or to poxvirus inoculation as trade-offs for enhanced immunity.One Sentence SummaryModern and ancient variants reveal a genetically tunable element for balancing immunity and microbial tolerance.

scholarly journals Evolution of Methyltransferase-Like (METTL) Proteins in Metazoa: A Complex Gene Family Involved in Epitranscriptomic Regulation and Other Epigenetic Processes

2021 ◽  
Author(s):  
Juliet M Wong ◽  
Jose M Eirin-Lopez
Keyword(s):  
Gene Family ◽  
Purifying Selection ◽  
Functional Differentiation ◽  
Similar Process ◽  
Phenotypic Traits ◽  
Functional Specialization ◽  
Evolutionary Mechanisms ◽  
Binding Domains ◽  
Rates Of Evolution ◽  
Basal Metazoan

Abstract The methyltransferase-like (METTL) proteins constitute a family of seven-beta-strand methyltransferases with S-adenosyl methionine-binding domains that modify DNA, RNA, and proteins. Methylation by METTL proteins contributes to the epigenetic, and in the case of RNA modifications, epitranscriptomic regulation of a variety of biological processes. Despite their functional importance, most investigations of the substrates and functions of METTLs within metazoans have been restricted to model vertebrate taxa. In the present work, we explore the evolutionary mechanisms driving the diversification and functional differentiation of 33 individual METTL proteins across Metazoa. Our results show that METTLs are nearly ubiquitous across the animal kingdom, with most having arisen early in metazoan evolution (i.e., occur in basal metazoan phyla). Individual METTL lineages each originated from single independent ancestors, constituting monophyletic clades, which suggests that each METTL was subject to strong selective constraints driving its structural and/or functional specialization. Interestingly, a similar process did not extend to the differentiation of nucleoside-modifying and protein-modifying METTLs (i.e., each METTL type did not form a unique monophyletic clade). The members of these two types of METTLs also exhibited differences in their rates of evolution. Overall, we provide evidence that the long-term evolution of METTL family members was driven by strong purifying selection, which in combination with adaptive selection episodes, led to the functional specialization of individual METTL lineages. This work contributes useful information regarding the evolution of a gene family that fulfills a variety of epigenetic functions, and can have profound influences on molecular processes and phenotypic traits.

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 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

2021 ◽  
Author(s):  
Liang Cheng ◽  
Xudong Han ◽  
Zijun Zhu ◽  
Changlu Qi ◽  
Ping Wang ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Purifying Selection ◽  
Virus Genome ◽  
Receptor Binding Domain ◽  
Evolutionary Trends ◽  
Synonymous Mutations ◽  
Almost All ◽  
Virus Strains ◽  
New Mutations

Abstract Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.

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.

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 Recent origin of low trabecular bone density in modern humans

2014 ◽  
Vol 112 (2) ◽  
pp. 366-371 ◽  
Author(s):  
Habiba Chirchir ◽  
Tracy L. Kivell ◽  
Christopher B. Ruff ◽  
Jean-Jacques Hublin ◽  
Kristian J. Carlson ◽  
...  
Keyword(s):  
Body Size ◽  
Trabecular Bone ◽  
Homo Sapiens ◽  
Modern Human ◽  
Homo Erectus ◽  
Lower Limbs ◽  
Modern Humans ◽  
Human Skeleton ◽  
Trabecular Density ◽  
Fossil Hominins

Humans are unique, compared with our closest living relatives (chimpanzees) and early fossil hominins, in having an enlarged body size and lower limb joint surfaces in combination with a relatively gracile skeleton (i.e., lower bone mass for our body size). Some analyses have observed that in at least a few anatomical regions modern humans today appear to have relatively low trabecular density, but little is known about how that density varies throughout the human skeleton and across species or how and when the present trabecular patterns emerged over the course of human evolution. Here, we test the hypotheses that (i) recent modern humans have low trabecular density throughout the upper and lower limbs compared with other primate taxa and (ii) the reduction in trabecular density first occurred in early Homo erectus, consistent with the shift toward a modern human locomotor anatomy, or more recently in concert with diaphyseal gracilization in Holocene humans. We used peripheral quantitative CT and microtomography to measure trabecular bone of limb epiphyses (long bone articular ends) in modern humans and chimpanzees and in fossil hominins attributed to Australopithecus africanus, Paranthropus robustus/early Homo from Swartkrans, Homo neanderthalensis, and early Homo sapiens. Results show that only recent modern humans have low trabecular density throughout the limb joints. Extinct hominins, including pre-Holocene Homo sapiens, retain the high levels seen in nonhuman primates. Thus, the low trabecular density of the recent modern human skeleton evolved late in our evolutionary history, potentially resulting from increased sedentism and reliance on technological and cultural innovations.

Chromosomal instability in different species of agricultural animals (review)

2021 ◽  
pp. 19-26
Author(s):  
V. A. Andreeva
Keyword(s):  
Chromosomal Instability ◽  
Animal Species ◽  
Western Siberia ◽  
Reproductive Function ◽  
Farm Animals ◽  
Chromosomal Disorders ◽  
Important Indicator ◽  
Karyotypic Analysis ◽  
Different Types ◽  
Almost All

The purpose of the work was to analyze the frequency of chromosomal instability in different species of agricultural animals in Western Siberia on the basis of literature data. The analysis of the literature on the topic of somatic chromosomal instability in agricultural animals has been carried out. Despite the stability of the chromosome set, deviations from it are quite common. It is noteworthy that chromosomal instability is characteristic of almost all individuals in the population and serves as an important indicator for assessing the natural mutability of chromosomes. It has been found if an aberration appeared in one tissue, it is very likely to occur in others. It has been noted that somatic chromosomal instability occurs in animals with reduced reproductive function, as well as those suffering from any pathology. For example, in calves with parakeratosis the increase in the frequency of chromatid and isochromatid breaks has been found. Analysis of the frequency of aberrations in sires, which differ in the level of perinatal mortality of offspring revealed the increased percentage of offspring mortality in fathers with the large number of chromosomal disorders. Therefore, low fertilization, spontaneous abortions and stillbirths may be indications for karyotypic analysis. It has been revealed that the lability of the karyotype is inherent in all animal species, regardless of the species, sex and age, as well as the morphofunctional state. The data on some types of somatic chromosomal instability in different types of farm animals in Western Siberia has been presented. Such indicators as the frequency of polyploidy, the number of cells with fragments of chromosomes, as well as single and paired fragments of chromosomes has been given. Different types of chromosomal instability varied depending on the animal species and climate zone. The presented data can be accepted as a physiological norm and used in veterinary medicine and animal science.

scholarly journals An ecocultural model predicts Neanderthal extinction through competition with modern humans

2016 ◽  
Vol 113 (8) ◽  
pp. 2134-2139 ◽  
Author(s):  
William Gilpin ◽  
Marcus W. Feldman ◽  
Kenichi Aoki
Keyword(s):  
Cultural Change ◽  
Human Population ◽  
Competitive Exclusion ◽  
Modern Human ◽  
Learning Ability ◽  
Volterra Model ◽  
Modern Humans ◽  
Interacting Species ◽  
The Difference ◽  
Cultural Competition

Archaeologists argue that the replacement of Neanderthals by modern humans was driven by interspecific competition due to a difference in culture level. To assess the cogency of this argument, we construct and analyze an interspecific cultural competition model based on the Lotka−Volterra model, which is widely used in ecology, but which incorporates the culture level of a species as a variable interacting with population size. We investigate the conditions under which a difference in culture level between cognitively equivalent species, or alternatively a difference in underlying learning ability, may produce competitive exclusion of a comparatively (although not absolutely) large local Neanderthal population by an initially smaller modern human population. We find, in particular, that this competitive exclusion is more likely to occur when population growth occurs on a shorter timescale than cultural change, or when the competition coefficients of the Lotka−Volterra model depend on the difference in the culture levels of the interacting species.

scholarly journals Homoplasy in the evolution of modern human-like joint proportions in Australopithecus afarensis

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Anjali M Prabhat ◽  
Catherine K Miller ◽  
Thomas Cody Prang ◽  
Jeffrey Spear ◽  
Scott A Williams ◽  
...  
Keyword(s):  
Upper Limb ◽  
Lower Limb ◽  
Modern Human ◽  
Homo Erectus ◽  
Australopithecus Afarensis ◽  
Modern Humans ◽  
Homo Habilis ◽  
Hominin Evolution ◽  
Parsimonious Explanation ◽  
Phylogenetic Hypotheses

The evolution of bipedalism and reduced reliance on arboreality in hominins resulted in larger lower limb joints relative to the joints of the upper limb. The pattern and timing of this transition, however, remains unresolved. Here, we find the limb joint proportions of Australopithecus afarensis, Homo erectus, and Homo naledi to resemble those of modern humans, whereas those of A. africanus, Australopithecus sediba, Paranthropus robustus, Paranthropus boisei, Homo habilis, and Homo floresiensis are more ape-like. The homology of limb joint proportions in A. afarensis and modern humans can only be explained by a series of evolutionary reversals irrespective of differing phylogenetic hypotheses. Thus, the independent evolution of modern human-like limb joint proportions in A. afarensis is a more parsimonious explanation. Overall, these results support an emerging perspective in hominin paleobiology that A. afarensis was the most terrestrially adapted australopith despite the importance of arboreality throughout much of early hominin evolution.

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