Journal articles on the topic 'Ancient DNA Human Evolution'
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Perry, George H., and Ludovic Orlando. "Ancient DNA and human evolution." Journal of Human Evolution 79 (February 2015): 1–3. http://dx.doi.org/10.1016/j.jhevol.2014.12.002.
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Montiel, Rafael, Assumpcio Malgosa, and Paolo Francalacci. "Authenticating Ancient Human Mitochondrial DNA." Human Biology 73, no. 5 (2001): 689–713. http://dx.doi.org/10.1353/hub.2001.0069.
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Zhenilo, S. V., A. S. Sokolov, and E. B. Prokhortchou. "Epigenetics of Ancient DNA." Acta Naturae 8, no. 3 (September 15, 2016): 72–76. http://dx.doi.org/10.32607/20758251-2016-8-3-72-76.
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Initially, the study of DNA isolated from ancient specimens had been based on the analysis of the primary nucleotide sequence. This approach has allowed researchers to study the evolutionary changes that occur in different populations and determine the influence of the environment on genetic selection. However, the improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression. It was discovered recently that the methylation status of the regulatory elements of the HOXD cluster and MEIS1 gene changed during human evolution. Epigenetic changes in these genes played a key role in the evolution of the limbs of modern humans. Recent works have demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes. In the nearest future, if a preserved fossils brain is found, it will be possible to identify the evolutionary changes in the higher nervous system associated with epigenetic differences.
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Llamas, Bastien, Eske Willerslev, and Ludovic Orlando. "Human evolution: a tale from ancient genomes." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1713 (February 5, 2017): 20150484. http://dx.doi.org/10.1098/rstb.2015.0484.
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The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
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Crubézy, Eric, Sylvain Amory, Christine Keyser, Caroline Bouakaze, Martin Bodner, Morgane Gibert, Alexander Röck, Walther Parson, Anatoly Alexeev, and Bertrand Ludes. "Human evolution in Siberia: from frozen bodies to ancient DNA." BMC Evolutionary Biology 10, no. 1 (2010): 25. http://dx.doi.org/10.1186/1471-2148-10-25.
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D.V., Nesheva. "Aspects of Ancient Mitochondrial DNA Analysis in Different Populations for Understanding Human Evolution." Balkan Journal of Medical Genetics 17, no. 1 (June 1, 2014): 5–14. http://dx.doi.org/10.2478/bjmg-2014-0019.
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Abstract The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data.
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Ermini, Luca, Clio Der Sarkissian, Eske Willerslev, and Ludovic Orlando. "Major transitions in human evolution revisited: A tribute to ancient DNA." Journal of Human Evolution 79 (February 2015): 4–20. http://dx.doi.org/10.1016/j.jhevol.2014.06.015.
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Schneider, Eberhard, Nady El Hajj, and Thomas Haaf. "Epigenetic Information from Ancient DNA Provides New Insights into Human Evolution." Brain, Behavior and Evolution 84, no. 3 (2014): 169–71. http://dx.doi.org/10.1159/000365650.
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Zink, Albert. "Paleogenetics and Mummies." Canarias Arqueológica 22, no. 22 (2021): 49–65. http://dx.doi.org/10.31939/canarq/2021.22.08.
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The molecular analysis of ancient DNA represents a unique oppor tunity for the study of human evolution, population dynamics, and disease evolution in mummified human remains.The investigation of ancient pathogen DNA has led to the detection of a wide range of bacterial, protozoal and viral infections in ancient tissue samples. In the 1990s and 2000s, Arthur C. Aufderheide, together with his colleagues, significantly contributed to the development of this field with his groundbreaking work on the molecular identification of tuberculosis and Chagas disease in South American mummies. More recently, the introduction of next generation sequencing (NGS) technologies and DNA capture techniques, has further improved the opportunity to study ancient human remains. One of the first mummies for which whole genome reconstruction was attempted successfully,is the 5,300-year-old TyroleanIceman. The sequencing revealed detailed infomation on his ancestry, his physical appearance, physiological parameters and the presence of pathogens and disease susceptibility.
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Hummel, S., and B. Herrmann. "Y-chromosome-specific DNA amplified in ancient human bone." Naturwissenschaften 78, no. 6 (June 1991): 266–67. http://dx.doi.org/10.1007/bf01134353.
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Llamas, Bastien, Xavier Roca Rada, and Evelyn Collen. "Ancient DNA helps trace the peopling of the world." Biochemist 42, no. 1 (January 31, 2020): 18–22. http://dx.doi.org/10.1042/bio04201018.
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Many of us are fascinated by narratives regarding the origin and evolution of our species. Who are we? How did we people the world? Answers to these simple questions remain elusive even though researchers have been quite successful in describing past human morphology and culture using evidence from anthropology, archaeology, history, sociology and linguistics. However, when they address human migrations, archaeologists are somewhat restricted to surviving artifactual evidence and limited to descriptions of culture expansions, which may have occurred by the movement of either ideas or people. The advent of genomics, by which one can sequence whole or part of an individual's DNA, provided a powerful means to dig into past human demographic history. Notably, the coalescent theory posits that individuals in a population share genetic variants that originated from a common ancestor. This powerful theory is the basis for a number of bioanalytical innovations that utilize genetic data to reconstruct human movements around the world.
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Nishimura, Luca, Naoko Fujito, Ryota Sugimoto, and Ituro Inoue. "Detection of Ancient Viruses and Long-Term Viral Evolution." Viruses 14, no. 6 (June 18, 2022): 1336. http://dx.doi.org/10.3390/v14061336.
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The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people’s skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people’s bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people’s diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Margaryan, Ashot, Henrik B. Hansen, Simon Rasmussen, Martin Sikora, Vyacheslav Moiseyev, Alexandr Khoklov, Andrey Epimakhov, et al. "Ancient pathogen DNA in human teeth and petrous bones." Ecology and Evolution 8, no. 6 (February 26, 2018): 3534–42. http://dx.doi.org/10.1002/ece3.3924.
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Kocher, Arthur, Luka Papac, Rodrigo Barquera, Felix M. Key, Maria A. Spyrou, Ron Hübler, Adam B. Rohrlach, et al. "Ten millennia of hepatitis B virus evolution." Science 374, no. 6564 (October 8, 2021): 182–88. http://dx.doi.org/10.1126/science.abi5658.
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Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa; however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that diverged about 20,000 years ago. —LMZ
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Jones, Elizabeth D., and Elsbeth Bösl. "Ancient human DNA: A history of hype (then and now)." Journal of Social Archaeology 21, no. 2 (February 18, 2021): 236–55. http://dx.doi.org/10.1177/1469605321990115.
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In this article on the history of ancient DNA research, we argue that the innovation of next-generation sequencing (NGS) of the early 2000s has ushered in a second hype cycle much like the first hype cycle the field experienced in the 1990s with the advent of the polymerase chain reaction (PCR). While the first hype cycle centered around the search for the oldest DNA, the field’s current optimism today promotes the rhetoric of revolution surrounding the study of ancient human gnomes. This is evidenced from written sources and personal interviews with researchers who feel the vast amount of data, the conclusions being made from this data, and the ever-increasing celebrity status of the field are perhaps moving too fast for their own good. Here, we use the concept of contamination, in both a literal and figurative understanding of the term, to explore the field’s continuities and disparities. We also argue that a number of additional, figurative interpretations of “contamination” are useful for navigating the current debate between geneticists and archaeologists regarding the origin, evolution, and migration of ancient humans across space and time. Our historical outlook on aDNA’s disciplinary development, we suggest, is necessary to accurately appreciate the state of the field, how it came to be, and where it might go in the future.
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McBride, Alison A. "Oncogenic human papillomaviruses." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1732 (September 11, 2017): 20160273. http://dx.doi.org/10.1098/rstb.2016.0273.
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Human papillomaviruses (HPVs) are an ancient group of viruses with small, double-stranded DNA circular genomes. They are species-specific and have a strict tropism for mucosal and cutaneous stratified squamous epithelial surfaces of the host. A subset of these viruses has been demonstrated to be the causative agent of several human cancers. Here, we review the biology, natural history, evolution and cancer association of the oncogenic HPVs. This article is part of the themed issue ‘Human oncogenic viruses’.
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Lamers, Ryan, Shana Hayter, and Carney D. Matheson. "Postmortem Miscoding Lesions in Sequence Analysis of Human Ancient Mitochondrial DNA." Journal of Molecular Evolution 68, no. 1 (December 6, 2008): 40–55. http://dx.doi.org/10.1007/s00239-008-9184-3.
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Arizmendi Cárdenas, Yami Ommar, Samuel Neuenschwander, and Anna-Sapfo Malaspinas. "Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study." PeerJ 10 (March 24, 2022): e12784. http://dx.doi.org/10.7717/peerj.12784.
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Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.
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Lee, Young Nam, Michael H. Malim, and Paul D. Bieniasz. "Hypermutation of an Ancient Human Retrovirus by APOBEC3G." Journal of Virology 82, no. 17 (June 18, 2008): 8762–70. http://dx.doi.org/10.1128/jvi.00751-08.
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ABSTRACT Human endogenous retroviruses (HERVs) comprise approximately 8% of the human genome, but all are remnants of ancient retroviral infections and harbor inactivating mutations that render them replication defective. Nevertheless, as viral “fossils,” HERVs may provide insights into ancient retrovirus-host interactions and their evolution. Indeed, one endogenous retrovirus [HERV-K(HML-2)], which has replicated in humans for the past few million years but is now thought to be extinct, was recently reconstituted in a functional form, and infection assays based on it have been established. Here, we show that several human APOBEC3 proteins are intrinsically capable of mutating and inhibiting infection by HERV-K(HML-2) in cell culture. We also present striking evidence that two HERV-K(HML-2) proviruses that are fixed in the modern human genome (HERV-K60 and HERV-KI) were subjected to hypermutation by a cytidine deaminase. Inspection of the spectrum of mutations that are found in HERV-K proviruses in the human genome and HERV-K DNA generated during in vitro replication in the presence of each of the human APOBEC3 proteins unequivocally identifies APOBEC3G as the cytidine deaminase responsible for hypermutation of HERV-K60 and HERV-KI. This is a rare example of the antiretroviral effects of APOBEC3G in the setting of natural human infection, whose consequences have been fossilized in human DNA, and a striking example of inactivation of ancient retroviruses in humans through enzymatic cytidine deamination.
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Malmström, Helena, Jan Storå, Love Dalén, Gunilla Holmlund, and Anders Götherström. "Extensive Human DNA Contamination in Extracts from Ancient Dog Bones and Teeth." Molecular Biology and Evolution 22, no. 10 (June 15, 2005): 2040–47. http://dx.doi.org/10.1093/molbev/msi195.
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Baroudi, Kusai, Rushabh Dagli, Namrata Dagli, and Bassel Tarakji. "Oral Paleomicrobiology: Study of Ancient Oral Microbiome." Journal of Contemporary Dental Practice 16, no. 7 (2015): 588–94. http://dx.doi.org/10.5005/jp-journals-10024-1726.
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ABSTRACT Background Paleomicrobiology is a special branch of micropaleontology concerned with the study of bacterial fossils. We have used the term ‘oral paleomicrobiology’, as in this review we have focused on the ancient oral microflora. Recently, dental calculus and dental pulp have been identified as rich sources of ancient microbial DNA. Study of this ancient genetic material opens a new door to the ancient world. This review gives an overview of history of ancient DNA research, various techniques of analyzing ancient DNA in dental calculus and dental pulp, and the implications of the oral paleomicrobiology. Materials and methods A comprehensive literature search was performed in the following databases—pubmed, medline and google scholar for studies published before 10 April, 2015. The following keywords were used—‘ancient DNA’, ‘ancient oral flora, ‘oral paleomicrobiology’ and ‘oral microbiome’, ‘16S rRNA sequencing’. To obtain additional data, a manual search was performed using the reference lists of selected articles. Result As a result of literature search, 27 articles were found in pubmed, 12 in google scholar and one in medline. Eight more articles were selected from the reference list of selected articles. Conclusion The combination of microbiology and paleontology has brought a revolution in the study of human evolution and microbial communities. The naturally well-preserved samples of microbial DNA from dental pulp and microbial colonies trapped in dental calculus are a potential source of microbial genetic material, which will prove invaluable in resolving mysteries of the past. This may be a beginning of a new era of oral paleomicrobiology, which will contribute in our studies about prevention of disease by establishing symbiosis between human beings and their microbiome. How to cite this article Dagli N, Dagli R, Baroudi K, Tarakji B. Oral Paleomicrobiology: Study of Ancient Oral Microbiome. J Contemp Dent Pract 2015;16(7):588-594.
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Enard, David, and Dmitri A. Petrov. "Ancient RNA virus epidemics through the lens of recent adaptation in human genomes." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1812 (October 5, 2020): 20190575. http://dx.doi.org/10.1098/rstb.2019.0575.
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Over the course of the last several million years of evolution, humans probably have been plagued by hundreds or perhaps thousands of epidemics. Little is known about such ancient epidemics and a deep evolutionary perspective on current pathogenic threats is lacking. The study of past epidemics has typically been limited in temporal scope to recorded history, and in physical scope to pathogens that left sufficient DNA behind, such as Yersinia pestis during the Great Plague. Host genomes, however, offer an indirect way to detect ancient epidemics beyond the current temporal and physical limits. Arms races with pathogens have shaped the genomes of the hosts by driving a large number of adaptations at many genes, and these signals can be used to detect and further characterize ancient epidemics. Here, we detect the genomic footprints left by ancient viral epidemics that took place in the past approximately 50 000 years in the 26 human populations represented in the 1000 Genomes Project. By using the enrichment in signals of adaptation at approximately 4500 host loci that interact with specific types of viruses, we provide evidence that RNA viruses have driven a particularly large number of adaptive events across diverse human populations. These results suggest that different types of viruses may have exerted different selective pressures during human evolution. Knowledge of these past selective pressures will provide a deeper evolutionary perspective on current pathogenic threats. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Leciej, Dawid, Karl-Heinz Herzig, and Olaf Thalmann. "Zoonoses and their traces in ancient genomes – a possible indicator for ancient life-style changes?" Journal of Medical Science 89, no. 3 (September 30, 2020): e467. http://dx.doi.org/10.20883/medical.e467.
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Humans are constantly exposed to health risks inherent to the environment in which they live, thereby including non-human fauna. Zoonoses are infectious diseases caused by agents such as bacteria, parasites, or viruses being transmitted to humans from wild animals and livestock. The close proximity of animals and humans facilitate the spread of zoonoses, so it is intriguing to hypothesize that populations accustomed to different lifestyles will also vary in the prevalence of zoonotic agents. The Neolithic era in human history is characterised by a dramatic transition in lifestyle, from hunting and gathering to farming. Thus, with the changes in the reservoir of animal species humans were exposed to zoonotic agents potentially penetrating human populations. Due to the rapid development of sequencing technologies and methodology in ancient DNA research, it is now possible to generate complete genomes of ancient specimens and pinpoint those genomic regions or epigenetic signatures that might be influenced by past zoonotic transmissions. Unravelling such traces, particularly on a population-scale, will help to overcome the lack of generalisation that hampered previous research focusing exclusively on the model fossils in human evolution, and facilitate a better understanding of the aetiology of diseases, including those caused by zoonotic agents.
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Allaby, Robin G., Rafal Gutaker, Andrew C. Clarke, Neil Pearson, Roselyn Ware, Sarah A. Palmer, James L. Kitchen, and Oliver Smith. "Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130377. http://dx.doi.org/10.1098/rstb.2013.0377.
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Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.
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Mühlemann, Barbara, Ashot Margaryan, Peter de Barros Damgaard, Morten E. Allentoft, Lasse Vinner, Anders J. Hansen, Andrzej Weber, et al. "Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans." Proceedings of the National Academy of Sciences 115, no. 29 (July 2, 2018): 7557–62. http://dx.doi.org/10.1073/pnas.1804921115.
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Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9–99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0–6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.
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Schofield, J. P. "Molecular studies on an ancient gene encoding for carbamoyl-phosphate synthetase." Clinical Science 84, no. 2 (February 1, 1993): 119–28. http://dx.doi.org/10.1042/cs0840119.
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1. Carbamoyl-phosphate synthetase (EC 6.3.5.5.) catalyses the synthesis of carbamoyl phosphate, the immediate precursor of arginine and pyrimidine biosynthesis, and is highly conserved throughout evolution. The large subunit of all carbamoyl-phosphate synthetases sequenced to date comprises two highly homologous halves, the product of a proposed ancestral gene duplication. The sequences of the enzymes of Escherichia coli, Drosophila melanogaster, Saccharomyces cerevisiae, rat and Syrian hamster all have duplications, suggesting that this event occurred in the progenote predating the separation of the major phylae. Until now, only limited data on carbamoyl-phosphate synthetase were available for the primitive eukaryote Dictyostelium discoideum and for the Archaea Methanosarcina barkeri MS. The DNA sequence of the D. discoideum carbamoylphosphate gene and additional sequence for the carbamoyl-phosphate synthetase gene of M. barkeri MS have been determined, and a duplicated structure for both is clearly demonstrated. 2. Genes with ancient duplications provide unique information on their evolution. A study of the intron/exon organization of the rat carbamoylphosphate synthetase I gene and the carbamoylphosphate synthetase hamster II gene in the CAD multi-gene complex shows that at least some of their introns are very old. Evidence is provided that some introns must have been present in the ancestral precursor before its duplication. 3. The human carbamoyl-phosphate synthetase I gene has been isolated and characterized. A human liver cDNA library was constructed and probed for carbamoyl-phosphate synthetase I. A human genomic DNA cosmid library was also probed for the carbamoyl-phosphate synthetase I gene. The cDNA sequence of the human carbamoyl-phosphate synthetase I gene has been determined, and work has been initiated to confirm that at least part of this gene is contained within two cosmids spanning 46 kb. This will enable future studies to be made on mutations in this gene in the rare autosomal recessive deficiency of carbamoyl-phosphate synthetase I.
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Pusch, C. M. "Spiking of Contemporary Human Template DNA with Ancient DNA Extracts Induces Mutations Under PCR and Generates Nonauthentic Mitochondrial Sequences." Molecular Biology and Evolution 21, no. 5 (January 22, 2004): 957–64. http://dx.doi.org/10.1093/molbev/msh107.
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Goncharov, A. E., and V. V. Kolodzhieva. "Medical paleomicrobiology: problems and prospects." Antibiotics and Chemotherapy 66, no. 5-6 (August 30, 2021): 72–77. http://dx.doi.org/10.37489/0235-2990-2021-66-5-6-72-77.
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The study of microbial DNA from paleontological and archaeological samples is a powerful tool for estimating the molecular evolution of human pathogens. The paper is a retrospective review of the most significant achievements in medical paleomicrobiology. The subject of the discussion is the genetic diversity of ancient microbiomes including pathogenicity and antibiotic resistance genes. Paleomicrobiological studies of permafrost as a repository of pathogenic microbiota are highly promising.
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Roy, Chandan. "Svante Pääbo." INDIAN JOURNAL OF PHYSIOLOGY AND ALLIED SCIENCES 74, no. 04 (December 29, 2022): 37. http://dx.doi.org/10.55184/ijpas.v74i04.85.
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Svante Pääbo was born on 20th April, 1955 at Stockholm, Sweden. He is a Swedish evolutionary geneticist whospecialized in the study of DNA from ancient specimens and who was the first to contribute to the sequencing of the Neanderthal genome. Pääbo also discovered the hominin Denisova. For his groundbreaking research on hominin genomes and human evolution, Pääbo was awarded the 2022 Nobel Prize for Physiology or Medicine.
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Liu, Xiaoming. "Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions." Molecular Biology and Evolution 37, no. 9 (May 5, 2020): 2691–98. http://dx.doi.org/10.1093/molbev/msaa112.
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Abstract The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.
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Dalal, Vasundhra, Nagarjuna Pasupuleti, Gyaneshwer Chaubey, Niraj Rai, and Vasant Shinde. "Advancements and Challenges in Ancient DNA Research: Bridging the Global North–South Divide." Genes 14, no. 2 (February 14, 2023): 479. http://dx.doi.org/10.3390/genes14020479.
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Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Malmstrom, H., E. M. Svensson, M. T. P. Gilbert, E. Willerslev, A. Gotherstrom, and G. Holmlund. "More on Contamination: The Use of Asymmetric Molecular Behavior to Identify Authentic Ancient Human DNA." Molecular Biology and Evolution 24, no. 4 (January 30, 2007): 998–1004. http://dx.doi.org/10.1093/molbev/msm015.
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Ottoni, Claudio, Dušan Borić, Olivia Cheronet, Vitale Sparacello, Irene Dori, Alfredo Coppa, Dragana Antonović, et al. "Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus." Proceedings of the National Academy of Sciences 118, no. 32 (July 26, 2021): e2102116118. http://dx.doi.org/10.1073/pnas.2102116118.
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Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
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Kim, Hie Lim, Takeshi Igawa, Ayaka Kawashima, Yoko Satta, and Naoyuki Takahata. "Divergence, demography and gene loss along the human lineage." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1552 (August 27, 2010): 2451–57. http://dx.doi.org/10.1098/rstb.2010.0004.
Full textAbstract:
Genomic DNA sequences are an irreplaceable source for reconstructing the vanished past of living organisms. Based on updated sequence data, this paper summarizes our studies on species divergence time, ancient population size and functional loss of genes in the primate lineage leading to modern humans ( Homo sapiens sapiens ). The inter- and intraspecific comparisons of DNA sequences suggest that the human lineage experienced a rather severe bottleneck in the Middle Pleistocene, throughout which period the subdivided African population played a predominant role in shaping the genetic architecture of modern humans. Also, published and newly identified human-specific pseudogenes (HSPs) are enumerated in order to infer their significance for human evolution. Of the 121 candidate genes obtained, authentic HSPs turn out to comprise only 25 olfactory receptor genes, four T cell receptor genes and nine other genes. The fixation of HSPs has been too rare over the past 6–7 Myr to account for species differences between humans and chimpanzees.
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Willemsen, Anouk, and Ignacio G. Bravo. "Origin and evolution of papillomavirus (onco)genes and genomes." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1773 (April 8, 2019): 20180303. http://dx.doi.org/10.1098/rstb.2018.0303.
Full textAbstract:
Papillomaviruses (PVs) are ancient viruses infecting vertebrates, from fishes to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the infection. Most PV genomes contain two small early genes E6 and E7 . In a bunch of closely related human papillomaviruses (HPVs), the E6 and E7 proteins provide the viruses with oncogenic potential. The recent discoveries of PVs without E6 and E7 in different fish species place a new root on the PV tree, and suggest that ancestral PVs consisted of the minimal PV backbone E1-E2-L2-L1 . Bayesian phylogenetic analyses date the most recent common ancestor of the PV backbone to 424 million years ago (Ma). Common ancestry tests on extant E6 and E7 genes indicate that they share a common ancestor dating back to at least 184 Ma. In AlphaPVs infecting Old World monkeys and apes, the appearance of the E5 oncogene 53–58 Ma concurred with (i) a significant increase in substitution rate, (ii) a basal radiation and (iii) key gain of functions in E6 and E7. This series of events was instrumental to construct the extant phenotype of oncogenic HPVs. Our results assemble the current knowledge on PV diversity and present an ancient evolutionary timeline punctuated by evolutionary innovations in the history of this successful viral family. This article is part of the theme issue ‘Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses’.
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CÔTÉ, NATHALIE M. L., and MATTHIEU LE BAILLY. "Palaeoparasitology and palaeogenetics: review and perspectives for the study of ancient human parasites." Parasitology 145, no. 5 (July 27, 2017): 656–64. http://dx.doi.org/10.1017/s003118201700141x.
Full textAbstract:
SUMMARYWhile some species of parasites can be identified to species level from archaeological remains using microscopy (i.e.Enterobius vermicularis,Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e.Tæniasp. andEchinococcussp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time. However, biomolecules can be poorly preserved and modern reference DNA is available only for a limited number of species of parasites, leading to the conclusion that classic microscopic observation should be combined with molecular analyses. Here we present a review of the molecular approaches used over the past two decades to identify human pathogenic helminths (Ascarissp.,Trichurissp.,E. vermicularis,Fasciolasp. etc.) or protists (Giardiasp.,Trypanosomasp.,Leishmaniasp. etc.). We also discuss the prospects for studying the evolution of parasites with genetics and genomics.
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Seuánez, Héctor N., Maria C. Viana, William C. Tavares, Vanessa Mendonça, Ayslan C. Brant, Mariana Boroniv, and Evandro Lucena. "Absence of Pathogenicity in Non-Human Primates of Mutations Related to Retinoblastoma in Humans." World Journal of Veterinary Research 1, no. 1 (June 1, 2019): 05–10. http://dx.doi.org/10.33597/wjvr.01-1002.
Full textAbstract:
The tumor suppressor, Human Retinoblastoma Susceptibility Gene (RB1) plays a prominent role in normal development, gene transcription, DNA replication, repair, and mitosis, and its complete biallelic dysfunction in retinoblasts is the main cause of retinoblastoma in humans. Comparisons between the reference, human RB1 coding region with its counterparts in 19 non-human primates showed that several RB1 alterations accompanying retinoblastoma in the human were present in several non-human primates without apparent pathological effects. Comparative analyses of molecular data were most useful for tracing the evolution of RB1, identifying the polarity of mutational events, the physico-chemical effects conferred by amino acid substitutions, and the number of codons under selection. These historic reconstructions indicated that several RB1 mutations found in retinoblastoma in the human were presumably atavistic, accounting for evolutionary regressions. Moreover, some same-sense RB1 mutations, despite specifying for the same amino acids, were probably ancient adaptations that took place in our evolutionary lineage.
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Kehlmaier, Christian, Axel Barlow, Alexander K. Hastings, Melita Vamberger, Johanna L. A. Paijmans, David W. Steadman, Nancy A. Albury, Richard Franz, Michael Hofreiter, and Uwe Fritz. "Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum." Proceedings of the Royal Society B: Biological Sciences 284, no. 1846 (January 11, 2017): 20162235. http://dx.doi.org/10.1098/rspb.2016.2235.
Full textAbstract:
Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas ( Chelonoidis alburyorum ) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galápagos ( C. niger complex) and Chaco tortoises ( C. chilensis ), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galápagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.
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Gancz, Abigail S., and Laura S. Weyrich. "Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases." F1000Research 12 (January 30, 2023): 109. http://dx.doi.org/10.12688/f1000research.129036.1.
Full textAbstract:
Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.
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Woods, Roseina, Ian Barnes, Selina Brace, and Samuel T. Turvey. "Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents." Molecular Biology and Evolution 38, no. 1 (October 9, 2020): 84–95. http://dx.doi.org/10.1093/molbev/msaa189.
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Abstract Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.
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Schnorr, Stephanie L. "The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1812 (October 5, 2020): 20190577. http://dx.doi.org/10.1098/rstb.2019.0577.
Full textAbstract:
In this study, I use microbiome datasets from global soil samples and diverse hosts to learn whether soil microbial taxa are found in host microbiomes, and whether these observations fit the narrative that environmental interaction influences human microbiomes. A major motivation for conducting host-associated microbiome research is to contribute towards understanding how the environment may influence host physiology. The microbial molecular network is considered a key vector by which environmental traits may be transmitted to the host. Research on human evolution seeks evidence that can inform about the living experiences of human ancestors. This objective is substantially enhanced by recent work on ancient biomolecules from preserved microbial tissues, such as dental calculus, faecal sediments and whole coprolites. A challenge yet is to distinguish authentic biomolecules from environmental contaminants deposited contemporaneously, primarily from soil. However, we do not have sound expectations about the soil microbial elements arriving to host-associated microbiomes in a modern context. One assumption in human microbiome research is that proximity to the natural environment should affect biodiversity or impart genetic elements. I present evidence supporting the assumption that environmental soil taxa are found among host-associated gut taxa, which can recapitulate the surrounding host habitat ecotype. Soil taxa found in gut microbiomes relate to a set of universal ‘core’ taxa for all soil ecotypes, demonstrating that widespread host organisms may experience a consistent pattern of external environmental cues, perhaps critical for development. Observed differentiation of soil feature diversity, abundance and composition among human communities, great apes and invertebrate hosts also indicates that lifestyle patterns are inferable from an environmental signal that is retrievable from gut microbiome amplicon data. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Williams, Matthew, and João Teixeira. "A genetic perspective on human origins." Biochemist 42, no. 1 (January 31, 2020): 6–10. http://dx.doi.org/10.1042/bio04201006.
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Who are we? Where did we come from? Why are we here? These fundamental questions have been widespread throughout human history, shared across different cultures from distant epochs and geographical locations. The search has been as much a philosophical as an empirical one, capturing the imagination of the philosopher, the theologian, the artist and the scientist alike. Hence, the quest for unveiling our origins is probably as old as humanity itself. From a scientific point of view, which we address in the present article, the question of human origins became deeply intertwined with Charles Darwin's theory of evolution in the late 19th century. This led to the development of scientific fields such as palaeoanthropology, which analyses fossil remains, stone tools and cultural artefacts to piece together our past. Recently, however, the possibility to assess genetic information from thousands of individuals across the world and, more importantly, to obtain DNA from specimens that lived thousands of years in the past (so-called ancient DNA [aDNA] analyses) is rapidly transforming long-held beliefs about our origins. As such, we have never been in a better position to ask what do our genomes have to tell us about where we came from. Ultimately, however, can they tell us who we are?
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Lullfitz, Alison, Margaret Byrne, Lynette Knapp, and Stephen D. Hopper. "Platysace (Apiaceae) of south-western Australia: silent story tellers of an ancient human landscape." Biological Journal of the Linnean Society 130, no. 1 (March 31, 2020): 61–78. http://dx.doi.org/10.1093/biolinnean/blaa035.
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Abstract High gene flow and a population structure corresponding to human rather than geographical drivers are likely to be genetic patterns of human-dispersed plant taxa. We examined variation in geographical structure and gene flow estimates based on three non-coding regions of plastid DNA in three south-west Australian members of the Platysace genus to identify whether a human influence on dispersion of utilized taxa was detectable. Edible tubers of Platysace deflexa and Platysace trachymenioides have been harvested historically by Noongar traditional owners, whereas Platysace effusa has no known cultural significance. We found differences between utilized and non-utilized taxa, particularly when considered against the generally complex phylogeographical patterning in south-west Australian plant taxa. Platysace effusa showed a pattern of high population divergence, low gene flow and multiple refugia, consistent with a long evolutionary history, past climatic oscillations and persistence in a highly fragmented landscape. In contrast, higher gene flow estimates, less divergence between populations and common haplotypes in P. deflexa and in P. trachymenioides over the south-eastern part of its range are consistent with anthropogenic influences. This study contributes to the understanding of human influences on south-west Australian plant taxa that have been present since the late Pleistocene, but to date have received little scientific attention.
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Ferrari, Giada, Heidi Lischer, Judith Neukamm, Enrique Rayo, Nicole Borel, Andreas Pospischil, Frank Rühli, Abigail Bouwman, and Michael Campana. "Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf." Genes 9, no. 9 (August 31, 2018): 436. http://dx.doi.org/10.3390/genes9090436.
Full textAbstract:
The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.
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Cabrera, Vicente M. "Updating the Phylogeography and Temporal Evolution of Mitochondrial DNA Haplogroup U8 with Special Mention to the Basques." DNA 2, no. 2 (April 7, 2022): 104–15. http://dx.doi.org/10.3390/dna2020008.
Full textAbstract:
Mitochondrial DNA phylogenetic and phylogeographic studies have been very useful in reconstructing the history of modern humans. In addition, recent advances in ancient DNA techniques have enabled direct glimpses of the human past. Taking advantage of these possibilities, I carried out a spatiotemporal study of the rare and little-studied mtDNA haplogroup U8. Today, U8, represented by its main branches U8a and U8b, has a wide western Eurasian range but both with average frequencies below 1%. It is known that, in Paleolithic times, U8 reached high frequencies in European hunter-gatherers. However, it is pertinent to precise that only lineages belonging to U8a and U8c, a sister branch of U8b, were detected at that time. In spite of its wide geographic implantation, U8c was extinct after the Last Glacial Maximum, but U8a subsisted until the present day, although it never reached its high Paleolithic frequencies. U8a is detected mainly in northern and western Europe including the Basques, testifying to a minor maternal Paleolithic continuity. In this respect, it is worth mentioning that Basques show more U8-based affinities with continental European than with Mediterranean populations. On the contrary, coalescent ages of the most ancient U8b clades point to a Paleolithic diversification in the Caucasus and the Middle Eastern areas. U8b-derived branches reached eastern Europe since the Mesolithic. Subsequent Neolithic and post-Neolithic expansions widen its ranges in continental Europe and the Mediterranean basin, including northern Africa, albeit always as a minor clade that accompanied other, more representative, mitochondrial lineages.
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Moorjani, Priya, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, and David Reich. "A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years." Proceedings of the National Academy of Sciences 113, no. 20 (May 2, 2016): 5652–57. http://dx.doi.org/10.1073/pnas.1514696113.
Full textAbstract:
The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen’s age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and 14C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the 14C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26–30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.
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Logsdon, Glennis A., Mitchell R. Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, et al. "The structure, function and evolution of a complete human chromosome 8." Nature 593, no. 7857 (April 7, 2021): 101–7. http://dx.doi.org/10.1038/s41586-021-03420-7.
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AbstractThe complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the β-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.
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Alcazer, Vincent, Paola Bonaventura, and Stephane Depil. "Human Endogenous Retroviruses (HERVs): Shaping the Innate Immune Response in Cancers." Cancers 12, no. 3 (March 6, 2020): 610. http://dx.doi.org/10.3390/cancers12030610.
Full textAbstract:
Human Endogenous Retroviruses (HERVs) are accounting for 8% of the human genome. These sequences are remnants from ancient germline infections by exogenous retroviruses. After million years of evolution and multiple integrations, HERVs have acquired many damages rendering them defective. At steady state, HERVs are mostly localized in the heterochromatin and silenced by methylation. Multiple conditions have been described to induce their reactivation, including auto-immune diseases and cancers. HERVs re-expression leads to RNA (simple and double-stranded) and DNA production (by reverse transcription), modulating the innate immune response. Some studies also argue for a role of HERVs in shaping the evolution of innate immunity, notably in the development of the interferon response. However, their exact role in the innate immune response, particularly in cancer, remains to be defined. In this review, we see how HERVs could be key-players in mounting an antitumor immune response. After a brief introduction on HERVs characteristics and biology, we review the different mechanisms by which HERVs can interact with the immune system, with a focus on the innate response. We then discuss the potential impact of HERVs expression on the innate immune response in cancer.
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MacKintosh, Carol, and David E. K. Ferrier. "Recent advances in understanding the roles of whole genome duplications in evolution." F1000Research 6 (August 31, 2017): 1623. http://dx.doi.org/10.12688/f1000research.11792.1.
Full textAbstract:
Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.
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MacKintosh, Carol, and David E. K. Ferrier. "Recent advances in understanding the roles of whole genome duplications in evolution." F1000Research 6 (March 29, 2018): 1623. http://dx.doi.org/10.12688/f1000research.11792.2.
Full textAbstract:
Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.