Статті в журналах: "Paleogenomic"

1

Clabby, Catherine. "Paleogenomic Puzzles." American Scientist 99, no. 3 (2011): 210. http://dx.doi.org/10.1511/2011.90.210.

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2

Dobrovolskaya, M. V., S. S. Kunizheva, T. V. Andreeva, and E. I. Rogaev. "Paleogenomic research in the context of modern Biomolecular Archaeology." VESTNIK ARHEOLOGII, ANTROPOLOGII I ETNOGRAFII, no. 1(56) (March 21, 2022): 244–49. http://dx.doi.org/10.20874/2071-0437-2022-56-1-21.

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Biomolecular Archaeology is a newly formed field of archaeological science. The 9th International Sympo-sium on Biomolecular Archaeology was held in June 2021 in Toulouse (France) with the participation of almost 500 delegates. Such conferences were originally organized in the beginning of the 21st c. for regular discussion the most relevant topics and the latest achievements in biomolecular archaeology. Thus, the materials of the symposium appear as a representative reflection of the processes taking place in modern science. Paleogenomics being one of the most actively developing components of biomolecular archaeology. The proposed review presents the most stri-king, in our opinion, reports on the topic, which enables understanding of the potential and prospects of modern pa-leogenomic research. Conclusions based on the results of paleogenomic studies are crucially important for the study of population formation, which makes it essential to comply with the rules of parity comprehensive research, which have been reflected in the publication of the basic ethical rules for organizing such studies.

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3

López-Sánchez, Paula, Javier C. Costas, and Horacio F. Naveira. "Paleogenomic Record of the Extinction of Human Endogenous Retrovirus ERV9." Journal of Virology 79, no. 11 (June 1, 2005): 6997–7004. http://dx.doi.org/10.1128/jvi.79.11.6997-7004.2005.

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ABSTRACT An outstanding question of genome evolution is what stops the invasion of a host genome by transposable elements (TEs). The human genome, harboring the remnants of many extinct TE families, offers an extraordinary opportunity to investigate this problem. ERV9 is an endogenous retrovirus repeatedly mobilized during primate evolution, 15 to 6 million years ago (MYA), which left a trace of over a hundred provirus-like copies and at least 4,000 solitary long terminal repeats (LTRs) in the human genome. Then, its proliferation ceased for unknown reasons, and the family went extinct. We have made a detailed reconstruction of its last active subfamily, ERV9_XII, by examining 115 solitary LTRs from it. These insertions were grouped into 11 sets according to shared nucleotide variants, which could be placed in a sequential order of 10 to 6 MYA. At least 75% of the subfamily was produced 8 to 6 MYA, during a stage of intense proliferation. With new analytical tools, we show that the youngest and most prolific sets may have been produced by effectively instantaneous expansions of corresponding single-sequence variants. The extinction of this family apparently was not a consequence of its slow gradual degeneration, but the outcome of the fixation of specific restrictive alleles in the human-chimpanzee ancestral population. Three species-specific insertions (two in humans and one in chimpanzees) were identified, further supporting that extinction took place when these two species were beginning to diverge. These are the only fixed differences of this kind so far observed between humans and chimpanzees, apart from those belonging to the human endogenous retrovirus K family.

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4

Nakatsuka, Nathan, Iosif Lazaridis, Chiara Barbieri, Pontus Skoglund, Nadin Rohland, Swapan Mallick, Cosimo Posth, et al. "A Paleogenomic Reconstruction of the Deep Population History of the Andes." Cell 181, no. 5 (May 2020): 1131–45. http://dx.doi.org/10.1016/j.cell.2020.04.015.

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5

Wales, Nathan, Jazmín Ramos Madrigal, Enrico Cappellini, Aldo Carmona Baez, José Alfredo Samaniego Castruita, J. Alberto Romero-Navarro, Christian Carøe, et al. "The limits and potential of paleogenomic techniques for reconstructing grapevine domestication." Journal of Archaeological Science 72 (August 2016): 57–70. http://dx.doi.org/10.1016/j.jas.2016.05.014.

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6

Mitchell, Kieren J. "Ancient DNA from the koala lemur puts Madagascar on the paleogenomic map." Proceedings of the National Academy of Sciences 118, no. 30 (July 22, 2021): e2110218118. http://dx.doi.org/10.1073/pnas.2110218118.

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7

Kistler, Logan, Roselyn Ware, Oliver Smith, Matthew Collins, and Robin G. Allaby. "A new model for ancient DNA decay based on paleogenomic meta-analysis." Nucleic Acids Research 45, no. 11 (May 9, 2017): 6310–20. http://dx.doi.org/10.1093/nar/gkx361.

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8

Sánchez-Quinto, Federico, Helena Malmström, Magdalena Fraser, Linus Girdland-Flink, Emma M. Svensson, Luciana G. Simões, Robert George, et al. "Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society." Proceedings of the National Academy of Sciences 116, no. 19 (April 15, 2019): 9469–74. http://dx.doi.org/10.1073/pnas.1818037116.

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Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic façade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.

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9

Shapiro, B., and M. Hofreiter. "A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA." Science 343, no. 6169 (January 23, 2014): 1236573. http://dx.doi.org/10.1126/science.1236573.

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10

Hofmanová, Zuzana, Susanne Kreutzer, Garrett Hellenthal, Christian Sell, Yoan Diekmann, David Díez-del-Molino, Lucy van Dorp, et al. "Early farmers from across Europe directly descended from Neolithic Aegeans." Proceedings of the National Academy of Sciences 113, no. 25 (June 6, 2016): 6886–91. http://dx.doi.org/10.1073/pnas.1523951113.

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Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

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11

Birchler, James A. "Insights from paleogenomic and population studies into the consequences of dosage sensitive gene expression in plants." Current Opinion in Plant Biology 15, no. 5 (November 2012): 544–48. http://dx.doi.org/10.1016/j.pbi.2012.08.005.

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12

Malyarchuk, B. A. "Полиморфизм локуса rs4264393 гена PRDM7 в популяциях коренного населения Сибири: возможная связь с особенностями пигментации кожи в условиях Крайнего Севера". Bulletin of the North-East Science Center, № 4 (30 грудня 2022): 85–93. http://dx.doi.org/10.34078/1814-0998-2022-4-85-93.

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The rs4264393-G allele of the PRDM7 gene belongs to the polymorphic variants very frequent only in indigenous populations of northeastern Siberia: in Eskimos, Chukchi, and Koryaks, its frequency is 64 %. The results of the paleogenomic data analysis suggest that the rs4264393-G variant was present in the north of modern Yakutia (Duvannyi Yar site) about 10 thousand years ago and probably appeared in Northeast Asia even earlier, during the presumed migrations of East Asian populations (20-18 thousand years ago), which mixed with the Upper Paleolithic groups of North Siberia and gave rise to the ancestors of Paleosiberian populations and Amerindians. The PRDM7 gene encodes for a methyltransferase, involved in histone modification, and appears to be an active regulator of gene activity in melanocytes. The findings are discussed in connection with the peculiarities of Eskimo and Paleo-Asiatic skin pigmentation and the possibility that the rs4264393-G variant of the PRDM7 gene may be involved in the evolution of the Arctic peoples pigmentation system.

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13

Bravo-Lopez, Miriam, Viridiana Villa-Islas, Carolina Rocha Arriaga, Ana B. Villaseñor-Altamirano, Axel Guzmán-Solís, Marcela Sandoval-Velasco, Julie K. Wesp, et al. "Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1812 (October 5, 2020): 20190580. http://dx.doi.org/10.1098/rstb.2019.0580.

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The ‘red complex’ is an aggregate of three oral bacteria ( Tannerella forsythia , Porphyromonas gingivalis and Treponema denticola ) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T. forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa . This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules'.

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14

Vai, Stefania, Maria Angela Diroma, Costanza Cannariato, Alicja Budnik, Martina Lari, David Caramelli, and Elena Pilli. "How a Paleogenomic Approach Can Provide Details on Bioarchaeological Reconstruction: A Case Study from the Globular Amphorae Culture." Genes 12, no. 6 (June 11, 2021): 910. http://dx.doi.org/10.3390/genes12060910.

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Ancient human remains have the potential to explain a great deal about the prehistory of humankind. Due to recent technological and bioinformatics advances, their study, at the palaeogenomic level, can provide important information about population dynamics, culture changes, and the lifestyles of our ancestors. In this study, mitochondrial and nuclear genome data obtained from human bone remains associated with the Neolithic Globular Amphorae culture, which were recovered in the Megalithic barrow of Kierzkowo (Poland), were reanalysed to gain insight into the social organisation and use of the archaeological site and to provide information at the individual level. We were able to successfully estimate the minimum number of individuals, sex, kin relationships, and phenotypic traits of the buried individuals, despite the low level of preservation of the bone samples and the intricate taphonomic conditions. In addition, the evaluation of damage patterns allowed us to highlight the presence of “intruders”—that is, of more recent skeletal remains that did not belong to the original burial. Due to its characteristics, the study of the Kierzkowo barrow represented a challenge for the reconstruction of the biological profile of the human community who exploited it and an excellent example of the contribution that ancient genomic analysis can provide to archaeological reconstruction.

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15

Malyarchuk, B. A. "Sources of the mitochondrial gene pool of Russians by the results of analysis of modern and paleogenomic data." Vavilov Journal of Genetics and Breeding 23, no. 5 (August 24, 2019): 588–93. http://dx.doi.org/10.18699/vj19.529.

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Paleogenomic studies of recent years have shown that the Bronze Age migrations of populations of the PontoCaspian steppes from the east to the west of Europe had a great influence on the formation of the genetic makeup of modern Europeans. The results of studies of the variability of mitochondrial genomes in the modern Russian populations of Eastern Europe also made it possible to identify an increase in the effective population size during the Bronze Age, which, apparently, could be related to the migration processes of this time. This paper presents the results of analysis of data on the variability of entire mitochondrial genomes in the modern Russian populations in comparison with the distribution of mtDNA haplogroups in the ancient populations of Europe and the Caucasus of the Neolithic and Bronze Age. It was shown that the formation of the modern appearance of the Russian mitochondrial gene pool began approximately 4 thousand years B.C. due to the influx of mtDNA haplotypes characteristic of the population of Central and Western Europe to the east of Europe. It is assumed that the migrations of the ancient populations of the Ponto-Caspian steppes in the western direction led to the formation of mixed populations in Central Europe, bearing mitochondrial haplogroups H, J, T, K, W characteristic of Western and Central Europeans. Further expansion of these populations to the east of Europe and further to Asia explains the emergence of new features of the mitochondrial gene pool in Eastern Europeans. The results of a phylogeographic analysis are also presented, showing that the features of the geographical distribution of the subgroups of the mitochondrial haplogroup R1a in Europe are a reflection of the “Caucasian” component that appeared in the gene pools of various groups of Europeans during the migration of the Bronze Age. The results of phylogeographic analysis of mitochondrial haplogroups U2e2a1d, U4d2, N1a1a1a1, H2b, and H8b1 testify to the migrations of ancient Eastern Europeans to Asia – the south of Siberia and the Indian subcontinent.

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16

ORGAN, C. L., A. CANOVILLE, R. R. REISZ, and M. LAURIN. "Paleogenomic data suggest mammal-like genome size in the ancestral amniote and derived large genome size in amphibians." Journal of Evolutionary Biology 24, no. 2 (November 22, 2010): 372–80. http://dx.doi.org/10.1111/j.1420-9101.2010.02176.x.

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17

González-Fortes, Gloria, Eppie R. Jones, Emma Lightfoot, Clive Bonsall, Catalin Lazar, Aurora Grandal-d’Anglade, María Dolores Garralda, et al. "Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin." Current Biology 27, no. 12 (June 2017): 1801–10. http://dx.doi.org/10.1016/j.cub.2017.05.023.

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18

Verdugo, Cristina, Kimberly Zhu, Kalina Kassadjikova, Lara Berg, Jannine Forst, Alison Galloway, James E. Brady, and Lars Fehren-Schmitz. "An investigation of ancient Maya intentional dental modification practices at Midnight Terror Cave using anthroposcopic and paleogenomic methods." Journal of Archaeological Science 115 (March 2020): 105096. http://dx.doi.org/10.1016/j.jas.2020.105096.

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19

White, Anna E., Toni de-Dios, Pablo Carrión, Gian Luca Bonora, Laia Llovera, Elisabetta Cilli, Esther Lizano, et al. "Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome." Biology 10, no. 12 (December 14, 2021): 1324. http://dx.doi.org/10.3390/biology10121324.

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The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.

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20

Torres-Rodríguez, Esperanza, Miguel Vallebueno-Estrada, Javier Martínez González, Angel García Cook, Rafael Montiel, and Jean-Philippe Vielle-Calzada. "AMS Dates of New Maize Specimens Found in Rock Shelters of the Tehuacan Valley." Radiocarbon 60, no. 3 (April 23, 2018): 975–87. http://dx.doi.org/10.1017/rdc.2018.29.

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ABSTRACTA large collection of maize macro-specimens has been gathered from archaeological sites across the American continent, but only a few have been directly dated by accelerator mass spectrometry (AMS). We recently conducted two new excavations in several rock shelters of Tehuacán valley (San Marcos, Coxcatlán, and Purrón) and uncovered 132 non-manipulated macro-specimens of maize suitable for morphological and paleogenomic analysis, including many complete cobs, stalks, internodes, and leaves. Direct AMS dates for 43 samples found in San Marcos or Coxcatlán confirm the previously reported chronologies for these sites. By contrast, a cob found in Purrón was dated to 3060±30 before present (3360–3180 cal BP) (2σ), demonstrating that maize was present at that site at least 1500 calendar years earlier than previously expected, and suggesting that other specimens of similar age are still likely to be found in the southeastern region of the Tehuacán valley. A global comparison of macro-specimen chronology across the continent shows that the current archaebotanical record does not yet reflect the chronology of dispersal from central Mexico to northern or southern regions, opening the possibility for finding the missing links in subsequent expeditions within Mexico and Central America.

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21

Kim, Jungeun, Sungwon Jeon, Jae-Pil Choi, Asta Blazyte, Yeonsu Jeon, Jong-Il Kim, Jun Ohashi, et al. "The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences." Genome Biology and Evolution 12, no. 5 (March 27, 2020): 553–65. http://dx.doi.org/10.1093/gbe/evaa062.

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Abstract Koreans are thought to be an ethnic group of admixed northern and southern subgroups. However, the exact genetic origins of these two remain unclear. In addition, the past admixture is presumed to have taken place on the Korean peninsula, but there is no genomic scale analysis exploring the origin, composition, admixture, or the past migration of Koreans. Here, 88 Korean genomes compared with 91 other present-day populations showed two major genetic components of East Siberia and Southeast Asia. Additional paleogenomic analysis with 115 ancient genomes from Pleistocene hunter-gatherers to Iron Age farmers showed a gradual admixture of Tianyuan (40 ka) and Devil’s gate (8 ka) ancestries throughout East Asia and East Siberia up until the Neolithic era. Afterward, the current genetic foundation of Koreans may have been established through a rapid admixture with ancient Southern Chinese populations associated with Iron Age Cambodians. We speculate that this admixing trend initially occurred mostly outside the Korean peninsula followed by continuous spread and localization in Korea, corresponding to the general admixture trend of East Asia. Over 70% of extant Korean genetic diversity is explained to be derived from such a recent population expansion and admixture from the South.

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22

Capriles, José M., Calogero M. Santoro, Richard J. George, Eliana Flores Bedregal, Douglas J. Kennett, Logan Kistler, and Francisco Rothhammer. "Pre-Columbian transregional captive rearing of Amazonian parrots in the Atacama Desert." Proceedings of the National Academy of Sciences 118, no. 15 (March 29, 2021): e2020020118. http://dx.doi.org/10.1073/pnas.2020020118.

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The feathers of tropical birds were one of the most significant symbols of economic, social, and sacred status in the pre-Columbian Americas. In the Andes, finely produced clothing and textiles containing multicolored feathers of tropical parrots materialized power, prestige, and distinction and were particularly prized by political and religious elites. Here we report 27 complete or partial remains of macaws and amazon parrots from five archaeological sites in the Atacama Desert of northern Chile to improve our understanding of their taxonomic identity, chronology, cultural context, and mechanisms of acquisition. We conducted a multiproxy archaeometric study that included zooarchaeological analysis, isotopic dietary reconstruction, accelerated mass spectrometry radiocarbon dating, and paleogenomic analysis. The results reveal that during the Late Intermediate Period (1100 to 1450 CE), Atacama oasis communities acquired scarlet macaws (Ara macao) and at least five additional translocated parrot species through vast exchange networks that extended more than 500 km toward the eastern Amazonian tropics. Carbon and nitrogen stable isotopes indicate that Atacama aviculturalists sustained these birds on diets rich in marine bird guano-fertilized maize-based foods. The captive rearing of these colorful, exotic, and charismatic birds served to unambiguously signal relational wealth in a context of emergent intercommunity competition.

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23

Roulin, Anne, Cristian Chaparro, Benoit Piégu, Scott Jackson, and Olivier Panaud. "Paleogenomic Analysis of the Short Arm of Chromosome 3 Reveals the History of the African and Asian Progenitors of Cultivated Rices." Genome Biology and Evolution 2 (January 1, 2010): 132–39. http://dx.doi.org/10.1093/gbe/evq005.

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Novak, Mario, Iñigo Olalde, Harald Ringbauer, Nadin Rohland, James Ahern, Jacqueline Balen, Ivor Janković, Hrvoje Potrebica, Ron Pinhasi, and David Reich. "Genome-wide analysis of nearly all the victims of a 6200 year old massacre." PLOS ONE 16, no. 3 (March 10, 2021): e0247332. http://dx.doi.org/10.1371/journal.pone.0247332.

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Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies.

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Lazagabaster, Ignacio A., Valentina Rovelli, Pierre-Henri Fabre, Roi Porat, Micka Ullman, Uri Davidovich, Tal Lavi, et al. "Rare crested rat subfossils unveil Afro–Eurasian ecological corridors synchronous with early human dispersals." Proceedings of the National Academy of Sciences 118, no. 31 (July 26, 2021): e2105719118. http://dx.doi.org/10.1073/pnas.2105719118.

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Biotic interactions between Africa and Eurasia across the Levant have invoked particular attention among scientists aiming to unravel early human dispersals. However, it remains unclear whether behavioral capacities enabled early modern humans to surpass the Saharo–Arabian deserts or if climatic changes triggered punctuated dispersals out of Africa. Here, we report an unusual subfossil assemblage discovered in a Judean Desert’s cliff cave near the Dead Sea and dated to between ∼42,000 and at least 103,000 y ago. Paleogenomic and morphological comparisons indicate that the specimens belong to an extinct subspecies of the eastern African crested rat, Lophiomys imhausi maremortum subspecies nova, which diverged from the modern eastern African populations in the late Middle Pleistocene ∼226,000 to 165,000 y ago. The reported paleomitogenome is the oldest so far in the Levant, opening the door for future paleoDNA analyses in the region. Species distribution modeling points to the presence of continuous habitat corridors connecting eastern Africa with the Levant during the Last Interglacial ∼129,000 to 116,000 y ago, providing further evidence of the northern ingression of African biomes into Eurasia and reinforcing previous suggestions of the critical role of climate change in Late Pleistocene intercontinental biogeography. Furthermore, our study complements other paleoenvironmental proxies with local—instead of interregional—paleoenvironmental data, opening an unprecedented window into the Dead Sea rift paleolandscape.

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26

Jeong, Choongwon, Shevan Wilkin, Tsend Amgalantugs, Abigail S. Bouwman, William Timothy Treal Taylor, Richard W. Hagan, Sabri Bromage, et al. "Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe." Proceedings of the National Academy of Sciences 115, no. 48 (November 5, 2018): E11248—E11255. http://dx.doi.org/10.1073/pnas.1813608115.

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Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.

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27

Froese, Duane, Mathias Stiller, Peter D. Heintzman, Alberto V. Reyes, Grant D. Zazula, André E. R. Soares, Matthias Meyer, et al. "Fossil and genomic evidence constrains the timing of bison arrival in North America." Proceedings of the National Academy of Sciences 114, no. 13 (March 13, 2017): 3457–62. http://dx.doi.org/10.1073/pnas.1620754114.

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The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada’s Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus. We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195–135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45–21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.

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Hernández, Candela L., Guillermo Pita, Bruno Cavadas, Saioa López, Luis J. Sánchez-Martínez, Jean-Michel Dugoujon, Andrea Novelletto, Pedro Cuesta, Luisa Pereira, and Rosario Calderón. "Human Genomic Diversity Where the Mediterranean Joins the Atlantic." Molecular Biology and Evolution 37, no. 4 (December 9, 2019): 1041–55. http://dx.doi.org/10.1093/molbev/msz288.

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Abstract Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.

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Keller, Marcel, Maria A. Spyrou, Christiana L. Scheib, Gunnar U. Neumann, Andreas Kröpelin, Brigitte Haas-Gebhard, Bernd Päffgen, et al. "Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)." Proceedings of the National Academy of Sciences 116, no. 25 (June 4, 2019): 12363–72. http://dx.doi.org/10.1073/pnas.1820447116.

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The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium’s spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

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Grange, Thierry, Jean-Philip Brugal, Laurence Flori, Mathieu Gautier, Antigone Uzunidis, and Eva-Maria Geigl. "The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters." Diversity 10, no. 3 (July 18, 2018): 65. http://dx.doi.org/10.3390/d10030065.

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Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.

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Bottjer, D. J., E. H. Davidson, K. J. Peterson, and R. A. Cameron. "Paleogenomics of Echinoderms." Science 314, no. 5801 (November 10, 2006): 956–60. http://dx.doi.org/10.1126/science.1132310.

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Добровольская, М. В. "RESEARCH OF PALEOANTHROPOLOGICAL REMAINS IN THE CONTEXT OF AN ARCHAEOLOGICAL SITE: MODERN STAGE." Краткие сообщения Института археологии (КСИА), no. 262 (November 15, 2021): 129–41. http://dx.doi.org/10.25681/iaras.0130-2620.262.129-141.

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Палеоантропологические материалы из археологических памятников традиционно исследуются физическими антропологами, на этом основана тесная взаимосвязь этих двух научных дисциплин. Поле их взаимодействия сохранилось в неизменном виде, в то время как теоретические и методические основы и возможности археологии и палеоантропологии коренным образом изменились. Концепции антропогенеза, этноса и расы переживают кризисные годы и даже десятилетия. Революционные изменения связаны с развитием палеогеномных исследований и биоархеологического направления. В статье предлагается определение специфики изучения палеоантропологических материалов в контексте археологического памятника. В рамках исторических целей имеют научную значимость как индивидуальные реконструкции образа жизни людей прошлого, так и воссоздание групповых и палеопопуляционных характеристик. Эти междисциплинарные исследования как по целям, так и по методам не сводимы к области физической антропологии. Направление, которое рассматривает культурную среду как сферу воздействия на биологические особенности человека, в разных научных традициях называют по-разному. Среди употребляемых терминов можно встретить «биоархеология», «историческая экология человека». Paleoanthropological remains from archaeological sites are traditionally examined by physical anthropologists, therefore, there are close links between these two scientific disciplines. The area of their interaction has remained unchanged whereas both theoretical and methodological principles and possibilities of archaeology and paleoanthropology have changed drastically. Concepts of anthropogenesis, ethnos and race have been going through crises for years and even decades. Revolutionary changes are related to development of paleogenomic studies and the bioarchaeological area of research. The paper contains description of specific features of studying paleoanthropological remnants in the context of an archaeological site. In accordance with historical objectives, both individual reconstructions of ancient people's lifestyle and recreation of group and paleopopulation characteristics have scientific value. In terms of objectives and methods, such cross-disciplinary studies do not come down to physical anthropology. The area of research that examines the cultural environment as the factor influencing human biological characteristics has different names in various traditions. Some common terms include «bioarchaeology» and «historical ecology of people».

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Lalueza-Fox, Carles, and M. Thomas P. Gilbert. "Paleogenomics of Archaic Hominins." Current Biology 21, no. 24 (December 2011): R1002—R1009. http://dx.doi.org/10.1016/j.cub.2011.11.021.

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Bankoff, Richard J., Heritiana D. D. Randrianatoandro, and George H. Perry. "Primate Conservation Genomics and Paleogenomics." American Anthropologist 117, no. 4 (November 10, 2015): 742–43. http://dx.doi.org/10.1111/aman.12368.

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35

Bardill, Jessica, Alyssa C. Bader, Nanibaa' A. Garrison, Deborah A. Bolnick, Jennifer A. Raff, Alexa Walker, and Ripan S. Malhi. "Advancing the ethics of paleogenomics." Science 360, no. 6387 (April 26, 2018): 384–85. http://dx.doi.org/10.1126/science.aaq1131.

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Cortez, Amanda Daniela, Deborah A. Bolnick, George Nicholas, Jessica Bardill, and Chip Colwell. "An ethical crisis in ancient DNA research: Insights from the Chaco Canyon controversy as a case study." Journal of Social Archaeology 21, no. 2 (March 3, 2021): 157–78. http://dx.doi.org/10.1177/1469605321991600.

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In recent years, the field of paleogenomics has grown into an exciting and rapidly advancing area of scientific inquiry. However, scientific work in this field has far outpaced the discipline’s dialogue about research ethics. In particular, Indigenous peoples have argued that the paleogenomics revolution has produced a “vampire science” that perpetuates biocolonialist traditions of extracting Indigenous bodies and heritage without the consent of, or benefits to, the communities who are most affected by this research. In this article, we explore these ethical issues through the case study of a project that sequenced the ancient DNA (aDNA) of nine Ancestral Puebloan people from Chaco Canyon, New Mexico. By providing a “thick description” of this controversy, we are able to analyze its metanarratives, periodization, path dependency, and historical contingencies. We conclude that the paleogenomics revolution needs to include an ethical revolution that remakes the field’s values, relationships, forms of accountability, and practices.

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Murat, Florent, Caroline Pont, and Jérôme Salse. "Paleogenomics in Triticeae for translational research." Current Plant Biology 1 (August 2014): 34–39. http://dx.doi.org/10.1016/j.cpb.2014.08.003.

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38

Malyarchuk, B. A. "Genetic markers on the distribution of ancient marine hunters in Priokhotye." Vavilov Journal of Genetics and Breeding 24, no. 5 (August 28, 2020): 539–44. http://dx.doi.org/10.18699/vj20.646.

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This is a review of studies on the genetic polymorphism of modern and ancient populations of the north of Asia and America, with the aim of reconstructing the history of migrations of ancient marine hunters in the Okhotsk Sea region. The data on mitochondrial DNA polymorphism and the “Arctic” mutation distribution – the rs80356779-A variant of the CPT1A gene – were analyzed. It is known that the “Arctic” variant of the CPT1A gene is widely distributed in modern populations of the Eskimos, Chukchis, Koryaks, and other peoples of the Okhotsk Sea region, whose economic structure is associated with marine hunting. According to paleogenomic data, the earliest cases of the “Arctic” variant of the CPT1A gene were found in the Greenland and Canadian Paleoeskimos (4 thousand years ago), among representatives of the Tokarev culture of the Northern Priokhotye (3 thousand years ago), and among the bearers of the culture of the late Jomon of Hokkaido (3.5–3.8 thousand years ago). The results of the analysis revealed several migration events associated with the spread of marine hunters in the Okhotsk Sea region. The latest migration, which left traces on bearers of the Epi-Jomon culture (2.0–2.5 thousand years ago), introduced the mitochondrial haplogroup G1b and the “Arctic” variant of the CPT1A gene from the north of Priokhotye to Hokkaido and neighboring territories of the Amur Region. Traces of earlier migration, which also brought the “Arctic” mutation, were recorded in the Hokkaido population of the late Jomon period (3.5–3.8 thousand years ago). A phylogenetic analysis of mitochondrial genomes belonging to the rare haplogroup C1a, found in populations of the Far East and Japan, but phylogenetically related to the C1-haplogroups of the Amerindians, was carried out. The results of the analysis showed that the divergence of mitochondrial lineages within the C1a haplogroup occurred in the range from 7.9 to 6.6 thousand years ago, and the age of the Japanese branch of the C1a haplogroup is approximately 5.2 thousand years. It is not yet known whether this migration is associated with the spread of the “Arctic” variant of the CPT1A gene or the presence of C1a haplotypes in the population of the Japanese islands marks another, earlier, episode of the migration history linking the populations of Northwest Pacific and North America.

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39

Choin, Jeremy, and Lluis Quintana-Murci. "Paleogenomics: The demographic past of prehistoric Europeans." Current Biology 32, no. 11 (June 2022): R535—R538. http://dx.doi.org/10.1016/j.cub.2022.04.081.

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40

Lysak, Martin A., Terezie Mandáková, and M. Eric Schranz. "Comparative paleogenomics of crucifers: ancestral genomic blocks revisited." Current Opinion in Plant Biology 30 (April 2016): 108–15. http://dx.doi.org/10.1016/j.pbi.2016.02.001.

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41

Birnbaum, Daniel, Fran�ois Coulier, Marie-Jos�phe P�busque, and Pierre Pontarotti. "?Paleogenomics?: Looking in the past to the future." Journal of Experimental Zoology 288, no. 1 (April 15, 2000): 21–22. http://dx.doi.org/10.1002/(sici)1097-010x(20000415)288:1<21::aid-jez2>3.0.co;2-q.

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42

Brunson, Katherine, and David Reich. "The Promise of Paleogenomics Beyond Our Own Species." Trends in Genetics 35, no. 5 (May 2019): 319–29. http://dx.doi.org/10.1016/j.tig.2019.02.006.

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43

Jiménez Arenas, Juan Manuel. "Evolución humana y paz. Una aproximación desde la teoría y la práctica." Vínculos de Historia. Revista del Departamento de Historia de la Universidad de Castilla-La Mancha, no. 7 (June 8, 2018): 15. http://dx.doi.org/10.18239/vdh_2018.07.01.

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Puede resultar paradójico investigar la paz en la prehistoria, y más concretamente, a partir de los restos de taxones humanos extintos, cuando no tenemos constancia ni del concepto ni, probablemente, la idea de paz. Sin embargo, considerar la paz como una categoría de análisis nos permite visibilizarla en todo tiempo, lugar y por parte de cualquier agente. Por otro lado, esta aportación se inserta dentro de la investigación para la paz, lo que implica que se centra en encontrar ejemplos históricos que permitan transformar la realidad pacíficamente. En este trabajotransitaremos desde la teoría a la práctica partiendo de una definición concreta de paz, la paz imperfecta, entendida como el desarrollo de las capacidades humanas deseables, desde una perspectiva procesual, inacabada, en continuo cambio, cotidiana y paradójica en el sentido de que convive con la violencia. A partir de aquí plantearé cómo la secuenciación del genoma de taxones extintos y la persistencia de trazas de neandertales y denisovanos en nuestro código genético han puesto de manifiesto que, durante la evolución humana, lejos de las lógicas de exterminioque han sido historiográficamente predominantes para explicar la expansión de los humanos anatómicamente modernos, cabe pensar que han primado los flujos y las interrelaciones, a pesar de las diferencias fenotípicas existentes. Como consecuencia, la variabilidad y la diversidad han sido y son fundamentales para la supervivencia de nuestra especie.PALABRAS CLAVE: paz imperfecta, prehistoria, Paleogenómica, violencia metaestructural, modelos ontológicos.ABSTRACTIt may appear paradoxical to investigate peace in prehistory, and more specifically, based upon the remains of extinct human taxa, when neither the concept nor, probably, the idea of peace existed. However, considering peace as a category of analysis allows us to visualize it in any time or place and via any agent. Furthermore, this contribution is framed within research for peace, which means that it focuses on finding historical examples that make it possible peacefully to transform reality. The work progresses from theory to practice, beginning with a precise definition of peace, imperfect peace, understood as the development of desirable human capabilities and from a complex perspective (contextual, fluctuating, unfinished, constantly changing, daily and paradoxical –in the sense of coexistence with violence–). This is followed by a consideration of how the sequencing of the genome of extinct taxa and the persistence of traces of Neanderthals and Denisovans in our genetic code have revealed that, during human evolution, contrary to the logics of extermination that have been historiographically predominant, there is reason to believe that interrelationships have prevailed despite the existing phenotypic differences. As a result, it is argued that variability and diversity have been and continue to be crucial to the survival of our species.KEY WORDS: imperfect peace, prehistory, paleogenomic, metastructural violence, ontological models.

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44

Poinar, Hendrik N., Carsten Schwarz, Ji Qi, Beth Shapiro, Ross D. E. MacPhee, Bernard Buigues, Alexei Tikhonov, et al. "Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA." Science 311, no. 5759 (December 20, 2005): 392–94. http://dx.doi.org/10.1126/science.1123360.

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We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

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45

Perry, George H., and Cheryl A. Makarewicz. "Horse Paleogenomes and Human–Animal Interactions in Prehistory." Trends in Genetics 35, no. 7 (July 2019): 473–75. http://dx.doi.org/10.1016/j.tig.2019.04.006.

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46

Serrano, Javier G., Alejandra C. Ordóñez, and Rosa Fregel. "Paleogenomics of the prehistory of Europe: human migrations, domestication and disease." Annals of Human Biology 48, no. 3 (April 3, 2021): 179–90. http://dx.doi.org/10.1080/03014460.2021.1942205.

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47

Olalde, Iñigo, and Carles Lalueza-Fox. "Modern humans' paleogenomics and the new evidences on the European prehistory." STAR: Science & Technology of Archaeological Research 1, no. 1 (February 24, 2015): 1–9. http://dx.doi.org/10.1179/2054892315y.0000000002.

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48

Jackson, D. J., L. Macis, J. Reitner, B. M. Degnan, and G. Worheide. "Sponge Paleogenomics Reveals an Ancient Role for Carbonic Anhydrase in Skeletogenesis." Science 316, no. 5833 (June 7, 2007): 1893–95. http://dx.doi.org/10.1126/science.1141560.

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49

Veeramah, Krishna R. "The importance of fine-scale studies for integrating paleogenomics and archaeology." Current Opinion in Genetics & Development 53 (December 2018): 83–89. http://dx.doi.org/10.1016/j.gde.2018.07.007.

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50

Thompson, Jeffrey R., Eric M. Erkenbrack, Veronica F. Hinman, Brenna S. McCauley, Elizabeth Petsios, and David J. Bottjer. "Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins." Proceedings of the National Academy of Sciences 114, no. 23 (June 5, 2017): 5870–77. http://dx.doi.org/10.1073/pnas.1610603114.

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Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes. Paleogenomics unites the fossil record and all aspects of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. Recent work on the regulatory genomic basis of development in cidaroid echinoids, sand dollars, heart urchins, and other nonmodel echinoderms provides an ideal dataset with which to explore GRN evolution in a comparative framework. Using divergence time estimation and ancestral state reconstructions, we have determined the age of the double-negative gate (DNG), the subcircuit which specifies micromeres and skeletogenic cells in Strongylocentrotus purpuratus. We have determined that the DNG has likely been used for euechinoid echinoid micromere specification since at least the Late Triassic. The innovation of the DNG thus predates the burst of post-Paleozoic echinoid morphological diversification that began in the Early Jurassic. Paleogenomics has wide applicability for the integration of deep time and molecular developmental data, and has wide utility in rigorously establishing timelines for GRN evolution.

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