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Journal articles on the topic 'Ancient Population'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Özer, İsmail, and Kazumichi Katayama. "Sex determination using the femur in an ancient Anatolian population." Anthropologischer Anzeiger 64, no. 4 (December 22, 2006): 389–98. http://dx.doi.org/10.1127/anthranz/64/2006/389.

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2

Esposito, Umberto, Ranajit Das, Syakir Syed, Mehdi Pirooznia, and Eran Elhaik. "Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians." Genes 9, no. 12 (December 12, 2018): 625. http://dx.doi.org/10.3390/genes9120625.

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The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient—and oftentimes haploid—DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.

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3

Storey, Glenn R. "The population of ancient Rome." Antiquity 71, no. 274 (December 1997): 966–78. http://dx.doi.org/10.1017/s0003598x00085859.

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What was the population of imperial Rome? City blocks in Pompeii and Ostia are sufficiently well explored that a fair estimate of population density can now be arrived at. That peoples the city of ancient Rome with roughly 450,000 inhabitants, within the known population and density range of pre-industrial and modern urban centres.

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4

Gaston, Anthony J. "Population Parameters of the Ancient Murrelet." Condor 92, no. 4 (November 1990): 998. http://dx.doi.org/10.2307/1368736.

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5

Buck, R. J., and John M. Fossey. "Topography and Population of Ancient Boiotia." Phoenix 47, no. 2 (1993): 165. http://dx.doi.org/10.2307/1088587.

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6

Dyer, Christopher, and J. C. Russell. "Late Ancient and Medieval Population Control." Economic History Review 39, no. 1 (February 1986): 161. http://dx.doi.org/10.2307/2596143.

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7

Garr, W. Randall. "A Population Estimate of Ancient Ugarit." Bulletin of the American Schools of Oriental Research 266 (May 1987): 31–43. http://dx.doi.org/10.2307/1356929.

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8

Relethford, John H. "Mitochondrial DNA and ancient population growth." American Journal of Physical Anthropology 105, no. 1 (January 1998): 1–7. http://dx.doi.org/10.1002/(sici)1096-8644(199801)105:1<1::aid-ajpa1>3.0.co;2-0.

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9

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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10

Vicente, Mário, and Carina M. Schlebusch. "African population history: an ancient DNA perspective." Current Opinion in Genetics & Development 62 (June 2020): 8–15. http://dx.doi.org/10.1016/j.gde.2020.05.008.

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11

Keyser, Christine, Clémence Hollard, Angela Gonzalez, Jean-Luc Fausser, Eric Rivals, Anatoly Nikolayevich Alexeev, Alexandre Riberon, Eric Crubézy, and Bertrand Ludes. "The ancient Yakuts: a population genetic enigma." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130385. http://dx.doi.org/10.1098/rstb.2013.0385.

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This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages.

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12

Brezis, Elise S., and Warren Young. "Population and economic growth: Ancient and modern." European Journal of the History of Economic Thought 23, no. 2 (February 21, 2014): 246–71. http://dx.doi.org/10.1080/09672567.2014.881897.

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13

Parks, M., S. Subramanian, C. Baroni, M. C. Salvatore, G. Zhang, C. D. Millar, and D. M. Lambert. "Ancient population genomics and the study of evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130381. http://dx.doi.org/10.1098/rstb.2013.0381.

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Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin ( Pygoscelis adeliae ). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.

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14

Eriksson, A., and A. Manica. "Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins." Proceedings of the National Academy of Sciences 109, no. 35 (August 14, 2012): 13956–60. http://dx.doi.org/10.1073/pnas.1200567109.

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15

Bennett, Casey C., and Frederika A. Kaestle. "Reanalysis of Eurasian Population History: Ancient DNA Evidence of Population Affinities." Human Biology 78, no. 4 (2006): 413–40. http://dx.doi.org/10.1353/hub.2006.0052.

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16

Zakrzewski, Sonia R. "Population continuity or population change: Formation of the ancient Egyptian state." American Journal of Physical Anthropology 132, no. 4 (2007): 501–9. http://dx.doi.org/10.1002/ajpa.20569.

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17

Ebenesersdóttir, S. Sunna, Marcela Sandoval-Velasco, Ellen D. Gunnarsdóttir, Anuradha Jagadeesan, Valdís B. Guðmundsdóttir, Elísabet L. Thordardóttir, Margrét S. Einarsdóttir, et al. "Ancient genomes from Iceland reveal the making of a human population." Science 360, no. 6392 (May 31, 2018): 1028–32. http://dx.doi.org/10.1126/science.aar2625.

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Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.

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18

Kılınç, Gülşah Merve, Natalija Kashuba, Dilek Koptekin, Nora Bergfeldt, Handan Melike Dönertaş, Ricardo Rodríguez-Varela, Dmitrij Shergin, et al. "Human population dynamics and Yersinia pestis in ancient northeast Asia." Science Advances 7, no. 2 (January 2021): eabc4587. http://dx.doi.org/10.1126/sciadv.abc4587.

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We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis. Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.

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19

Lima, Valdirene S., Alena M. Iniguez, Koko Otsuki, Luiz Fernando Ferreira, Adauto Araújo, Ana Carolina P. Vicente, and Ana Maria Jansen. "Chagas Disease in Ancient Hunter-Gatherer Population, Brazil." Emerging Infectious Diseases 14, no. 6 (June 2008): 1001–2. http://dx.doi.org/10.3201/eid1406.0707.

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20

Lima, Valdirene S., Alena M. Iniguez, Koko Otsuki, Luiz Fernando Ferreira, Adauto Araújo, Ana Carolina P. Vicente, and Ana Maria Jansen. "Chagas Disease in Ancient Hunter-Gatherer Population, Brazil." Emerging Infectious Diseases 14, no. 6 (June 2008): 1001–2. http://dx.doi.org/10.3201/eid1406.070707.

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21

Nichols, Johanna. "MODELING ANCIENT POPULATION STRUCTURES AND MOVEMENT IN LINGUISTICS." Annual Review of Anthropology 26, no. 1 (October 21, 1997): 359–84. http://dx.doi.org/10.1146/annurev.anthro.26.1.359.

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22

Feliciani, Claudio, and Pierluigi Amerio. "Madelung's Disease: Inherited from an Ancient Mediterranean Population?" New England Journal of Medicine 340, no. 19 (May 13, 1999): 1481. http://dx.doi.org/10.1056/nejm199905133401906.

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23

Razi, Zvi, and Josiah Cox Russell. "The Control of Late Ancient and Medieval Population." American Historical Review 91, no. 2 (April 1986): 369. http://dx.doi.org/10.2307/1858155.

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24

Zhang, X., J. Dai, Y. X. Han, and J. L. Shao. "Prevalence Profile of Oral Disease in Ancient Population." Open Anthropology Journal 3, no. 2 (February 1, 2010): 12–15. http://dx.doi.org/10.2174/1874912701003020012.

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25

Stone, Anne C., and Mark Stoneking. "Ancient DNA from a pre-Columbian Amerindian population." American Journal of Physical Anthropology 92, no. 4 (December 1993): 463–71. http://dx.doi.org/10.1002/ajpa.1330920405.

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26

Rudych, Tetiana, and Oleksandra Kozak. "Population of Kyiv Podil in Ancient Rus Period." Archaeology, no. 2 (June 9, 2021): 63–79. http://dx.doi.org/10.15407/arheologia2021.02.063.

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27

Raveane, A., S. Aneli, F. Montinaro, G. Athanasiadis, S. Barlera, G. Birolo, G. Boncoraglio, et al. "Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe." Science Advances 5, no. 9 (September 2019): eaaw3492. http://dx.doi.org/10.1126/sciadv.aaw3492.

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European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non–steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

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28

Mineta, Katsuhiko, Kosuke Goto, Takashi Gojobori, and Fowzan S. Alkuraya. "Population structure of indigenous inhabitants of Arabia." PLOS Genetics 17, no. 1 (January 11, 2021): e1009210. http://dx.doi.org/10.1371/journal.pgen.1009210.

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Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world’s major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world’s major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.

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29

Stone, Anne C., and Mark Stoneking. "Analysis of ancient DNA from a prehistoric Amerindian cemetery." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1379 (January 29, 1999): 153–59. http://dx.doi.org/10.1098/rstb.1999.0368.

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The Norris Farms No. 36 cemetery in central Illinois has been the subject of considerable archaeological and genetic research. Both mitochondrial DNA (mtDNA) and nuclear DNA have been examined in this 700–year–old population. DNA preservation at the site was good, with about 70% of the samples producing mtDNA results and approximately 15% yielding nuclear DNA data. All four of the major Amerindian mtDNA haplogroups were found, in addition to a fifth haplogroup. Sequences of the first hypervariable region of the mtDNA control region revealed a high level of diversity in the Norris Farms population and confirmed that the fifth haplogroup associates with Mongolian sequences and hence is probably authentic. Other than a possible reduction in the number of rare mtDNA lineages in many populations, it does not appear as if European contact significantly altered patterns of Amerindian mtDNA variation, despite the large decrease in population size that occurred. For nuclear DNA analysis, a novel method for DNA–based sex identification that uses nucleotide differences between the X and Y copies of the amelogenin gene was developed and applied successfully in approximately 20 individuals. Despite the well–known problems of poor DNA preservation and the ever–present possibility of contamination with modern DNA, genetic analysis of the Norris Farms No. 36 population demonstrates that ancient DNA can be a fruitful source of new insights into prehistoric populations.

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Krzewińska, Maja, Gro Bjørnstad, Pontus Skoglund, Pall Isolfur Olason, Jan Bill, Anders Götherström, and Erika Hagelberg. "Mitochondrial DNA variation in the Viking age population of Norway." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130384. http://dx.doi.org/10.1098/rstb.2013.0384.

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The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.

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31

Djuraeva, Sanabar. "Ceremonies And Actions Performed By The Population At The Pilgrimage." American Journal of Interdisciplinary Innovations and Research 02, no. 11 (November 6, 2020): 1–6. http://dx.doi.org/10.37547/tajiir/volume02issue11-01.

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This article mentions that after the introduction of the Islamic religion in Central Asia, ancient religious customs became Islamic, and these rituals and act were held for centuries by the population. Based on the places of pilgrimage of the Surkhandarya region, a scientific analysis was conducted.

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32

Simón, Marc, Rafael Montiel, Andrea Smerling, Eduvigis Solórzano, Nancy Díaz, Brenda A. Álvarez-Sandoval, Andrea R. Jiménez-Marín, and Assumpció Malgosa. "Molecular analysis of ancient caries." Proceedings of the Royal Society B: Biological Sciences 281, no. 1790 (September 7, 2014): 20140586. http://dx.doi.org/10.1098/rspb.2014.0586.

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An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains.

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33

Chang, Dan, and Beth Shapiro. "Using ancient DNA and coalescent-based methods to infer extinction." Biology Letters 12, no. 2 (February 2016): 20150822. http://dx.doi.org/10.1098/rsbl.2015.0822.

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DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction.

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34

lo Cascio, Elio. "The Size of the Roman Population: Beloch and the Meaning of the Augustan Census Figures." Journal of Roman Studies 84 (November 1994): 23–40. http://dx.doi.org/10.2307/300868.

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The importance of Beloch's Bevölkerung der griechisch-römischen Welt and its influence on subsequent research in ancient demography can hardly be overstated. This book represents the key-stone of all modern investigation on size, structure, and, to a certain extent, dynamics of ancient populations. It was the first overall scientific treatment of the subject and it is still unparalleled in its scope. An attempt at its critical evaluation is not just an historiographical exercise: we must come to terms with Beloch's Bevölkerung, because its detailed treatment of most of the topics concerning the population of the ancient world is at the root of all modern debates and controversies.

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35

Mkrtchyan, Rusan Albertovna, and Alla Armenovna Movsesian. "Ancient population of the Lake Sevan basin (paleophenetic analysis)." Moscow University Anthropology Bulletin (Vestnik Moskovskogo Universiteta. Seria XXIII. Antropologia), no. 4 (December 30, 2020): 79–89. http://dx.doi.org/10.32521/2074-8132.2020.4.079-089.

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36

Raff, Jennifer A., Deborah A. Bolnick, Justin Tackney, and Dennis H. O'Rourke. "Ancient DNA perspectives on American colonization and population history." American Journal of Physical Anthropology 146, no. 4 (September 13, 2011): 503–14. http://dx.doi.org/10.1002/ajpa.21594.

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37

Turchin, P., and W. Scheidel. "Coin hoards speak of population declines in Ancient Rome." Proceedings of the National Academy of Sciences 106, no. 41 (October 5, 2009): 17276–79. http://dx.doi.org/10.1073/pnas.0904576106.

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38

Chengzhi, Xie, Li Chunxiang, Cui Yinqiu, Cai Dawei, Wang Haijing, Zhu Hong, and Zhou Hui. "Mitochondrial DNA analysis of ancient Sampula population in Xinjiang." Progress in Natural Science 17, no. 8 (August 1, 2007): 927–33. http://dx.doi.org/10.1080/10002007088537493.

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39

E.Deniz, OĞUZ-KIRCA. "The ancient population of a Chersonessian Heir: Phoinix Kersonesoslu." Ankara Üniversitesi Dil ve Tarih-Coğrafya Fakültesi Tarih Bölümü Tarih Araştırmaları Dergisi 34, no. 58 (2015): 445–88. http://dx.doi.org/10.1501/tarar_0000000614.

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40

Brace, Selina, Yoan Diekmann, Thomas J. Booth, Lucy van Dorp, Zuzana Faltyskova, Nadin Rohland, Swapan Mallick, et al. "Ancient genomes indicate population replacement in Early Neolithic Britain." Nature Ecology & Evolution 3, no. 5 (April 15, 2019): 765–71. http://dx.doi.org/10.1038/s41559-019-0871-9.

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41

Chaput, Michelle A., and Konrad Gajewski. "Radiocarbon dates as estimates of ancient human population size." Anthropocene 15 (September 2016): 3–12. http://dx.doi.org/10.1016/j.ancene.2015.10.002.

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42

Schillaci, Michael A., Joel D. Irish, and Carolan C. E. Wood. "Further analysis of the population history of ancient Egyptians." American Journal of Physical Anthropology 139, no. 2 (June 2009): 235–43. http://dx.doi.org/10.1002/ajpa.20976.

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43

Mkrtchyan, Rusan Albertovna, and Alla Armenovna Movsesian. "Ancient population of the Lake Sevan basin (paleophenetic analysis)." Moscow University Anthropology Bulletin (Vestnik Moskovskogo Universiteta. Seria XXIII. Antropologia), no. 4 (December 30, 2020): 79–89. http://dx.doi.org/10.32521/2074-8132.2020.4.079-089.

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44

Mathieson, Iain, Federico Abascal, Lasse Vinner, Pontus Skoglund, Cristina Pomilla, Peter Mitchell, Charles Arthur, et al. "An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa." Genome Biology and Evolution 12, no. 4 (February 5, 2020): 407–12. http://dx.doi.org/10.1093/gbe/evaa019.

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Abstract Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa—indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.

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Koupadi, Kyriaki, Francesco Fontani, Marta Maria Ciucani, Elena Maini, Sara De Fanti, Maurizio Cattani, Antonio Curci, et al. "Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age." Genes 11, no. 12 (November 26, 2020): 1409. http://dx.doi.org/10.3390/genes11121409.

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Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.

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Speidel, Leo, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, and Simon R. Myers. "Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies." Molecular Biology and Evolution 38, no. 9 (June 15, 2021): 3497–511. http://dx.doi.org/10.1093/molbev/msab174.

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Abstract Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k−15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.

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Heupink, Tim H., John van den Hoff, and David M. Lambert. "King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times." Biology Letters 8, no. 4 (February 22, 2012): 586–89. http://dx.doi.org/10.1098/rsbl.2012.0053.

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Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.

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de la Fuente, Constanza, María C. Ávila-Arcos, Jacqueline Galimany, Meredith L. Carpenter, Julian R. Homburger, Alejandro Blanco, Paloma Contreras, et al. "Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia." Proceedings of the National Academy of Sciences 115, no. 17 (April 9, 2018): E4006—E4012. http://dx.doi.org/10.1073/pnas.1715688115.

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Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

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Miller, Eleanor F., Andrea Manica, and William Amos. "Global demographic history of human populations inferred from whole mitochondrial genomes." Royal Society Open Science 5, no. 8 (August 2018): 180543. http://dx.doi.org/10.1098/rsos.180543.

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The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.

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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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