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Ancient and Archaic Genomes
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Ancient and Archaic Genomes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 46902

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. David Caramelli

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Guest Editor
Department of Biology, University of Florence, 50122 Florence, Italy
Interests: ancient DNA; human evolution; human population genetics; forensics genetics; wildlife forensics genetics
Prof. Martina Lari

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Guest Editor
Laboratorio di Antropologia Molecolare e Paleogenetica, Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
Interests: molecular anthropology and paleogenetics; recovery and analysis of ancient and degraded DNA from human, animal and plant ancient remain. NGS methods; phylogenetic analysis; genetic history of past populations; ancient microbiome reconstruction; molecular and genetic methods applied to the preservation and valorization of cultural heritage
Dr. Stefania Vai

E-Mail Website
Guest Editor
Laboratorio di Antropologia Molecolare e Paleogenetica, Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
Interests: molecular anthropology and paleogenetics; recovery and analysis of ancient and degraded DNA from human, animal and plant ancient remain; NGS methods; phylogenetic analysis; genetic history of past human populations; domestication processes; molecular and genetic methods applied to the preservation and valorization of cultural heritage

Special Issue Information

The development of high-throughput sequencing has triggered a revolution in the study of ancient DNA. In the last decade, methodological  advances have allowed researchers to overcome some of the limits linked to the degradation and preservation of nucleic acids, improving the capacity of recovery and analysis of the ancient molecules. This fact, along with a wider accessibility to the Next-Generation Sequencing platforms, has contributed to increase the number of genomic studies on ancient remains. The applications of paleogenomics span several research fields. Genomic data from archaic hominins are providing exceptional information for the study of human evolution, detecting interbreeding between different human forms. Genome-level studies of prehistorical and historical human samples are helping to understand genetic variability through time and to unravel past population dynamics. Genomic data from ancient animal and plant remains allow researchers to reconstruct the evolutionary history of wild and domesticated populations and directly observe genetic changes linked to natural and artificial selection, and contribute to management decisions in conservation projects. Pathogen paleogenomics is leading to the discovery of extinct microbial lineages and to the characterization of the evolutionary history of microorganisms that are still relevant today. 

This Special Issue will collect reviews and original contributions concerning the study of ancient and archaic genomes from different organisms, considering accomplishments and challenges, methodological approaches, bioinformatics and analytical tools, current status, and future prospects of paleogenomic research.

Sincerely

Prof. David Caramelli
Prof. Martina Lari
Dr. Stefania Vai
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Next-Generation Sequencing (NGS)
  • ancient DNA
  • paleogenomics
  • archaic humans
  • archeogenetics
  • extinct species
  • conservation genomics
  • domestication
  • paleopathogens
  • evolutionary genomics

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Published Papers (7 papers)

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Editorial

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3 pages, 174 KiB  
Editorial
Ancient and Archaic Genomes
by Stefania Vai, Martina Lari and David Caramelli
Genes 2021, 12(9), 1411; https://doi.org/10.3390/genes12091411 - 13 Sep 2021
Viewed by 2309
Abstract
The first data obtained from ancient DNA samples were published more than thirty years ago [...] Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)

Research

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21 pages, 4192 KiB  
Article
How a Paleogenomic Approach Can Provide Details on Bioarchaeological Reconstruction: A Case Study from the Globular Amphorae Culture
by Stefania Vai, Maria Angela Diroma, Costanza Cannariato, Alicja Budnik, Martina Lari, David Caramelli and Elena Pilli
Genes 2021, 12(6), 910; https://doi.org/10.3390/genes12060910 - 11 Jun 2021
Cited by 3 | Viewed by 3370
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)
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14 pages, 1491 KiB  
Article
First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy)
by Francesco Fontani, Elisabetta Cilli, Fabiola Arena, Stefania Sarno, Alessandra Modi, Sara De Fanti, Adam Jon Andrews, Adriana Latorre, Paolo Abondio, Felice Larocca, Martina Lari, David Caramelli, Emanuela Gualdi-Russo and Donata Luiselli
Genes 2021, 12(5), 636; https://doi.org/10.3390/genes12050636 - 25 Apr 2021
Cited by 5 | Viewed by 5468
Abstract
The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA [...] Read more.
The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies. Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)
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19 pages, 4172 KiB  
Article
Maternal Lineages from 10–11th Century Commoner Cemeteries of the Carpathian Basin
by Kitti Maár, Gergely I. B. Varga, Bence Kovács, Oszkár Schütz, Zoltán Maróti, Tibor Kalmár, Emil Nyerki, István Nagy, Dóra Latinovics, Balázs Tihanyi, Antónia Marcsik, György Pálfi, Zsolt Bernert, Zsolt Gallina, Sándor Varga, László Költő, István Raskó, Tibor Török and Endre Neparáczki
Genes 2021, 12(3), 460; https://doi.org/10.3390/genes12030460 - 23 Mar 2021
Cited by 15 | Viewed by 12180
Abstract
Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the [...] Read more.
Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10–11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians). Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)
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15 pages, 1962 KiB  
Article
Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania)
by Alexandra Gînguță, Ioana Rusu, Cristina Mircea, Adrian Ioniță, Horia L. Banciu and Beatrice Kelemen
Genes 2021, 12(3), 436; https://doi.org/10.3390/genes12030436 - 19 Mar 2021
Cited by 3 | Viewed by 11568
Abstract
The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such [...] Read more.
The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe. Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)
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15 pages, 1436 KiB  
Article
Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations
by Mariya A. Kusliy, Nadezhda V. Vorobieva, Alexey A. Tishkin, Alexey I. Makunin, Anna S. Druzhkova, Vladimir A. Trifonov, Tumur-O. Iderkhangai and Alexander S. Graphodatsky
Genes 2021, 12(3), 412; https://doi.org/10.3390/genes12030412 - 12 Mar 2021
Cited by 8 | Viewed by 5581
Abstract
The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data [...] Read more.
The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged. Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)
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15 pages, 530 KiB  
Article
A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach
by Maria Teresa Vizzari, Andrea Benazzo, Guido Barbujani and Silvia Ghirotto
Genes 2020, 11(12), 1510; https://doi.org/10.3390/genes11121510 - 16 Dec 2020
Cited by 5 | Viewed by 4231
Abstract
There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question [...] Read more.
There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago. Full article
(This article belongs to the Special Issue Ancient and Archaic Genomes)
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