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Advances in Ancient Genomes
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Advances in Ancient 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 (15 January 2024) | Viewed by 17888

Special Issue Editors

Prof. Dr. Xulong Lai

E-Mail Website
Guest Editor
School of Earth Science, China University of Geosciences, Wuhan 430074, China
Interests: ancient DNA; palaeogenomics; Pleistocene; evolution; vertebrate paleontology; phylogenetic analysis; next generation sequencing (NGS); genetic diversity; genetic history of past population
Dr. Junxia Yuan

E-Mail Website
Guest Editor
Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
Interests: ancient DNA; palaeogenomics; ancient animal remain; Pleistocene; phylogenetic analysis; domestication; gene folw
Prof. Dr. Guilian Sheng

E-Mail Website
Guest Editor
School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
Interests: ancient DNA; palaeogenomics; molecular evolution; phylogenetics; phylogeography; population genetics; next generation sequencing (NGS)

Special Issue Information

Dear Colleagues,

In recent years, the rapidly increasing advancements of next-generation sequencing (NGS) technologies have revolutionized our approach to ancient DNA research. Much research has contributed to overcoming earlier limitations, including the degradation and preservation of endogenous ancient DNA molecules, as well as the contamination by modern DNA. With the technological improvements regarding the capacity of recovery and the analysis of the ancient molecules, it is now possible to retrieve complete genomes from fossil remains or even sediment. Palaeogenomics offers a high-resolution means to uncover long-standing issues of confusion, for example, accurately identifying the taxon of an extinct species, detecting the possible information of interspecies interactions, and investigating the patterns of animal domestication. Genome-level study also greatly contributes to understanding the genetic variability of endangered species through time and helps conservation projects. Ancient genomes are providing a more comprehensive and a more complete perspective on the evolutionary history of modern and extinct species, which are challenging as they can only be inferred from the morphological analysis of fossil or subfossil materials.

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

Prof. Dr. Xulong Lai
Dr. Junxia Yuan
Prof. Dr. Guilian Sheng
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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

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

  • ancient DNA
  • paleogenomics
  • paleogenetics
  • next generation sequencing (NGS)
  • target enrichment
  • extinct species
  • domestication
  • genomic history
  • gene flow

Published Papers (6 papers)

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Research

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14 pages, 2711 KiB  
Article
Ancient Mitochondrial Genomes Provide New Clues to the Origin of Domestic Cattle in China
by Naifan Zhang, Xinyue Shao, Yaqi Guo, Xinyu Zhang, Yawei Zhou, Jing Yuan, Zhuowei Tang, Songmei Hu, Sergey Stepanovich Minyaev and Dawei Cai
Genes 2023, 14(7), 1313; https://doi.org/10.3390/genes14071313 - 22 Jun 2023
Viewed by 1883
Abstract
Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they [...] Read more.
Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they were introduced to China is unknown. In this study, we extracted the mitochondrial genomes of 34 cases of ancient taurine cattle (from the late Neolithic to Qin and Han dynasties) excavated from sites in northern China and the eastern Eurasian steppe, and successfully obtained 14 mitochondrial genome sequences. The results of ancient DNA analysis reveal that with cultural exchange and trade, there was close genetic exchange between domestic taurine cattle in different regions. The haplotypes shared by domestic cattle have genetic continuity, reflecting the strong cultural influence of the large capital city sites such as Taosi, Shimao and Erlitou on the surrounding areas. This study suggests that ancient northern Chinese taurine cattle may have accompanied the westward transmission of agricultural or painted pottery culture and thus had a maternal genetic contribution to modern Tibetan cattle. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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10 pages, 1549 KiB  
Article
Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows
by Shiwen Song, Bo Xiao, Jiaming Hu, Haifeng Lin, Zhicheng Du, Kunpeng Xiang, Dong Pan, Xindong Hou, Junxia Yuan, Xulong Lai and Guilian Sheng
Genes 2023, 14(6), 1187; https://doi.org/10.3390/genes14061187 - 29 May 2023
Cited by 1 | Viewed by 1165
Abstract
As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on [...] Read more.
As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74–2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37–0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225–160 and 90–50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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11 pages, 2221 KiB  
Article
Deciphering the West Eurasian Genetic Footprints in Ancient South India
by Bhavna Ahlawat, Lomous Kumar, Parayil John Cherian, Jagmahender Singh Sehrawat, Niraj Rai and Kumarasamy Thangaraj
Genes 2023, 14(5), 963; https://doi.org/10.3390/genes14050963 - 23 Apr 2023
Viewed by 3275
Abstract
Since 2006, Pattanam coastal village of the Ernakulam District in Kerala, India, has witnessed multi-disciplinary archaeological investigations in collaboration with leading research institutions across the world. The results confirm that the Pattanam site could be an integral part of the lost ancient port [...] Read more.
Since 2006, Pattanam coastal village of the Ernakulam District in Kerala, India, has witnessed multi-disciplinary archaeological investigations in collaboration with leading research institutions across the world. The results confirm that the Pattanam site could be an integral part of the lost ancient port of Muziris, which, as per the material evidence from Pattanam and its contemporary sites, played an important role in the transoceanic exchanges between 100 BCE (Before Common Era) and 300 CE (Common Era). So far, the material evidence with direct provenance to the maritime exchanges related to ancient cultures of the Mediterranean, West Asian, Red Sea, African, and Asian regions have been identified at Pattanam. However, the genetic evidence supporting the impact of multiple cultures or their admixing is still missing for this important archaeological site of South India. Hence, in the current study, we tried to infer the genetic composition of the skeletal remains excavated from the site in a broader context of South Asian and worldwide maternal affinity. We applied the MassArray-based genotyping approach of mitochondrial makers and observed that ancient samples of Pattanam represent a mixed maternal ancestry pattern of both the West Eurasian ancestry and the South Asian ancestry. We observed a high frequency of West Eurasian haplogroups (T, JT, and HV) and South Asian-specific mitochondrial haplogroups (M2a, M3a, R5, and M6). The findings are consistent with the previously published and ongoing archaeological excavations, in which material remains from over three dozen of sites across the Indian Ocean, Red Sea, and Mediterranean littoral regions have been unearthed. This study confirms that people belonging to multiple cultural and linguistic backgrounds have migrated, probably settled, and eventually died on the South-western coast of India. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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12 pages, 1205 KiB  
Article
Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data
by Draga Toncheva, Maria Marinova, Todor Chobanov and Dimitar Serbezov
Genes 2023, 14(3), 727; https://doi.org/10.3390/genes14030727 - 16 Mar 2023
Viewed by 2553
Abstract
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. [...] Read more.
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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Review

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17 pages, 2148 KiB  
Review
Advancements and Challenges in Ancient DNA Research: Bridging the Global North–South Divide
by Vasundhra Dalal, Nagarjuna Pasupuleti, Gyaneshwer Chaubey, Niraj Rai and Vasant Shinde
Genes 2023, 14(2), 479; https://doi.org/10.3390/genes14020479 - 14 Feb 2023
Cited by 1 | Viewed by 4243
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The [...] Read more.
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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16 pages, 584 KiB  
Review
Methodological Changes in the Field of Paleogenetics
by Mikołaj Danielewski, Joanna Żuraszek, Aleksandra Zielińska, Karl-Heinz Herzig, Ryszard Słomski, Jarosław Walkowiak and Karolina Wielgus
Genes 2023, 14(1), 234; https://doi.org/10.3390/genes14010234 - 16 Jan 2023
Cited by 3 | Viewed by 3468
Abstract
Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound [...] Read more.
Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges. Full article
(This article belongs to the Special Issue Advances in Ancient Genomes)
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