Revealing the Puzzle of the Past through Ancient Biomolecules: From Wild to Tame Faunal Diversity

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (1 May 2023) | Viewed by 16849

Special Issue Editors


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Guest Editor
1. "Emil Racoviță" Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711 Bucharest, Romania
2. Emil G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
3. Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
4. Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
Interests: ancient DNA; cave; ecology; population genomics

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Guest Editor
Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, 5-7 Clinicilor Street, 400006 Cluj-Napoca, Romania
Interests: bioarchaeology; molecular anthropology; ancient DNA; historical domesticated stocks

Special Issue Information

Dear Colleagues,

Starting four decades ago, the study of ancient biomolecules gave us the opportunity to disentangle the complexity of processes that shaped the ancient faunal diversity across millennia at an unprecedented molecular level. Studies addressing demographic dynamics, divergence and admixture among populations, determining probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species first used short mitochondrial DNA fragments, then eventually whole genomes, epigenomes, proteomes, and even lipids. However, even now, few studies explore the possibility of interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropic impact.

In this Special Issue of Diversity we aim to bring the story of extinct and extant faunal diversity to life, from wild to domesticated populations, retrieved from subsurface and surface archaeological and palaeontological deposits, by analysing ancient biomolecules (DNA, proteins, lipids, and stable isotopes). The manuscripts should provide insight and present new challenges and perspectives on the spatio-temporal ancient faunal diversity within palaeoecological contexts.

We hope this Special Issue will approach a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient and medieval wild and domestic stocks, and offer a better understanding of drivers of past faunal diversity on Earth.

Papers proposing meaningful contributions on faunal diversity, independently of analysed marker source and specific topic, are welcome.

Dr. Ioana Nicoleta Meleg
Dr. Beatrice Simona Kelemen
Guest Editors

Manuscript Submission Information

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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

  • ancient DNA
  • wild and domestic ancient fauna
  • genomics
  • epigenomics
  • proteomics
  • ancient biomolecules (DNA, proteins, lipids, stable isotopes)
  • sedimentary ancient DNA
  • bimolecular archaeology and palaeontology, palaeoecology

Published Papers (6 papers)

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Research

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23 pages, 6412 KiB  
Article
Stable Isotopes and Herding Strategies in Middle Uruk Period in Tell Humeida (Syrian Euphrates Valley)
by Aurora Grandal-d’Anglade, Ana García-Vázquez, Marta Moreno-García, Leonor Peña-Chocarro, Jorge Sanjurjo-Sánchez and Juan Luís Montero-Fenollós
Diversity 2023, 15(6), 709; https://doi.org/10.3390/d15060709 - 26 May 2023
Viewed by 1218
Abstract
The techniques of agriculture and animal husbandry at Tell Humeida, a Middle Uruk Period (Late Chalcolithic) site on the middle Syrian Euphrates, were studied using stable isotopes of bone collagen of domestic and wild mammals and from cereal and ruderal plant seeds. Two [...] Read more.
The techniques of agriculture and animal husbandry at Tell Humeida, a Middle Uruk Period (Late Chalcolithic) site on the middle Syrian Euphrates, were studied using stable isotopes of bone collagen of domestic and wild mammals and from cereal and ruderal plant seeds. Two archaeological campaigns in 2009 and 2011 yielded a small collection of bones, most of which were taxonomically indeterminable. The work had to be interrupted due to the political conflict. The faunal study comprised collagen peptide fingerprinting for taxonomic identification, followed by isotopic analysis. Multiple 14C dating were performed to date the infill to around 3600 cal BC. An isotopic analysis of the sparse plant remains suggested that irrigation and manuring were common practices. Sheep and equids predominated in the faunal assemblage. Sheep grazed on manured soils, and their diet could include millet or another C4 plant, of which, however, no carpological remains were found. The diet of equids differed from that of sheep but also that of other wild ungulates (cervids/gazelles). Their isotopic signatures indicated that they grazed in humid areas, near the watercourse. These finds indicated a settlement that was closely linked to the availability of water, which made it possible to grow crops in an almost desert-like area, and the rearing of sheep. Full article
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17 pages, 2324 KiB  
Article
The mtDNA D-Loop Legacy of Cattle: Fluctuations in Diversity from the Neolithic to Early Medieval Times in Switzerland
by José Granado, Elizabeth Wright, Robert Blatter, Jürg Lange, Meral Turgay, Laura Bañuelos, Sabine Deschler-Erb, Barbara Stopp, Elisabeth Marti-Grädel, Marguerita Schäfer, Idoia Grau-Sologestoa, Sandra Ammann, Debora Schmid, Alex R. Furger, Reto Marti, Jörg Schibler and Angela Schlumbaum
Diversity 2023, 15(5), 687; https://doi.org/10.3390/d15050687 - 19 May 2023
Viewed by 1554
Abstract
Fluctuations in the size of taurine cattle (Bos taurus) have been regularly demonstrated using archaeozoological data from across time and space in Europe, and have been linked to cultural, social and economic changes, but little is known about whether phenotypic change [...] Read more.
Fluctuations in the size of taurine cattle (Bos taurus) have been regularly demonstrated using archaeozoological data from across time and space in Europe, and have been linked to cultural, social and economic changes, but little is known about whether phenotypic change is accompanied by changes in genetic diversity. Here, we performed PCR-typed analysis of the partial mtDNA d-loop fragments of 99 cattle from the Neolithic to Early Medieval times from a number of different sites across Switzerland, combining newly presented data with previously published data (n = 20). We found that most cattle included (84) were members of the common European macro-haplogroup T3. However, cattle belonging to the haplogroups T1, T2, Q and P were identified as early as the Neolithic period, before 2690 cal. BCE. The highest diversity was found in the Neolithic period, during the 1st century CE and during the 7th–8th centuries CE. Bottleneck phases with low genetic diversity were detected during the Late Iron Age and from the fifth to the seventh century CE. Based on the FST values, Horgen, Corded Ware and cattle populations from the seventh to the ninth century CE were plotted away from the clusters of all other populations. The periods with larger-sized cattle correspond with those of high mtDNA d-loop diversity. Phenotype and genotype both appear to respond to the same socio-economic and cultural processes. Full article
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11 pages, 3323 KiB  
Article
Holocene Genetic Evolution of Pig (Sus scrofa) on Romanian Territory in a European Time and Space Frame
by Margareta Simina Stanc, Monica Luca, Adrian Bălășescu and Luminița Bejenaru
Diversity 2022, 14(4), 288; https://doi.org/10.3390/d14040288 - 11 Apr 2022
Cited by 1 | Viewed by 1799
Abstract
Romanian territory represents a key point in the dispersal of domestic pigs into Europe, due to its geographical position. Our study gathers a high number of samples from different archaeological sites on Romanian territory in order to establish a more accurate chronological view [...] Read more.
Romanian territory represents a key point in the dispersal of domestic pigs into Europe, due to its geographical position. Our study gathers a high number of samples from different archaeological sites on Romanian territory in order to establish a more accurate chronological view of the spread of domestic pig into Europe and to investigate the possibility of a local domestication process. Approximately 200 samples from 45 archaeological sites on Romanian territory, covering a large period of time, from the Neolithic to the Middle Ages, were subjected to DNA analysis. The sequencing of a short fragment from the D-loop region of the mitochondrial DNA identified a different prevalence of domestic pig genetic signature between two periods of time: the Neolithic period and the Early Bronze Age–Middle Ages period. While the Neolithic period is characterized by the presence of domestic pigs with a Near-Eastern signature, during the Early Bronze Age–Middle Ages period this genetic signature is replaced with a European one. Two European and two Near-Eastern signatures were described for all the analysed samples, each of them prevailing within the wild, respectively domestic Sus scrofa. The data also revealed the introgression process as a form of domestication in Romanian territory. Full article
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15 pages, 1251 KiB  
Article
MtDNA D-Loop Diversity in Alpine Cattle during the Bronze Age
by José Granado, Marianna Harmath, Umberto Tecchiati, Klaus Oeggl, Jörg Schibler and Angela Schlumbaum
Diversity 2021, 13(9), 449; https://doi.org/10.3390/d13090449 - 19 Sep 2021
Cited by 6 | Viewed by 2188
Abstract
The Bronze Age in Europe is characterized by major socio-economic changes, including certain aspects of animal husbandry. In the Alpine region archaeozoological data, though not very abundant, reveal that cattle were the most important domestic animals in this time period. They were probably [...] Read more.
The Bronze Age in Europe is characterized by major socio-economic changes, including certain aspects of animal husbandry. In the Alpine region archaeozoological data, though not very abundant, reveal that cattle were the most important domestic animals in this time period. They were probably used differently in the lowlands than at higher altitude, traction became more important and people increasingly exploited them for dairy products rather than for meat. Thus, a crucial question in this context is whether these major events are accompanied by changes in genetic diversity of cattle. Here we report partial mtDNA d-loop data (320 bp) obtained by PCR from 40 alpine cattle excavated at different sites in South Tyrol, Italy, and Grisons, Switzerland. Most cattle belong to the main European taurine T3 haplogroup, but a few members of T2 and Q haplogroups were identified. Moreover, genetic diversity measures and population genetic statistics indicate different cattle histories at different sites, including bottlenecks and potential admixture. However, Bronze Age Alpine cattle appear to be linked to modern rural cattle mainly from Italy. Full article
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17 pages, 4866 KiB  
Article
Shedding Light on the Dark Ages: Sketching Potential Trade Relationships in Early Medieval Romania through Mitochondrial DNA Analysis of Sheep Remains
by Arina Acatrinei, Ioana Rusu, Cristina Mircea, Cezara Zagrean-Tuza, Emese Gál, Doru Păceșilă, Oana Gâza, Claudia Urduzia, Zeno Karl Pinter, Cătălin Dobrinescu, Vitalie Bodolică, Adela Pintea and Beatrice Kelemen
Diversity 2021, 13(5), 208; https://doi.org/10.3390/d13050208 - 13 May 2021
Cited by 1 | Viewed by 3198
Abstract
Southeast Europe has played an important role in shaping the genetic diversity of sheep due to its proximity to the Danubian route of transport from the Near East into Europe, as well as its possible role as a post-domestication migration network and long [...] Read more.
Southeast Europe has played an important role in shaping the genetic diversity of sheep due to its proximity to the Danubian route of transport from the Near East into Europe, as well as its possible role as a post-domestication migration network and long tradition of sheep breeding. The history of Romania and, in particular, the historical province of Dobruja, located on the shore of the Black Sea, has been influenced by its geographical position at the intersection between the great powers of the Near East and mainland Europe, with the Middle Ages being an especially animated time in terms of trade, migration, and conflict. In this study, we analyzed the mitochondrial control region of five sheep originating from the Capidava archaeological site (Dobruja, Southeast Romania), radiocarbon dated to the Early Middle Ages (5–10th century AD), in order to better understand the genetic diversity of local sheep populations and human practices in relation to this particular livestock species. The analyses illustrate high haplotype diversity in local medieval sheep, as well as possible genetic continuity in the region. A higher tendency for North to South interaction, rather than East to West, is apparent, together with a lack of interaction along the Asian route. Continuous interaction between the First Bulgarian Empire, which occupied Dobruja starting with the 7th century AD, and the Byzantine Empire is indicated. These results might suggest expanding trade in Southeast Romania in the Early Middle Ages. Full article
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Review

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31 pages, 7525 KiB  
Review
Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches
by Erika Rosengren, Arina Acatrinei, Nicolae Cruceru, Marianne Dehasque, Aritina Haliuc, Edana Lord, Cristina I. Mircea, Ioana Rusu, Emilio Mármol-Sánchez, Beatrice S. Kelemen and Ioana N. Meleg
Diversity 2021, 13(8), 370; https://doi.org/10.3390/d13080370 - 10 Aug 2021
Cited by 6 | Viewed by 4747
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, [...] Read more.
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth. Full article
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