Ancient and Modern DNA for Diversity and Domestication of Animals

A special issue of Animals (ISSN 2076-2615).

Deadline for manuscript submissions: 31 July 2024 | Viewed by 391

Special Issue Editor


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Guest Editor
Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
Interests: ancient DNA (paleogenomics); animal domestication; population genetics; phylogenetics; conservation biology; equine genomics; camelus genomics
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Special Issue Information

Dear Colleagues,

The domestication of animals led to a major shift in human subsistence strategies, from hunting of wild animals and gathering of wild plants in nature, to a sedentary agricultural lifestyle, which eventually resulted in the development of complex societies. During domestication, the phenotype and genotype of various animal species, such as dogs, pigs, sheep, goats, cattle, and horses, have been substantially altered, allowing them to adapt to the human niche. Over the past millennia, farmers have managed their livestock in a sustainable way; however, over the last two centuries, selective pressures have increased to produce hundreds of well-defined breeds with desirable traits, leading to the loss of highly valuable farm animal genetic resources. The maintenance of genomic diversity is vital for selection and genetic improvement strategies, adaptation to environmental changes and pathogens, and population conservation. Therefore, comparative genomic studies on ancient and modern specimens are particularly important to reconstruct the process by which animals entered domestic relationships with humans and were subjected to novel selection pressures. With such genomic information, we can recognize and restore marginal and rare breeds and improve the genetic diversity in industrial breeds. The main goal of this Special Issue is to cover studies investigating past and present genomic diversities and biological consequences of domestication, particularly, but not only, in major farmed species and companion animals.

Dr. Elmira Mohandesan
Guest Editor

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Keywords

  • animal domestication
  • ancient DNA
  • livestock
  • genetic diversity
  • feral populations
  • selection
  • adaptation

Published Papers (1 paper)

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Research

16 pages, 2391 KiB  
Article
Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples
by Alexandra A. Abdelmanova, Tatiana E. Deniskova, Veronika R. Kharzinova, Roman Yu Chinarov, Oksana I. Boronetskaya, Johann Sölkner, Gottfried Brem, Huashui Ai, Lusheng Huang, Vladimir I. Trukhachev and Natalia A. Zinovieva
Animals 2024, 14(11), 1629; https://doi.org/10.3390/ani14111629 - 30 May 2024
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Abstract
The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people’s pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding [...] Read more.
The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people’s pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775–1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs. Full article
(This article belongs to the Special Issue Ancient and Modern DNA for Diversity and Domestication of Animals)
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