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Diversity
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Ancient and Modern DNA for Diversity and Evolution of Animal...
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Ancient and Modern DNA for Diversity and Evolution of Animal and Plant Species

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

Deadline for manuscript submissions: closed (15 October 2022) | Viewed by 7006

Special Issue Editor

Dr. Elmira Mohandesan

E-Mail Website1 Website2
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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past few centuries, the world has witnessed tremendous turnovers in species distributions and biodiversity due to climatic and anthropogenic impacts. Until recently, our reconstruction of the past heavily relied on the interpretation of modern molecular data and on archaeological hypotheses. However, these days, research involving ancient DNA (aDNA) has revolutionized our understanding of the evolutionary past and yields snapshots of a vanished world of biodiversity. Although the majority of studies have focused on retrieving aDNA from biological specimens from hominids, or relatively large-bodied mammalian taxa, the field has grown rapidly with the help of researchers trying to use sedimentary ancient DNA (sedaDNA) and ancient proteins (Paleoproteomics) as promising tools to reconstruct the past biodiversity. In this Special Issue of Diversity, we present a set of review and research articles focused on “Ancient and Modern DNA for Diversity and Evolution of Animal and Plant Species”. The collection of works in this issue highlights review and primary research articles representing the state of knowledge on ancient and modern DNA/protein research focusing on reconstructing species past biodiversity, ecosystem, diet, disease, and behavior. The issue also includes methodological research articles focusing on the development of new and promising tools with the application in paleogenomics, paleoproteomics, and paleoepigenomics research.

Dr. Elmira Mohandesan
Guest Editor

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. Diversity 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 (aDNA)
  • Paleogenomics
  • Paleoproteomics
  • Paleoepigenomics
  • Environmental ancient DNA (eaDNA)
  • Metagenomics
  • Sedimentary ancient DNA (sedaDNA)
  • Genetic diversity
  • Biodiversity

Published Papers (3 papers)

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Research

13 pages, 1133 KiB  
Article
Evaluation of Genetic Diversity and Parasite-Mediated Selection of MHC Class I Genes in Emberiza godlewskii (Passeriformes: Emberizidae)
by Wei Huang, Xinyi Wang, Boye Liu, Tobias L. Lenz, Yangyang Peng, Lu Dong and Yanyun Zhang
Diversity 2022, 14(11), 925; https://0-doi-org.brum.beds.ac.uk/10.3390/d14110925 - 29 Oct 2022
Viewed by 1401
Abstract
The major histocompatibility complex (MHC) is a multi-copy immune gene family in vertebrates. Its genes are highly variable and code for antigen-presenting molecules. Characterization of MHC genes in different species and investigating the mechanisms that shape MHC diversity is an important goal in [...] Read more.
The major histocompatibility complex (MHC) is a multi-copy immune gene family in vertebrates. Its genes are highly variable and code for antigen-presenting molecules. Characterization of MHC genes in different species and investigating the mechanisms that shape MHC diversity is an important goal in understanding the evolution of biological diversity. Here we developed a next-generation sequencing (NGS) protocol to genotype the MHC class I genes of 326 Godlewski’s buntings (Emberiza godlewskii) sampled in the Western mountain area of Beijing from 2014 to 2016. A total of 184 functional alleles were identified, including both non-classical and classical alleles, clustering into nine supertypes. Compared with other passerine birds, the number of MHC class I alleles per individual in Godlewski’s buntings is high (mean 16.1 ± 3.3, median 16). In addition, we demonstrated signatures of historical and contemporary selection on MHC genes. Reflecting historical selection, ten amino acid sites in the antigen-binding domain showed signatures of balancing selection, eight of which exhibit high amino acid polymorphism. In terms of contemporary selection, we found that specific MHC supertypes were nominally associated with the infection of two malaria parasite lineages. These findings indicate the action of historical and possibly also contemporary balancing selection and suggest negative frequency-dependent or fluctuating selection as possible selection mechanisms. Full article
(This article belongs to the Special Issue Ancient and Modern DNA for Diversity and Evolution of Animal and Plant Species)
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14 pages, 2992 KiB  
Article
Genetic Variability within the Murgese Horse Breed Inferred from Genealogical Data and Morphometric Measurements
by Grazia Bramante, Elisa Pieragostini and Elena Ciani
Diversity 2022, 14(6), 422; https://0-doi-org.brum.beds.ac.uk/10.3390/d14060422 - 25 May 2022
Cited by 4 | Viewed by 1979
Abstract
The Murgese horse (MH) is a native breed from Apulia (Italy). This study aimed to evaluate the population status with regard to the available pedigree information (6923 animals born between 1900 and 2020), as well as its demographic and morphological evolution. The mean [...] Read more.
The Murgese horse (MH) is a native breed from Apulia (Italy). This study aimed to evaluate the population status with regard to the available pedigree information (6923 animals born between 1900 and 2020), as well as its demographic and morphological evolution. The mean equivalent generations were 5.88. The average relatedness, inbreeding coefficient and increase in inbreeding by equivalent generation (ΔF) were 9.88%, 5.22%, 1.05%, respectively. The effective population size based on ΔF was 47.46. The effective number of founders (fe) was 36, and that of ancestors (fa) was 19. The ratio fe/fa was 1.89 witnessing a bottleneck effect. The ratio fa/fe indicates a 52% reduction of the genetic diversity as expected, given the fact that, for the current population (now recovered to 5000 breeding animals), the fe is 34 and the fa only 17, with 50% of diversity being explained by only six ancestors. Basically, the results reflect a substantial loss of genetic diversity in the MH breed over generations since its official founding, and unbalanced use of sires in the population, highlighting the importance of continuous monitoring and implementation of more effective conservation measures, especially in view of the growing request for boosting genetic improvement for MH morpho-functional traits. Full article
(This article belongs to the Special Issue Ancient and Modern DNA for Diversity and Evolution of Animal and Plant Species)
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14 pages, 1393 KiB  
Article
Defining Management Units for Wild Nile Tilapia Oreochromis niloticus from Nine River Basins in Ghana
by Gifty Anane-Taabeah Attu, Emmanuel A. Frimpong and Eric M. Hallerman
Diversity 2022, 14(2), 73; https://0-doi-org.brum.beds.ac.uk/10.3390/d14020073 - 21 Jan 2022
Cited by 5 | Viewed by 2783
Abstract
Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused [...] Read more.
Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused on characterizing genetic differentiation at finer scales. We assessed genetic variation in O. niloticus within and among nine drainage basins in Ghana using nuclear microsatellite DNA markers as the basis for identifying potential units of conservation among wild populations. We screened 312 wild individuals using eight nuclear microsatellite DNA markers. We found moderate genetic diversity within and differentiation among all wild populations studied, with strong signals of recent demographic bottlenecks in several populations. Genetic structure among 11 populations suggested the presence of up to ten management units (MUs). In particular, the Black Volta and the Tano–Asuhyea populations, which were the most genetically distinct and geographically isolated and may be most at risk of loss of genetic diversity over time, may well represent evolutionary significant units. Therefore, at the minimum, the Black Volta and Tano–Asuhyea populations should be prioritized for conservation actions to sustain them over the long-term. Full article
(This article belongs to the Special Issue Ancient and Modern DNA for Diversity and Evolution of Animal and Plant Species)
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