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Wildlife Genetic Diversity and Genomics
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Wildlife Genetic Diversity and Genomics

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 (20 December 2024) | Viewed by 5900

Special Issue Editor

Dr. Wenping Zhang

E-Mail Website
Guest Editor
Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China
Interests: genetic diversity; genome; population genetics; metagenome; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biodiversity is a key component of ecosystems, responsible for driving variation in ecosystem productivity, stability, and resilience. Therefore, the ecological consequences of genetic diversity lie at the core of efforts to understand the links between biodiversity and ecosystem function. The nature of genomics and genetic diversity in wildlife has always been the basic problem of evolutionary genetics, as well as gene flow, population depression, population growth, and so on. However, despite its cardinal role in evolutionary theory and application, the maintenance of genetic diversity remains largely enigmatic, notwithstanding the dramatic discoveries of molecular biology, which revealed the abundant genetic diversity in nature. Moreover, it is unclear how widely the ecological effects of genetic diversity apply in wildlife, and little is known about the relative importance of genetic diversity vs. other factors that influence the ecological processes of interest in wildlife.

Therefore, this Special Issue will focus on the genomics and genetic diversity of wildlife, including animals, plants, and microorganisms and will aim to fill these gaps in research by evaluating the following aspects: (1) the genomics and genetic diversity in wildlife through all kinds of molecular markers, (2) the mechanisms by which environment- and genetic-driven trait variation occur in wildlife, (3) the ecological and evolutionary consequences of genotypic diversity effects on interactions in wildlife, (4) the genetic diversity consequences among stress factors, and (5) the linkages between the evolutionary forces that shape the expression of additive genetic variation and ecological genetic diversity effects.

Dr. Wenping Zhang
Guest Editor

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Keywords

  • animal
  • plant
  • microorganism
  • genome
  • metagenome
  • genetic diversity
  • genomic diversity
  • molecular marker
  • mitochondrial DNA
  • chloroplast DNA

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Published Papers (4 papers)

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Research

14 pages, 4107 KiB  
Article
Polymorphism of Genes Potentially Affecting Growth and Body Size Suggests Genetic Divergence in Wild and Domestic Reindeer (Rangifer tarandus) Populations
by Anna A. Krutikova, Natalia V. Dementieva, Yuri S. Shcherbakov, Vasiliy V. Goncharov, Darren K. Griffin and Michael N. Romanov
Genes 2024, 15(12), 1629; https://doi.org/10.3390/genes15121629 - 20 Dec 2024
Viewed by 1343
Abstract
Background/Objectives: A combination of increased human presence in the Arctic zone alongside climate change has led to a decrease in the number of wild reindeer (Rangifer tarandus). Studying the genetic potential of this species will aid in conservation efforts, while [...] Read more.
Background/Objectives: A combination of increased human presence in the Arctic zone alongside climate change has led to a decrease in the number of wild reindeer (Rangifer tarandus). Studying the genetic potential of this species will aid in conservation efforts, while simultaneously promoting improved meat productivity in domestic reindeer. Alongside reducing feed costs, increasing disease resistance, etc., acquiring genetic variation information is a crucial task for domestic reindeer husbandry. This study thus identified highly informative molecular genetic markers usable for assessing genetic diversity and breeding purposes in reindeer. Methods: We analyzed gene polymorphism that may potentially affect animal growth and development in populations of wild (Taimyr Peninsula) and domestic reindeer, including Nenets and Evenk breeds. We screened these populations for polymorphisms by sequencing the GH, GHR, LCORL and BMP2 genes. Results: Following generation of gene sequences, we compared the alleles frequency in the surveyed populations and their genetic divergence. Some loci lacked polymorphism in wild reindeer, unlike domestic breeds. This could suggest a selection-driven microevolutionary divergence in domestic reindeer populations. An isolated domestic population from Kolguyev Island appeared to be genetically remote from continental reindeer. Conclusions: Molecular genetic markers associated with economically important traits in reindeer can be further developed using the data obtained. Monitoring wild reindeer populations and better utilizing the genetic potential of domestic animals will depend on a panel of these marker genes. By using this marker panel, the amount of time spent on selection efforts will be greatly reduced to enhance meat performance during reindeer breeding. Full article
(This article belongs to the Special Issue Wildlife Genetic Diversity and Genomics)
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11 pages, 2887 KiB  
Article
Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of Pinus sylvestris L. Populations in the Urals
by Nikita Chertov, Yana Sboeva, Yulia Nechaeva, Svetlana Boronnikova, Andrei Zhulanov, Victoria Pechenkina and Ruslan Kalendar
Genes 2024, 15(10), 1343; https://doi.org/10.3390/genes15101343 - 21 Oct 2024
Viewed by 1161
Abstract
Background: Scots Pine is one of the main forest-forming species in boreal forests; it has great economic and ecological significance. This study aimed to develop and test primers for detecting nucleotide polymorphisms in genes that are promising for detecting adaptive genetic variability in [...] Read more.
Background: Scots Pine is one of the main forest-forming species in boreal forests; it has great economic and ecological significance. This study aimed to develop and test primers for detecting nucleotide polymorphisms in genes that are promising for detecting adaptive genetic variability in populations of Pinus sylvestris in the Urals and adjacent territories. Objectives: The objects of the study were 13 populations of Scots Pine located in the Perm Territory, Chelyabinsk Region, and the Republic of Bashkortostan. Results: Sixteen pairs of primers to loci of potentially adaptively significant genes were developed, from which three pairs of primers were selected to detect the nucleotide diversity of the studied populations. The indicator of total haplotype diversity determined in the three studied loci varied from 0.620 (Pinus-12 locus) to 0.737 (Pinus-11 locus) and, on average, amounted to 0.662. The nucleotide diversity indicators in P. sylvestris in the study region were, on average, low (π = 0.004, θW = 0.013). Their highest values were found at the Pinus-12 locus (π = 0.005; θW = 0.032), and the lowest were found at the Pinus-15 locus (π = 0.003; θW = 0.002). This indicates that Pinus-15 is the most conserved of the three studied loci. In the three studied P. sylvestris loci associated with adaptation to environmental factors, 97 polymorphic positions were identified. The 13 populations of P. sylvestris are characterized by an average level of genetic diversity (Hd = 0.662; π = 0.004; θ = 0.013). Conclusions: The polymorphic loci of adaptively significant genes of P. sylvestris can help identify the adaptive potential of pine forests in conditions of increasing ambient temperatures. Full article
(This article belongs to the Special Issue Wildlife Genetic Diversity and Genomics)
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11 pages, 2535 KiB  
Article
Agouti-Signaling Protein and Melanocortin-1-Receptor Mutations Associated with Coat Color Phenotypes in Fallow Deer (Dama dama)
by Monika Reissmann, Evelin Ullrich, Uwe Bergfeld and Arne Ludwig
Genes 2024, 15(8), 1055; https://doi.org/10.3390/genes15081055 - 11 Aug 2024
Viewed by 1499
Abstract
Four dominant coat color phenotypes are found in fallow deer (Dama dama). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals [...] Read more.
Four dominant coat color phenotypes are found in fallow deer (Dama dama). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals (772 brown, 62 black, 126 menil, and 38 white) were examined for mutations in the ASIP, MC1R, TYR, and SLC45A2 genes. In ASIP, two mutations (ASIP-M-E2, located at the boundary from exon 2 to intron 2; and ASIP-M-E3, an InDel of five nucleotides) were found, leading to black fallow deer being either homozygous or heterozygous in combination. There were also two mutations found in MC1R. Whereby the mutation MC1R-M1 (leucine to proline, L48P) homozygous leads to a white coat, while the mutation MC1R-M2 (glycine to aspartic acid, G236D) homozygous is associated with the menil phenotype. When both mutations occur together in a heterozygous character state, it results in a menil coat. Since the mutations in the two genes are only present alternatively, 36 genotypes can be identified that form color clusters to which all animals can be assigned. No mutations were found in the TYR and SLC45A2 genes. Our investigations demonstrate that the four dominant coat colors in fallow deer can be explained by ASIP and MC1R mutations only. Full article
(This article belongs to the Special Issue Wildlife Genetic Diversity and Genomics)
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11 pages, 5481 KiB  
Article
Complete Mitochondrial Genome and Phylogenetic Analysis of the Blue Whistling Thrush (Myophonus caeruleus)
by Zhenfeng Yuan, Peng Liu, Xi Lu, Dong Zhu, Jun Liu, Qiang Guo, Wenping Zhang and Yubao Duan
Genes 2024, 15(7), 830; https://doi.org/10.3390/genes15070830 - 24 Jun 2024
Cited by 1 | Viewed by 1368
Abstract
The blue whistling thrush (Myophonus caeruleus) is a bird belonging to the order Passeriformes and family Muscicapidae. M. caeruleus is widely distributed in China, Pakistan, India, and Myanmar and is a resident bird in the southern part of the Yangtze River [...] Read more.
The blue whistling thrush (Myophonus caeruleus) is a bird belonging to the order Passeriformes and family Muscicapidae. M. caeruleus is widely distributed in China, Pakistan, India, and Myanmar and is a resident bird in the southern part of the Yangtze River in China and summer migratory bird in the northern part of the Yangtze River. At present, there are some controversies about the classification of M. caeruleus. We use complete mitochondrial genomes to provide insights into the phylogenetic position of M. caeruleus and its relationships among Muscicapidae. The mitochondrial genome (GenBank: MN564936) is 16,815 bp long and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region (D-loop). The thirteen PCGs started with GTG and ATG and ended with five types of stop codons. The nucleotide composition of T was 23.71%, that of C was 31.45%, that of A was 30.06%, and that of G was 14.78%. The secondary structures of 22 tRNAs were predicted, all of which could form typical cloverleaf structures. There were 24 mismatches, mainly G–U mismatches. Through phylogenetic tree reconstruction, it was found that Saxicola, Monticola, Oenanthe, and Phoenicurus were clustered into one clade, together with the sister group of Myophonus. Full article
(This article belongs to the Special Issue Wildlife Genetic Diversity and Genomics)
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