Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethical Statement
2.2. Study Area and Sampling
2.3. DNA Extraction and MHC Genotyping by Sequencing
2.4. MHC Diversity
2.4.1. Sequence Diversity
2.4.2. Clusters/Populations Genetic Parameters and Molecular Variance
2.4.3. Clustering of DRB Exon 2 Alleles
2.4.4. Detecting Signatures of Recombination and Selection in MHC DRB Exon 2 Alleles in Roe Deer
2.5. Determination of Genetic Variability among Groups and Clusters Based on Neutral Microsatellite Loci
3. Results
3.1. Diversity of MHC DRB Alleles
3.2. Clusters/Populations Genetic Parameters and Molecular Variance
3.3. Recombination and Natural Selection in MHC DRB Alleles in Roe Deer
3.4. Evolutionary Relationships among DRB Exon 2 Alleles in Roe Deer
3.5. Genetic Diversity and Genetic Structure Based on Neutral Loci
4. Discussion
4.1. Genetic Diversity and Population Structure
4.2. Selection and Recombination
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Constent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Parameters Related to Nucleotide Differences | Overall Nucleotide Evolutionary Distance | Amino Acid Evolutionary Distance | |||||
---|---|---|---|---|---|---|---|
k | S | All Sites | ABS | Non-ABS | All Sites | ABS | Non-ABS |
9.833 | 22 + 1 indel (13 + 1 indel) * | 0.05 (0.01) | 0.17 (0.06) | 0.02 (0.01) | 0.09 (0.03) | 0.43 (0.22) | 0.03 (0.02) |
Geographical Group | Abbr. | n | A | AR | Ho | He | π (SD) | θ | Tajima’s D |
---|---|---|---|---|---|---|---|---|---|
Overall | 156 | 10 | 10.000 | 0.529 | 0.739 | 0.045 (0.004) | 0.015 | 2.263 | |
Southwestern | SW | 29 | 8 | 8.000 | 0.414 | 0.713 | 0.028 (0.004) | 0.022 | 0.579 |
Central | C | 68 | 10 | 8.357 | 0.524 | 0.724 | 0.029 (0.002) | 0.017 | 1.610 |
Northeastern | NE | 59 | 9 | 8.602 | 0.593 | 0.759 | 0.027 (0.002) | 0.017 | 1.428 |
Main Parameters | Overall | ABS | Non-ABS |
---|---|---|---|
N | 83 | 16 | 67 |
dS (SE) | 0.02 (0.01) | 0.02 (0.02) | 0.03 (0.01) |
dN (SE) | 0.05 (0.02) | 0.20 (0.08) | 0.02 (0.01) |
ω dN/dS) | 1.40 | 2.60 | −0.40 |
p-value | 0.08 | 0.01 | 1.00 |
Codon Sites under Positive Selection | Selection Model |
---|---|
12, 13, 16, 57, 67, 70, 71, 86 | M2a |
12, 13, 16, 57, 67, 70, 71, 86 | M8 |
Event | Recombinant Sequence | Major/Minor Parent | Consensus Score | Beginning/Ending Breakpoint | Probability (MC Corrected) * | Methods |
---|---|---|---|---|---|---|
1 | Caca-DRB*0403 | Unknown/ Caca-DRB*0401 | 0.534 | 170/242 | 0.0235 | MaxChi, SiScan, 3Seq |
2 | Caca-DRB*0401 | Caca-DRB*0404/Unknown | 0.481 | 84/266 | 0.0177 | MaxChi |
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Buzan, E.; Potušek, S.; Duniš, L.; Pokorny, B. Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia. Animals 2022, 12, 723. https://doi.org/10.3390/ani12060723
Buzan E, Potušek S, Duniš L, Pokorny B. Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia. Animals. 2022; 12(6):723. https://doi.org/10.3390/ani12060723
Chicago/Turabian StyleBuzan, Elena, Sandra Potušek, Luka Duniš, and Boštjan Pokorny. 2022. "Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia" Animals 12, no. 6: 723. https://doi.org/10.3390/ani12060723
APA StyleBuzan, E., Potušek, S., Duniš, L., & Pokorny, B. (2022). Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia. Animals, 12(6), 723. https://doi.org/10.3390/ani12060723