Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples, DNA Extraction, and Library Preparation
2.2. Sequencing Data Processing (FASTQ to Genotypes/Likelihoods)
2.3. Quality Control (Depth of Coverage and Contamination)
2.4. Genotype Likelihoods and SNP Calling
2.5. Genetic Sexing from Coverage
2.6. Relatedness Test
2.7. Population Structure Assessment
2.8. Heterozygosity Estimates
2.9. Estimation of Runs of Homozygosity and Inbreeding Coefficients
2.10. Past and Present Demographic History
2.11. Assessment of Gene Flow and Connectivity
3. Results
3.1. Single Hairs as a Source for Genomic DNA
3.2. Increased Resolution of Western Gorilla Population Structure
3.3. Genetic Diversity among Gorilla Species
3.4. Strong Bottleneck in Cross River Gorillas
3.5. Past Gene Flow among Gorilla Subspecies
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Alvarez-Estape, M.; Pawar, H.; Fontsere, C.; Trujillo, A.E.; Gunson, J.L.; Bergl, R.A.; Bermejo, M.; Linder, J.M.; McFarland, K.; Oates, J.F.; et al. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs. Genes 2023, 14, 743. https://doi.org/10.3390/genes14030743
Alvarez-Estape M, Pawar H, Fontsere C, Trujillo AE, Gunson JL, Bergl RA, Bermejo M, Linder JM, McFarland K, Oates JF, et al. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs. Genes. 2023; 14(3):743. https://doi.org/10.3390/genes14030743
Chicago/Turabian StyleAlvarez-Estape, Marina, Harvinder Pawar, Claudia Fontsere, Amber E. Trujillo, Jessica L. Gunson, Richard A. Bergl, Magdalena Bermejo, Joshua M. Linder, Kelley McFarland, John F. Oates, and et al. 2023. "Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs" Genes 14, no. 3: 743. https://doi.org/10.3390/genes14030743