Understanding the patterns of mutational load in admixed human and other mammalian populations
Creators: name: Ramasamy, Umayal
Publisher: name: University of the Sunshine Coast, Queensland
Year: 2023
Subjects: subject: genetic admixture
subject: deleterious mutations
subject: single nucleotide polymorphism
subject: effective population size
subject: population bottleneck
subject: founder effect
subject: genetic diversity and introgression
subject: Bioinformatics and computational biology
subject: Genetics
subject: FOS: Biological sciences

description: The out-of-Africa theory suggests that humans migrated out of Africa around 70,000 years ago, and during this process, only a subsample of the population migrated out of Africa. Over time, subsequent migrations progressively populated various regions of the globe. This process resulted in a serial subsampling of human populations that led to serial founder effects on the genetic variants carried by the populations. This resulted in significant variation in the SNPs of different populations, and the magnitude of this variation was correlated with geographic distance from Africa. However, the pattern of Single Nucleotide Polymorphisms (SNPs) of the individuals resulting from interbreeding between different populations is unknown.
description: Here I investigated this using the genomes of populations resulting from admixture between two (Africans and Europeans) and three (Africans, Europeans, and Native Americans) populations. For this purpose, I used the whole genome data of African Americans (61), Caribbeans (96), Peruvians (65), Colombians (94), Mexicans (64), and Puerto Ricans (104). The results of this investigation showed that the mean number of SNPs for admixed genomes was intermediate to those of their parental populations. For instance, the mean number of heterozygous SNPs in Caribbeans (2,25,480 SNPs) was greater than that of Europeans (1,67,907 SNPs) but less than that estimated for Africans (2,27,889 SNPs). In contrast, the average number of homozygous SNPs of Caribbeans (1,79,737 SNPs) was higher than that of Africans (1,78,865 SNPs) but lower than that observed for Europeans (2,07,060 SNPs). The difference between these mean values were statistically significant (P&lt;0.0001). A similar trend was detected for the Caribbean and Latin American populations. The results also revealed a correlation between the number of SNPs and the level of genetic admixture of the interbred populations. While this correlation was positive for heterozygous SNPs, it was negative for homozygous SNPs.
description: In order to explore the universality of these trends in non-human genomes, I performed similar analyses using whole genomes of cattle (275), canines (dogs and wolves) (54), and mouse (40) populations. The results were almost identical to those observed for humans. The mean number of hetero- and homozygous SNPs of admixed Bos taurus X Bos indicus breeds was intermediate between the parental Bos taurus and Bos indicus breeds. Likewise, the SNPs of dog-wolf and Mus musculus musculus-Mus musculus castaneus hybrids were also observed to be in between those of their parental populations. The correlation between the admixture proportions and SNP counts was positive for heterozygous and negative for homozygous SNPs, which was similar to that observed for humans. These results suggest that genetic admixture results in reducing the homozygous SNPs and increasing heterozygous SNPs.
description: The analyses using deleterious mutations produced results that were very similar to those observed for SNPs. These results imply that admixed humans have lower chances of getting recessive genetic diseases but higher chances of getting dominant genetic diseases. The outcomes of this study also suggest the importance of genetic admixture in dairy sciences to understanding the limitations of the breeding methods. Furthermore, the results could also be used to assess the impact of interbreeding between domesticated (e.g., dogs) and wild animals (e.g., wolves), which is important for the conservation of the latter.