Shaping the genomes of modern humans: Admixture and genetic diversity in africa and the americas

Throughout the course of human history, we have witnessed intricate patterns of migration, isolation, and gene flow between populations, known as admixture. This phenomenon has led to the blending of genetic lineages, enhancing genetic diversity within populations. In addition to admixture among modern human populations, our ancient ancestors interbred with other hominin groups like Neanderthals and Denisovans, resulting in the inheritance of fragments of DNA from these ancient lineages in modern humans, a process called introgression.

Recently, two studies published in Genome Biology and Evolution have shed light on patterns of admixture in Africa and the Americas, revealing how this process has shaped the genomes of present-day humans in these regions.

Africa, as the birthplace of humanity, is characterized by the highest levels of genetic diversity and population structure among humans. Non-African populations largely represent a subset of the genetic variation found in Africa. African genomes contain mixtures of multiple ancestries, each with unique evolutionary histories.

In a publication titled “Evolutionary Genetics and Admixture in African Populations,” researchers from the Georgia Institute of Technology and Mediclinic Precise Southern Africa reviewed the various demographic events that have shaped African genomes over time.

According to Joseph Lachance, one of the authors of the review, “What is striking is the immense complexity of human demographic history, particularly in Africa. Our genomes bear the imprints of numerous instances of population divergence followed by subsequent contact.”

For instance, ancient introgression from archaic hominin populations that no longer exist has contributed around 4-6% of the ancestry in present-day Khoe-San, Mbuti, and western African populations. More recent demographic events occurring within the past 10,000 years have also led to admixture among modern humans, including gene flow between different click-speaking Khoe-San populations, the spread of pastoralism from eastern to southern Africa, and the migrations of Bantu speakers across the continent.

It is important to note that biomedical studies often fail to capture this genetic diversity, which has implications for the health and disease outcomes of individuals with African ancestry. A better understanding of the genetic architecture can aid in predicting disease risks within populations and inform clinical decision-making for individual patients. Recognizing the significance of this information, the authors of the study call for more ethically conducted research on genetic variation in Africa to ensure equitable biomedical studies.

Joseph Lachance emphasizes the urgent need for more African genetic data, stating, “A critical point right now is the relative lack of African genetic data. Most genomic studies have focused on Eurasian populations, and this limitation can worsen existing health disparities.”

To gain a better understanding of African genomes, the study of ancient DNA is becoming increasingly prevalent. Researchers anticipate that future studies will delve into the fine-scale population structure within Africa. However, logistical and financial obstacles still hinder progress. Funding mechanisms that support research capacity in Africa are essential.

Another recent article in Genome Biology and Evolution, titled “The impact of modern admixture on archaic human ancestry in human populations,” explores admixture in the Americas. The continent was colonized more recently, with the initial migration of Indigenous Americans from Siberia. Subsequent migrations, such as those driven by European colonization and the Transatlantic slave trade, led to admixed populations with genetic contributions from various continents.

The study, conducted by researchers from Brown University, the Universidad Nacional Autónoma de México, and the University of California-Merced, examines how gene flow between modern humans redistributed archaic ancestry in admixed genomes. The analysis utilized data from the 1000 Genomes Project, focusing on several admixed populations, including Colombians from Medellin, individuals of Mexican ancestry from Los Angeles, Peruvians from Lima, and Puerto Ricans from Puerto Rico. These genomes were compared to the high-coverage genomes of Neanderthals and Denisovans, ancient hominins that diverged from modern humans approximately 500,000 years ago and interbred with humans in Eurasia before becoming extinct around 40,000 years ago.

Kelsey Witt, one of the study’s authors from Brown University, highlights the relatively understudied nature of these admixed populations compared to more homogeneous populations. Witt explains, “It is common in studies like this for admixed populations to be excluded because the multiple ancestry sources can make those questions harder to answer. For this work, we wanted to focus on admixed populations to determine what we could learn from them and whether admixed populations could provide information about all of the ancestry sources that contributed to them.”

The study’s findings reveal that the extent of introgression from Neanderthals and Denisovans correlates with the amount of Indigenous American or European ancestry within each population. While Neanderthal variants are approximately evenly distributed between European and Indigenous American tracts in these admixed genomes, Denisovan variants are predominantly found in Indigenous American tracts. This pattern reflects the shared ancestry between Indigenous Americans and Asian populations, which also exhibit higher levels of Denisovan introgression.

The research findings also identified several genes as potential candidates for adaptive introgression by searching for archaic alleles that are highly prevalent in admixed American populations but have low frequencies in East Asian populations. These genes encompass various pathways, including immunity, metabolism, and brain development. These discoveries have potential implications for the health of individuals within these admixed populations.

Kelsey Witt points out the existence of genetic mismatches, where certain variants were once adaptive in the past but currently have adverse effects on health due to changes in the environment. Moreover, in admixed populations, the interaction of genetic variants unique to different ancestral sources can lead to unexpected, and sometimes negative, outcomes within individuals. The study suggests that certain archaic variants are specific to particular ancestral sources, highlighting the complexity of their effects.

Similar to Joseph Lachance, Witt acknowledges the need for further research to untangle the impacts of admixture on modern humans. Witt highlights the relative simplicity of studying admixed populations in the Americas due to the knowledge of the timing and number of gene flow events. However, she also expresses the desire to apply this research to other admixed populations, where the timing and contributing populations may be less well-known or more closely related. Exploring such cases could contribute to a better understanding of recent admixture events.

These studies underscore the significant role of admixture in shaping human evolution, both in Africa and the Americas. Admixture not only reshuffles genetic variation within and between populations but also introduces new sources of variation with potential adaptability. By comparing the genomes of admixed populations with those of their ancestral groups and archaic humans, these studies shed light on how the mixing and matching of alleles have influenced the evolution of our species.

Source: Society for Molecular Biology and Evolution

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