Human evolution sped up by admixture of isolated populations

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Human evolution is often thought of as slow, taking many generations for new traits to emerge. However, evidence suggests that admixture, the exchange of genes between populations previously isolated from one another, can cause rapid adaptations. Dr King Jordan at the Georgia Institute of Technology has been investigating admixture in Latin American populations. His analysis revealed admixture-enabled selection of genes involved in the adaptive immune system strongly associated with African ancestry, whilst genes in the innate immune system showed evidence of Native American ancestry. Admixture-enabled selection therefore facilitated the emergence of hybrid immune systems that allowed rapid adaptation to new environments.

Throughout their evolution, the migration of human populations from their ancestral homelands of Africa to new, unexplored areas has led to humans inhabiting all corners of the Earth. A key consequence of this migratory behaviour is that populations can often remain isolated from one another for thousands, or even tens of thousands of years. During these periods of isolation, natural selection and genetic drift lead to distinct genetic differences between populations as each one adapts to the specific conditions of their environment. Recent studies of ancient DNA have revealed that human evolution has been defined by these periods of isolation followed by the convergence of one or more populations, which results in a process called admixture.

Admixture refers to the exchange of genes between populations that had previously been isolated from one another. The resulting combinations of two previously distinct sets of genes lead to the creation of an evolutionarily novel genome, that being the complete set of genes in an organism. These novel genomes provide a blueprint for adaptations to new environments, calling on traits inherited from both, or all, of the original populations.

fizkes/Shutterstock.com

The Columbian Exchange, the mass transfer of human populations, animals, plants, and ideas between the Americas, Europe and West Africa in the 15th and 16th centuries, is one of the biggest and most rapid admixture events in the history of human evolution. Modern Latin American populations are therefore descended from a mixture of African, European and Native American ancestry; three populations that came together during the Columbian Exchange having been separated for tens of thousands of years.

“Novel genomes provide a blueprint for adaptations to new environments, calling on traits inherited from the original, ancestrally diverse populations.”

Adapting to the new

The introduction of new, ancestry-specific haplotypes, a collection of specific genes on a chromosome that is likely to be inherited together, into a shared population enables adaptive evolutions through admixture-enabled selection.

Dr King Jordan at the Georgia Institute of Technology has been investigating the admixture of Latin American populations, theorising that admixture-enabled selection is a mechanism that allows for rapid adaptive evolution in human populations. Dr Jordan specialises in population genomics, which is the large-scale comparison of the DNA sequences across whole populations. Using biotechnology to analyse the genome allows characterisation of things like genetic variation and furthers our understanding of how certain genes relate to diseases or contribute to our overall health and wellbeing.

Research in the Jordan Lab studies the relationship between human ancestry and genomic determinants of health and fitness with an emphasis on admixed populations from Latin America. Sarfina Portrait/Shutterstock.com

To test his hypothesis, Dr Jordan and his team led by PhD student Emily Norris analysed the genomes of admixed populations in four Latin American countries: Colombia, Peru, Mexico and Puerto Rico.

Previous studies into admixture-enabled selection have returned conflicting results. Independent studies investigating populations in Mexico, Puerto Rico and Colombia found evidence of admixture-enabled selection on a collection of genes called the major histocompatibility complex (MHC), which plays a key role in the adaptive immune system. However, other studies on a different cohort of African-Americans found no such evidence and concluded that previous examples of admixture-enabled selection may have been due to chance.

Admixture is the exchange of genes between populations previously isolated from one another.

Dr Jordan’s study attempted to investigate these conflicting results by performing integrated analyses that used information from both single gene loci, that being the place on a chromosome that a gene is found, and multiple loci that encode for traits that are determined by more than one gene, known as polygenic traits. Overall, he found evidence of admixture-enabled selection at the MHC locus in several Latin American populations, supporting the findings of the earlier studies. In addition, the polygenic screen revealed new evidence for adaptive evolution on several traits related to immunity, blood and inflammation.

A varied ancestry

Overall, the genetic screen revealed that all four of these populations showed predominantly European ancestry, followed by Native American and African components. However, each population showed a different proportion of each ancestry. Puerto Rican populations have the highest percentage of European ancestry, whilst Peruvian populations have the highest percentage of Native American ancestry and Colombian populations showed the highest level of three-way admixture. Furthermore, individual genomes showed a wide variety in patterns of ancestry, but this is to be expected in admixed genomes as the process is random.

Christopher Columbus arriving in the New World.

To identify genes that might have been amplified in these populations due to admixture Dr Jordan performed a gene enrichment analysis, a technique used to identify genes that appear over-represented in a large set. The strongest signals of single gene ancestry enrichment were seen for African ancestry at the MHC, which is found on chromosome 6. Three of the four populations showed constant African ancestry enrichment at the MHC. This was particularly evident in Mexican and Colombian populations.

Further analysis concluded that this enrichment from African ancestry was highly unlikely to have been caused by chance alone, and in fact, provided evidence that several of the genes that make up the MHC were positively selected for over the last few hundred years. Several of these genes were human leukocyte antigen (HLA) encoding genes, including HLA-A, HLA-DRB5 and HLA-DRB1. These genes make up part of the MHC and are involved in an antigen-presenting pathway as part of the adaptive immune system. On the other hand, polygenic analysis found that several interconnected pathways of the innate immune system showed evidence of largely Native American ancestry.

Dr Jordan’s results suggest that admixture can enable much more rapid adaptive evolution.

Increased immunity

The immune system is widely known to be a target of selection. It acts as an interface between humans and their environment and therefore a strong immune system is highly advantageous. The innate immune system provides the rapid initial immune response to a variety of viral and bacterial pathogens, whilst the adaptive immune system provides a secondary defence that develops slowly. It thought that the vast reduction in Native American populations following the Columbian Exchange is partly due to the introduction of novel pathogens that their immune systems had no natural defence against.

“Admixture-enabled selection facilitated the emergence of new, hybrid immune systems that provided defence against both native and non-native pathogens.”

The results of this study suggest that the admixed populations in Latin America were able to adapt more quickly to their environment due to inherited traits from two of its ancestral populations. The Native American innate immune system provided a defence against pathogens that were native to the ‘New World’, whilst the newly introduced African adaptive immune system provided defence against pathogens that were introduced to the area during the Columbian Exchange. Admixture-enabled selection, therefore, facilitated the emergence of new, hybrid immune systems that provided defence against both native and non-native pathogens.

Norris, E.T., Rishishwar, L., Chande, A.T. et al. Genome Biol 21,
29 (2020). https://doi.org/10.1186/s13059-020-1946-2

Speeding up evolution

The process of human evolution is usually thought of as a very slow process, elongated by both the low rate of mutation and long periods between each new generation. Any new mutations that are introduced into a population are by nature found at a very low frequency and positive selection for new advantageous traits is gradual. However, Dr Jordan’s results, which support previous findings of admixture-enabled selection at the MHC in Latin American populations, suggest that admixture can enable much more rapid adaptive evolution, in this case over the last 500 years. The time since then accounts for approximately 20 generations or about 1% of the time since modern humans evolved, a much shorter period than it is thought evolution takes place over. Therefore, he has proposed that admixture should be considered a fundamental mechanism for the acceleration of human evolution.

Each set of genes inherited from the three ancestral source populations evolved separately for thousands of years, and likely provided a selective advantage in their original environments. These genes then provided the raw material for rapid evolution following the sudden mixture of each population, allowing the resulting descendants to adapt quickly to their new environment and resulting in the Latin American populations seen today.


Is admixture likely to have had a similar evolutionary effect in other populations affected by colonisation e.g., Australian populations?

Yes, admixture is absolutely expected to have similar evolutionary effects on other modern, cosmopolitan populations. Indeed, the process of admixture that we study in Latin America has played out multiple times in different regions around the world. Trade along the Indian Ocean rim, for example, led to admixture among diverse African, Middle Eastern, and Asian populations. Admixture will become even more common in the modern era of global travel and migration. For this reason, we believe that admixture-enabled selection has been, and will continue to be, a fundamental mechanism of human adaptive evolution.

 

References

  • Norris, E.T., et al. (2018). Genetic ancestry, admixture and health determinants in Latin America. BMC Genomics. 19(Suppl 8):861, pp. 75-87. https://doi.org/10.1186/s12864-018-5195-7
  • Norris, E.T., et al. (2020). Admixture-enabled selection for rapid adaptive evolution in the Americas. Genome Biology [online]. 21(29). https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1946-2
  • Norris, E.T., Rishishwar, L. & Jordan, I. K. (2021). ‘Rapid adaptive human evolution facilitated by admixture in the Americas’, in: Muñoz, M.L., Crawford, M.H. (Eds.), Human Migration: Biocultural Perspectives. Oxford University Press.
DOI
10.26904/RF-135-1229606489

Research Objectives

Research in the Jordan Lab studies the relationship between human ancestry and genomic determinants of health and fitness with an emphasis on admixed populations from Latin America.

Funding

Applied Bioinformatics Laboratory (ABiL); https://www.abil.ihrc.com/
Georgia Institute of Technology Bioinformatics Graduate Program

Collaborators

Emily T. Norris, Lavanya Rishishwar, Augusto Valderrama-Aguirre

Bio

Dr I. King Jordan is Professor in the School of Biological Sciences and Director of the Bioinformatics Graduate Program at the Georgia Institute of Technology. Members of Dr Jordan’s laboratory conduct bioinformatics research with an emphasis on human population genomics and genetic ancestry inference in support of health equity.

Dr I. King Jordan

Contact
950 Atlantic Drive
Atlanta, GA
30332 USA

E: king.jordan@biology.gatech.edu
T: +1 (404) 385-2224
W: http://jordan.biology.gatech.edu

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