Immune Gene Diversity in Archaic and Present-day Humans

Pathogen communities can vary substantially between geographical regions due to different environmental conditions. However, little is known about how host immune systems respond to environmental variation across macro-ecological and evolutionary scales. Here, we select 37 species of songbird that inhabit diverse environments, including African and Palaearctic residents and Afro-Palaearctic migrants, to address how climate and habitat have influenced the evolution of key immune genes, the major histocompatibility complex class I (MHC-I). Resident species living in wetter regions, especially in Africa, had higher MHC-I diversity than species living in drier regions, irrespective of the habitats they occupy. By contrast, no relationship was found between MHC-I diversity and precipitation in migrants. Our results suggest that the immune system of birds has evolved greater pathogen recognition in wetter tropical regions. Furthermore, evolving transcontinental migration appears to have enabled species to escape wet, pathogen-rich areas at key periods of the year, relaxing selection for diversity in immune genes and potentially reducing immune system costs.

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Immune gene diversity in archaic and present-day humans

10.1101/348581 ◽

2018 ◽

Author(s):

David Reher ◽

Felix M. Key ◽

Aida M. Andrés ◽

Janet Kelso

Keyword(s):

Gene Diversity ◽

Innate Immune ◽

Immune Gene ◽

Similar Reduction ◽

Protein Coding ◽

Immune Genes ◽

Genome Wide ◽

Show Evidence ◽

Functional Consequences ◽

Immune Related Genes

Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, and particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups and at different time points on the Neandertal lineage with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC).We find that the two Neandertals and the Denisovan have similar gene diversity, both significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared to the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.

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Low innate immune-gene diversity in the critically endangered orange-bellied parrot (Neophema chrysogaster)

Emu - Austral Ornithology ◽

10.1080/01584197.2019.1686994 ◽

2019 ◽

Vol 120 (1) ◽

pp. 56-64 ◽

Cited By ~ 2

Author(s):

Caitlin E. Morrison ◽

Carolyn J. Hogg ◽

Rosemary Gales ◽

Rebecca N. Johnson ◽

Catherine E. Grueber

Keyword(s):

Gene Diversity ◽

Innate Immune ◽

Critically Endangered ◽

Immune Gene ◽

Innate Immune Gene

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Evidence for reduced immune gene diversity and activity during the evolution of termites

10.1101/2020.07.09.192013 ◽

2020 ◽

Author(s):

Shulin He ◽

Thorben Sieksmeyer ◽

Yanli Che ◽

M. Alejandra Esparza Mora ◽

Petr Stiblik ◽

...

Keyword(s):

Gene Family ◽

Gene Diversity ◽

Immune Gene ◽

Gene Repertoire ◽

Individual Level ◽

Social Defense ◽

Major Transition ◽

Species Comparisons ◽

Organismal Complexity ◽

Multicellular Organisms

AbstractThe evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well studied immunity at the cell and individual level, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We identified five significant immune gene family contractions and one immune gene family expansion along the spine of a time-calibrated phylogeny, correlating with key transitions in termite sociality. In cross-species comparisons of immune gene expression, we find that termites appear to have evolved a caste-specific social defense system at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity entailed a fundamental reshaping of the immune system optimized for group over individual defense.

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Evidence for reduced immune gene diversity and activity during the evolution of termites

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.3168 ◽

2021 ◽

Vol 288 (1945) ◽

pp. 20203168

Author(s):

Shulin He ◽

Thorben Sieksmeyer ◽

Yanli Che ◽

M. Alejandra Esparza Mora ◽

Petr Stiblik ◽

...

Keyword(s):

Gene Diversity ◽

Immune Gene ◽

Gene Repertoire ◽

Evolutionary Transition ◽

Immune Systems ◽

Immune Gene Expression ◽

Major Transition ◽

Species Comparisons ◽

Organismal Complexity ◽

Multicellular Organisms

The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We find that key transitions in termite sociality are correlated with immune gene family contractions. In cross-species comparisons of immune gene expression, we find evidence for a caste-specific social defence system in termites, which appears to operate at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity may have entailed a fundamental reshaping of the immune system optimized for group over individual defence.

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Allelic diversity of DQA2 exon 2 gene in Egyptian goat populations

Indian Journal of Animal Research ◽

10.18805/ijar.v0iof.7660 ◽

2017 ◽

Author(s):

Sahar S. Ahmed ◽

Salah M. Abdel-Rahman ◽

Paul J. Grobler ◽

Antoinette Kotzé

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Allelic Diversity ◽

Single Strand Conformation Polymorphism ◽

Immune Gene ◽

Exon 2 ◽

Goat Population ◽

Allele Composition ◽

The Difference ◽

Conformation Polymorphism

The study aimed to assess the genetic diversity of 2-decyl-4-quinazolinyl amine exon2 (DQA2 exon2) gene among the Egyptian goat populations from different agro-climatic areas. Data of diseases distribution as well as blood samples were collected. The data collected for diseases distribution showed differences in the types of diseases between the agro-climatic areas. The Single Strand Conformation Polymorphism technique (SSCP) was used to assess the genetic diversity of DQA2 exon2 gene among the goat populations. The results showed that the DQA2 exon2 gene locus displayed 21 alleles with different frequencies in each of goat population. The gene diversity values among the populations ranged from 0.950± 0.022 to 0.887± 0.033. The difference between the most southern population (Aswan) and the remaining populations translate to significant (P less than 0.05) differentiation for only one population pair (Aswan – Baladi, with FST= 0.055; P= 0.001). Scrutiny of allele composition in these two goat populations showed unique alleles in each population (six in Aswan and four in Baladi). The results of the study suggested that the allelic numbers and allelic composition for the DQA2 exon2 gene among the Egyptian goat populations showed diversity in the immune gene due to the different pathogens exposure.

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Comment on: Assessment of the dunnocks’ introduction to New Zealand using innate immune-gene diversity, by Lara et al

Evolutionary Ecology ◽

10.1007/s10682-021-10122-z ◽

2021 ◽

Author(s):

Pipek Pavel

Keyword(s):

New Zealand ◽

Gene Diversity ◽

Innate Immune ◽

Immune Gene ◽

Innate Immune Gene

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Immune gene diversity in grey wolves (Canis lupus)

Journal of Veterinary Behavior ◽

10.1016/j.jveb.2013.04.022 ◽

2013 ◽

Vol 8 (4) ◽

pp. e33

Author(s):

A.K. Niskanen ◽

L. Kennedy ◽

I. Kojola ◽

H. Lohi ◽

M. Ruokonen ◽

...

Keyword(s):

Canis Lupus ◽

Gene Diversity ◽

Immune Gene

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High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice

10.1101/2020.02.03.932590 ◽

2020 ◽

Cited By ~ 1

Author(s):

Martin Stervander ◽

Elisa G. Dierickx ◽

Jack Thorley ◽

M. de L. Brooke ◽

Helena Westerdahl

Keyword(s):

Mate Choice ◽

Gene Diversity ◽

Gene Copy Number ◽

Small Population ◽

Critically Endangered ◽

Gene Copy ◽

Immune Gene ◽

Class I Mhc ◽

Mhc I ◽

Island Endemic

AbstractSmall population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7 km2 islet of Raso (Cape Verde) since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by co-segregation of multiple haplotypes comprising 2–8 linked MHC-I loci. Within-locus homozygosity is high, contributing to comparably low population-wide diversity. Conversely, each individual had comparably many alleles, 6–16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species’ adaptive potential.

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