Neutral Genetic Processes Influence MHC Evolution in Threatened Gopher Tortoises (Gopherus polyphemus)

Elbers, Jean P.; Clostio, Rachel W.; Taylor, Sabrina S.

doi:10.1093/jhered/esx034

Cited by 7 publications

(9 citation statements)

References 55 publications

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“…We recovered high MHC class I α polymorphism in both species based on sequence diversity and number of recovered alleles. Low immunogenetic diversity following population bottlenecks has been documented in amphibians [89], birds [90] and non-avian reptiles [53]; however, despite historical reductions in Ch. mydas population sizes [31] and threats to Ca.…”

Section: Discussionmentioning

confidence: 99%

“…However, this polymorphism is potentially overestimated, as the alleles we recovered come from multiple unidentified loci. By comparison, studies of Testudines that were able to assign MHC class I alleles to loci found that across 18 populations of Gopher tortoise ( Gopherus polyphemus ) at MHC class I exon 3, there were 13% segregating sites and nucleotide diversity was 0.03 [53]; furthermore, in a population of Diamondback terrapins ( Malaclemys terrapin ), the MHC class I locus was fixed for a single allele [50]. By contrast, our conservative criteria for retaining alleles means we are probably underestimating total alleles, and additional sea turtle MHC studies will almost certainly reveal further MHC class I α diversity.…”

Section: Discussionmentioning

confidence: 99%

“…mydas lends insight into how MHC has evolved in sea turtles and more broadly facilitates our understanding of reptilian acquired immune systems. While a relationship between pathogen susceptibility and MHC genetic variation has been documented in tortoises [53,54], associations between MHC and disease in sea turtles remain unexplored. By sampling immature Ch.…”

Section: Introductionmentioning

confidence: 99%

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Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles

2022

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Characterizing polymorphism at the major histocompatibility complex (MHC) genes is key to understanding the vertebrate immune response to disease. Despite being globally afflicted by the infectious tumour disease fibropapillomatosis (FP), immunogenetic variation in sea turtles is minimally explored. We sequenced the α 1 peptide-binding region of MHC class I genes (162 bp) from 268 juvenile green ( Chelonia mydas ) and 88 loggerhead ( Caretta caretta ) sea turtles in Florida, USA. We recovered extensive variation (116 alleles) and trans-species polymorphism. Supertyping analysis uncovered three functional MHC supertypes corresponding to the three well-supported clades in the phylogeny. We found significant evidence of positive selection at seven amino acid sites in the class I exon. Random forest modelling and risk ratio analysis of Ch. mydas alleles uncovered one allele weakly associated with smooth FP tumour texture, which may be associated with disease outcome. Our study represents the first characterization of MHC class I diversity in Ch. mydas and the largest sample of sea turtles used to date in any study of adaptive genetic variation, revealing tremendous genetic variation and high adaptive potential to viral pathogen threats. The novel associations we identified between MHC diversity and FP outcomes in sea turtles further highlight the importance of evaluating genetic predictors of disease, including MHC and other functional markers.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles

2022

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“…However, it is important to acknowledge how particular pathogens affect immune genetic diversity and, vice versa, how genetic variation influences adaptation to emerging zoonosis, habitat fragmentation, and climate change [40]. MHC genes play an important role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation [41]. While innate immunity is an efficient first protection against many pathogens but rather less specific, adaptive (or acquired) immunity is a highly specific immune response, and its variability is subject to different selective pressures [30,31].…”

Section: Nucleotide Diversity In Important Immune Gene Groupsmentioning

confidence: 99%

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Lado¹,

Elbers²,

Rogers

et al. 2020

BMC Genomics

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Background: Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species' survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes. Results: In this work, we improved the genome assemblies of the three Old World camel speciesdomestic dromedary and Bactrian camel, and the two-humped wild camelvia different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex.

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“…However, it is important to acknowledge how particular pathogens affect immune genetic diversity and, vice versa, how genetic variation in uences adaptation to emerging zoonosis, habitat fragmentation, and climate change [32]. MHC genes play an important role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation [33]. While innate immunity is an e cient rst protection against many pathogens but rather less speci c, adaptive (or acquired) immunity is a highly speci c immune response, and its variability is subject to different selective pressures [22,23].…”

Section: Old World Camelids Genome Assemblies´ Improvementmentioning

confidence: 99%

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Lado¹,

Elbers²,

Rogers

et al. 2020

Preprint

Self Cite

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Background Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, genetic diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes. Results In this work, we improved the genome assemblies in the three Old World camel species – domestic dromedary and Bactrian camel, and the two-humped wild camel – via different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex. Conclusions The new camel genome assemblies were greatly improved in terms of contiguity and increased size with fewer scaffolds, which is of general value for the scientific community. This allowed us to perform in-depth studies on genetic diversity in immunity-related regions of the genome. Our results suggest that differences of diversity across classes of genes appear compatible with being caused by a combination of population history coupled with possible distinct exposures to pathogens and consequent different selective pressures.

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Neutral Genetic Processes Influence MHC Evolution in Threatened Gopher Tortoises (Gopherus polyphemus)

Cited by 7 publications

References 55 publications

Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles

Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

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