Adaptive Potential of Genomic Structural Variation in Human and Mammalian Evolution

Overview

Journal Brief Funct Genomics

Publisher Oxford University Press

Date 2015 May 25

PMID 26003631

Citations 12

Authors

David W Radke

Charles Lee

Affiliations

Soon will be listed here.

Abstract

Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.

Citing Articles

Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus.

Ferguson S, Jones A, Murray K, Andrew R, Schwessinger B, Bothwell H Gigascience. 2024; 13.

PMID: 38869149 PMC: 11170218. DOI: 10.1093/gigascience/giae029.

The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data.

Lesack K, Wasmuth J PeerJ. 2024; 12:e17101.

PMID: 38500526 PMC: 10946394. DOI: 10.7717/peerj.17101.

Recent advances and current challenges in population genomics of structural variation in animals and plants.

Pokrovac I, Pezer Z Front Genet. 2022; 13:1060898.

PMID: 36523759 PMC: 9745067. DOI: 10.3389/fgene.2022.1060898.

Saitou M, Masuda N, Gokcumen O Mol Biol Evol. 2021; 39(3).

PMID: 34718708 PMC: 8896759. DOI: 10.1093/molbev/msab313.

The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi.

Gorkovskiy A, Verstrepen K Genes (Basel). 2021; 12(5).

PMID: 34066718 PMC: 8150848. DOI: 10.3390/genes12050699.

References

Ren J, Mao H, Zhang Z, Xiao S, Ding N, Huang L . A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs. Heredity (Edinb). 2010; 106(5):862-8. PMC: 3186233. DOI: 10.1038/hdy.2010.129. View

Iskow R, Gokcumen O, Lee C . Exploring the role of copy number variants in human adaptation. Trends Genet. 2012; 28(6):245-57. PMC: 3533238. DOI: 10.1016/j.tig.2012.03.002. View

Henrichsen C, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, Schutz F . Segmental copy number variation shapes tissue transcriptomes. Nat Genet. 2009; 41(4):424-9. DOI: 10.1038/ng.345. View

Haase B, Rieder S, Tozaki T, Hasegawa T, Penedo M, Jude R . Five novel KIT mutations in horses with white coat colour phenotypes. Anim Genet. 2011; 42(3):337-9. DOI: 10.1111/j.1365-2052.2011.02173.x. View

Liu S, Yao L, Ding D, Zhu H . CCL3L1 copy number variation and susceptibility to HIV-1 infection: a meta-analysis. PLoS One. 2011; 5(12):e15778. PMC: 3012711. DOI: 10.1371/journal.pone.0015778. View

Petersen J, Mickelson J, Rendahl A, Valberg S, Andersson L, Axelsson J . Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet. 2013; 9(1):e1003211. PMC: 3547851. DOI: 10.1371/journal.pgen.1003211. View

Lu D, Willard D, Patel I, Kadwell S, Overton L, Kost T . Agouti protein is an antagonist of the melanocyte-stimulating-hormone receptor. Nature. 1994; 371(6500):799-802. DOI: 10.1038/371799a0. View

Poptsova M, Banerjee S, Gokcumen O, Rubin M, Demichelis F . Impact of constitutional copy number variants on biological pathway evolution. BMC Evol Biol. 2013; 13:19. PMC: 3563492. DOI: 10.1186/1471-2148-13-19. View

Handsaker R, Van Doren V, Berman J, Genovese G, Kashin S, Boettger L . Large multiallelic copy number variations in humans. Nat Genet. 2015; 47(3):296-303. PMC: 4405206. DOI: 10.1038/ng.3200. View

10.

Orozco L, Cokus S, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A . Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet. 2009; 18(21):4118-29. PMC: 2758141. DOI: 10.1093/hmg/ddp360. View

11.

Burns J, Shimizu C, Gonzalez E, Kulkarni H, Patel S, Shike H . Genetic variations in the receptor-ligand pair CCR5 and CCL3L1 are important determinants of susceptibility to Kawasaki disease. J Infect Dis. 2005; 192(2):344-9. PMC: 2894631. DOI: 10.1086/430953. View

12.

Joerg H, Fries H, Meijerink E, Stranzinger G . Red coat color in Holstein cattle is associated with a deletion in the MSHR gene. Mamm Genome. 1996; 7(4):317-8. DOI: 10.1007/s003359900090. View

13.

Berglund J, Nevalainen E, Molin A, Perloski M, Andre C, Zody M . Novel origins of copy number variation in the dog genome. Genome Biol. 2012; 13(8):R73. PMC: 4053742. DOI: 10.1186/gb-2012-13-8-r73. View

14.

Fontanesi L, Scotti E, Colombo M, Beretti F, Forestier L, DallOlio S . A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with the Japanese brindling coat colour in rabbits (Oryctolagus cuniculus). BMC Genet. 2010; 11:59. PMC: 3236303. DOI: 10.1186/1471-2156-11-59. View

15.

Dauber A, Yu Y, Turchin M, Chiang C, Meng Y, Demerath E . Genome-wide association of copy-number variation reveals an association between short stature and the presence of low-frequency genomic deletions. Am J Hum Genet. 2011; 89(6):751-9. PMC: 3234379. DOI: 10.1016/j.ajhg.2011.10.014. View

16.

Fontanesi L, Martelli P, Scotti E, Russo V, Rogel-Gaillard C, Casadio R . Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization. Genomics. 2012; 100(4):245-51. DOI: 10.1016/j.ygeno.2012.07.001. View

17.

Hou Y, Liu G, Bickhart D, Matukumalli L, Li C, Song J . Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Funct Integr Genomics. 2011; 12(1):81-92. DOI: 10.1007/s10142-011-0252-1. View

18.

Young J, Endicott R, Parghi S, Walker M, Kidd J, Trask B . Extensive copy-number variation of the human olfactory receptor gene family. Am J Hum Genet. 2008; 83(2):228-42. PMC: 2495065. DOI: 10.1016/j.ajhg.2008.07.005. View

19.

Perry G, Dominy N, Claw K, Lee A, Fiegler H, Redon R . Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007; 39(10):1256-60. PMC: 2377015. DOI: 10.1038/ng2123. View

20.

Schmutz S, Dreger D . Interaction of MC1R and PMEL alleles on solid coat colors in Highland cattle. Anim Genet. 2012; 44(1):9-13. DOI: 10.1111/j.1365-2052.2012.02361.x. View