Skip to main content

The Adaptations That Have Made Us Human: The Genome

  • Chapter
  • First Online:
Illuminating Human Evolution: 150 Years after Darwin

Part of the book series: Evolutionary Studies ((EVOLUS))

  • 469 Accesses

Abstract

Identifying what makes us humans and understanding the genetic basis of our uniqueness are issues of interest and debate in biology. By analyzing genomic data we can detect and use the footprints that adaptive (positive) natural selection leaves in our genome to identify human adaptations at different timescales, as well as the resulting phenotypical traits that in current populations define us as humans. Although genomics has allowed us to recognize some of these adaptations from the pattern of variation expected under the classical or hard selective sweep model, the field starts to address novel approaches. These new strategies include not only methods to identify polygenic adaptations but also multidisciplinary procedures to understand the relationship between the genomic footprints of selection, the underlying functional genetic variants, the adaptive phenotype they determine, and the selective pressure that has driven each adaptation.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Akey JM (2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 19:711–722

    Article  CAS  Google Scholar 

  • Amorim G, Nunes CE, Meyer K et al (2017) Genetic signature of natural selection in first Americans. Proc Natl Acad Sci U S A 114:2195–2199

    Article  CAS  Google Scholar 

  • Borda V, Alvim I, Mendes M et al (2020) The genetic structure and adaptation of Andean highlanders and Amazonians are influenced by the interplay between geography and culture. Proc Natl Acad Sci U S A 117:32557–32565

    Article  CAS  Google Scholar 

  • Dannemann M, Andrés AM, Kelso J (2016) Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. Am J Hum Genet 98:22–33

    Article  CAS  Google Scholar 

  • Darwin C, Wallace A (1858) On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. J Proc Linn Soc London Zool 3:45–62

    Article  Google Scholar 

  • Daub JT, Hofer T, Cutivet E et al (2013) Evidence for polygenic adaptation to pathogens in the human genome. Mol Biol Evol 30:1544–1558

    Article  CAS  Google Scholar 

  • Fay JC, Wu C (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405–1413

    Article  CAS  Google Scholar 

  • Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R (2014) On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol 31:1275–1291

    Article  CAS  Google Scholar 

  • Field Y, Boyle EA, Telis N et al (2016) Detection of human adaptation during the past 2000 years. Science 354:760–764

    Article  CAS  Google Scholar 

  • Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925

    Article  CAS  Google Scholar 

  • Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709

    Article  CAS  Google Scholar 

  • Fumagalli M, Moltke I, Grarup N et al (2015) Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349:1343–1347

    Article  CAS  Google Scholar 

  • Garud NR, Rosenberg NA (2015) Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps. Theor Popul Biol 102:94–101

    Article  Google Scholar 

  • Grossman SR, Shlyakhter I, Shylakhter I et al (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883–886

    Article  CAS  Google Scholar 

  • Hancock AM, Witonsky DB, Alkorta-Aranburu G et al (2011) Adaptations to climate-mediated selective pressures in humans. PLoS Genet 7:e1001375

    Article  CAS  Google Scholar 

  • Huerta-Sánchez E, DeGiorgio M, Pagani L et al (2013) Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations. Mol Biol Evol 30:1877–1888

    Article  Google Scholar 

  • Huerta-Sánchez E, Jin X, Asan et al (2014) Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512:194–197

    Article  Google Scholar 

  • Jarvis JP, Scheinfeldt LB, Soi S et al (2012) Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies. PLoS Genet 8:e1002641

    Article  CAS  Google Scholar 

  • Kronenberg ZN, Fiddes IT, Gordon D et al (2018) High-resolution comparative analysis of great ape genomes. Science 360:eaar6343

    Article  Google Scholar 

  • Marques-Bonet T, Kidd JM, Ventura M et al (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457:877–881

    Article  CAS  Google Scholar 

  • Mendizabal I, Marigorta UM, Lao O, Comas D (2012) Adaptive evolution of loci covarying with the human African pygmy phenotype. Hum Genet 131:1305–1317

    Article  Google Scholar 

  • Mondal M, Casals F, Xu T et al (2016) Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet 48:1066–1070

    Article  CAS  Google Scholar 

  • Pritchard JK, Pickrell JK, Coop G (2010) The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Curr Biol 20:R208–R215

    Article  CAS  Google Scholar 

  • Pybus M, Luisi P, Dall’Olio GM et al (2015) Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. Bioinformatics 31:3946–3952

    CAS  PubMed  Google Scholar 

  • Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E (2015) Evidence for archaic adaptive introgression in humans. Nat Rev Genet 16:359–371

    Article  CAS  Google Scholar 

  • Rees JS, Castellano S, Andrés AM (2020) The genomics of human local adaptation. Trends Genet 36:415–428

    Article  CAS  Google Scholar 

  • Refoyo-Martínez A, Da Fonseca RR, Halldórsdóttir K et al (2019) Identifying loci under positive selection in complex population histories. Genome Res 29:1506–1520

    Article  Google Scholar 

  • Sabeti PC, Schaffner SF, Fry B et al (2006) Positive natural selection in the human lineage. Science 312:1614–1620

    Article  CAS  Google Scholar 

  • Sabeti PC, Varilly P, Fry B et al (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918

    Article  CAS  Google Scholar 

  • Speidel L, Forest M, Shi S, Myers SR (2019) A method for genome-wide genealogy estimation for thousands of samples. Nat Genet 51:1321–1329

    Article  CAS  Google Scholar 

  • Szpak M, Mezzavilla M, Ayub Q et al (2018) FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 19:5

    Article  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    Article  CAS  Google Scholar 

  • Vitti JJ, Grossman SR, Sabeti PC (2013) Detecting natural selection in genomic data. Annu Rev Genet 47:97–120

    Article  CAS  Google Scholar 

  • Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72

    Article  Google Scholar 

  • Walsh EC, Sabete P, Hutcheson HB et al (2006) Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet 119:92–102

    Article  CAS  Google Scholar 

  • Wang L, Sinnott-Armstrong N, Wagschal A et al (2020) A MicroRNA linking human positive selection and metabolic disorders. Cell 183:684–701

    Article  CAS  Google Scholar 

  • Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908–917

    Article  CAS  Google Scholar 

  • Yi X, Liang Y, Huerta-Sanchez E et al (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329:75–78

    Article  CAS  Google Scholar 

  • Zhang J, Nielsen R, Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–2479

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This review has been possible thanks to the support of the “Dirección General de Investigación, Generalidad de Cataluña” (2017SGR702), the “Ministerio de Ciencia e Innovación,” and the “Agencia Estatal de Investigación (AEI)” through the project PID2019-110933GB-E00/AEI/10.13039/501100011033 and the “Unidad de Excelencia María de Maeztu” funded by the MCIN and the AEI (Doi: 10.13039/501100011033; Ref: CEX2018-000792-M).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Elena Bosch .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bosch, E. (2022). The Adaptations That Have Made Us Human: The Genome. In: Bertranpetit, J., Peretó, J. (eds) Illuminating Human Evolution: 150 Years after Darwin. Evolutionary Studies. Springer, Singapore. https://doi.org/10.1007/978-981-19-3246-5_11

Download citation

Publish with us

Policies and ethics