4 Types of Natural Selection and Tests of Selection
85
Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams
MD, Schmidt S, Sninsky JJ, Sunyaev SR et al (2008) Assessing the evolutionary impact of
amino acid mutations in the human genome. PLoS Genet 4(5):e1000083
Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum
DM, White TJ, Sninsky JJ, Hernandez RD et al (2005) Natural selection on protein-coding
genes in the human genome. Nature 437(7062):1153–1157
Charlesworth D (2006) Balancing selection and its effects on sequences in nearby genome regions.
PLoS Genet 2(4):e64
Charlesworth B, Charlesworth D (2010) Elements of evolutionary genetics. Roberts and Company
Publishers, Greenwood Village
Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral
molecular variation. Genetics 134(4):1289–1303
Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment bias in
studies of human genome-wide polymorphism. Genome Res 15(11):1496–1502
DeGiorgio M, Lohmueller KE, Nielsen R (2014) A model-based approach for identifying
signatures of ancient balancing selection in genetic data. PLoS Genet 10(8):e1004561
Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB (2012) The structure of allelic diversity in the
presence of purifying selection. Theor Popul Biol 81(2):144–157
Enard D, Messer PW, Petrov DA (2014) Genome-wide signals of positive selection in human
evolution. Genome Res 24(6):885–895
Eyre-Walker A (2002) Changing effective population size and the McDonald-Kreitman test.
Genetics 162(4):2017–2024
Eyre-Walker A, Keightley PD (2009) Estimating the rate of adaptive molecular evolution in
the presence of slightly deleterious mutations and population size change. Mol Biol Evol
26(9):2097–2108
Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155(3):1405–1413
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(5):1275–1291
Hamilton M (2009) Population genetics. Wiley-Blackwell, Hoboken
Hartl DL, Clark AG (2007) Principles of population genetics. Sinauer, Sunderland
Hermisson J, Pennings PS (2005) Soft sweeps: molecular population genetics of adaptation from
standing genetic variation. Genetics 169(4):2335–2352
Hernandez RD, Williamson SH, Bustamante CD (2007) Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol 24(8):1792–1800
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M
(2011) Classic selective sweeps were rare in recent human evolution. Science 331(6019):920–
924
Huber CD, Nordborg M, Hermisson J, Hellmann I (2014) Keeping it local: evidence for positive
selection in Swedish Arabidopsis thaliana. Mol Biol Evol 31(11):3026–3039
Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD (2005) Distinguishing between
selective sweeps and demography using DNA polymorphism data. Genetics 170(3):1401–1410
Kaplan NL, Hudson RR, Langley CH (1989) The “hitchhiking effect” revisited. Genetics
123(4):887–899
Kim Y, Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining
chromosome. Genetics 160(2):765–777
Leffler EM, Gao Z, Pfeifer S, Segurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella
G et al (2013) Multiple instances of ancient balancing selection shared between humans and
chimpanzees. Science 339(6127):1578–1582
Li H, Stephan W (2005) Maximum-likelihood methods for detecting recent positive selection and
localizing the selected site in the genome. Genetics 171(1):377–384
Li Y, Willer C, Sanna S, Abecasis G (2009) Genotype imputation. Annu Rev Genomics Hum Genet
10:387–406
85
Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams
MD, Schmidt S, Sninsky JJ, Sunyaev SR et al (2008) Assessing the evolutionary impact of
amino acid mutations in the human genome. PLoS Genet 4(5):e1000083
Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum
DM, White TJ, Sninsky JJ, Hernandez RD et al (2005) Natural selection on protein-coding
genes in the human genome. Nature 437(7062):1153–1157
Charlesworth D (2006) Balancing selection and its effects on sequences in nearby genome regions.
PLoS Genet 2(4):e64
Charlesworth B, Charlesworth D (2010) Elements of evolutionary genetics. Roberts and Company
Publishers, Greenwood Village
Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral
molecular variation. Genetics 134(4):1289–1303
Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment bias in
studies of human genome-wide polymorphism. Genome Res 15(11):1496–1502
DeGiorgio M, Lohmueller KE, Nielsen R (2014) A model-based approach for identifying
signatures of ancient balancing selection in genetic data. PLoS Genet 10(8):e1004561
Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB (2012) The structure of allelic diversity in the
presence of purifying selection. Theor Popul Biol 81(2):144–157
Enard D, Messer PW, Petrov DA (2014) Genome-wide signals of positive selection in human
evolution. Genome Res 24(6):885–895
Eyre-Walker A (2002) Changing effective population size and the McDonald-Kreitman test.
Genetics 162(4):2017–2024
Eyre-Walker A, Keightley PD (2009) Estimating the rate of adaptive molecular evolution in
the presence of slightly deleterious mutations and population size change. Mol Biol Evol
26(9):2097–2108
Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155(3):1405–1413
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(5):1275–1291
Hamilton M (2009) Population genetics. Wiley-Blackwell, Hoboken
Hartl DL, Clark AG (2007) Principles of population genetics. Sinauer, Sunderland
Hermisson J, Pennings PS (2005) Soft sweeps: molecular population genetics of adaptation from
standing genetic variation. Genetics 169(4):2335–2352
Hernandez RD, Williamson SH, Bustamante CD (2007) Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol Biol Evol 24(8):1792–1800
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M
(2011) Classic selective sweeps were rare in recent human evolution. Science 331(6019):920–
924
Huber CD, Nordborg M, Hermisson J, Hellmann I (2014) Keeping it local: evidence for positive
selection in Swedish Arabidopsis thaliana. Mol Biol Evol 31(11):3026–3039
Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD (2005) Distinguishing between
selective sweeps and demography using DNA polymorphism data. Genetics 170(3):1401–1410
Kaplan NL, Hudson RR, Langley CH (1989) The “hitchhiking effect” revisited. Genetics
123(4):887–899
Kim Y, Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining
chromosome. Genetics 160(2):765–777
Leffler EM, Gao Z, Pfeifer S, Segurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella
G et al (2013) Multiple instances of ancient balancing selection shared between humans and
chimpanzees. Science 339(6127):1578–1582
Li H, Stephan W (2005) Maximum-likelihood methods for detecting recent positive selection and
localizing the selected site in the genome. Genetics 171(1):377–384
Li Y, Willer C, Sanna S, Abecasis G (2009) Genotype imputation. Annu Rev Genomics Hum Genet
10:387–406