8 Inferring Human Demographic History from Genetic Data
201
Keinan A, Mullikin JC, Patterson N, Reich D (2009) Accelerated genetic drift on chromosome X
during the human dispersal out of Africa. Nat Genet 41:66–70
Kim BY, Lohmueller KE (2015) Selection and reduced population size cannot explain higher
amounts of Neandertal ancestry in East Asian than in European human populations. Am J Hum
Genet 96:454–461
Klein RG (2000) The earlier Stone age of southern Africa. S Afr Archaeol Bull 55:107–122
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Paabo S (1997) Neandertal DNA
sequences and the origin of modern humans. Cell 90:19–30
Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo
TB, Rebbeck TR et al (2012) Evolutionary history and adaptation from high-coverage wholegenome sequences of diverse African hunter-gatherers. Cell 150:457–469
Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S et al (2014) Ancient human genomes
suggest three ancestral populations for present-day Europeans. Nature 513:409–413
Li H, Durbin R (2011) Inference of human population history from individual whole-genome
sequences. Nature 475:493–496
Li WH, Sadler LA (1991) Low nucleotide diversity in man. Genetics 129:513–523
Lipson M, Szécsényi-Nagy A, Mallick S, Pósa A, Stégmár B et al (2017) Parallel palaeogenomic
transects reveal complex genetic history of early European farmers. Nature 551:368–372
Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M et al (2018) Ancient genomes
document multiple waves of migration in Southeast Asian prehistory. Science 361:92–95
Livingston RJ, von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, Rieder MJ,
Gowrisankar S, Aronow BJ, Weiss RB, Nickerson DA (2004) Pattern of sequence variation
across 213 environmental response genes. Genome Res 14:1821–1831
Lohmueller KE, Degenhardt JD, Keinan A (2010) Sex-averaged recombination and mutation rates
on the X chromosome: a comment on Labuda et al. Am J Hum Genet 86:978–980
Lu D, Xu S (2013) Principal component analysis reveals the 1000 genomes project does not
sufficiently cover the human genetic diversity in Asia. Front Genet 4:127
Luca F, Hudson RR, Witonsky DB, Di Rienzo A (2011) A reduced representation approach to
population genetic analyses and applications to human evolution. Genome Res 21:1087–1098
Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis
G, Cheng JY, Crawford JE et al (2016) A genomic history of Aboriginal Australia. Nature
538:207–214
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt
S, Tandon A, Skoglund P et al (2016) The Simons Genome Diversity Project: 300 genomes from
142 diverse populations. Nature 538:201–206
Malmstrom H, Gilbert MTP, Thomas MG, Brandstrom M, Stora J, Molnar P, Andersen PK,
Bendixen C, Holmlund G, Gotherstrom A et al (2009) Ancient DNA reveals lack of continuity
between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol 19:1758–1762
Marjoram P, Donnelly P (1994) Pairwise comparisons of mitochondrial DNA sequences in
subdivided populations and implications for early human evolution. Genetics 136:673–683
Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genomewide human variation data reveals signals of differential demographic history in three large
world populations. Genetics 166:351–372
McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T et al (2018) The prehistoric peopling of
Southeast Asia. Science 361:88–92
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de
Filippo C et al (2012) A high-coverage genome sequence from an archaic Denisovan individual.
Science 338:222–226
Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martinez I, Gracia A, Bermudez
de Castro JM, Carbonell E, Pääbo S (2014) A mitochondrial genome sequence of a hominin
from Sima de los Huesos. Nature 505:403–406
Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price
AL, Reich D (2011) The history of African gene flow into Southern Europeans, Levantines, and
Jews. PLoS Genet 7:e1001373
201
Keinan A, Mullikin JC, Patterson N, Reich D (2009) Accelerated genetic drift on chromosome X
during the human dispersal out of Africa. Nat Genet 41:66–70
Kim BY, Lohmueller KE (2015) Selection and reduced population size cannot explain higher
amounts of Neandertal ancestry in East Asian than in European human populations. Am J Hum
Genet 96:454–461
Klein RG (2000) The earlier Stone age of southern Africa. S Afr Archaeol Bull 55:107–122
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Paabo S (1997) Neandertal DNA
sequences and the origin of modern humans. Cell 90:19–30
Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo
TB, Rebbeck TR et al (2012) Evolutionary history and adaptation from high-coverage wholegenome sequences of diverse African hunter-gatherers. Cell 150:457–469
Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S et al (2014) Ancient human genomes
suggest three ancestral populations for present-day Europeans. Nature 513:409–413
Li H, Durbin R (2011) Inference of human population history from individual whole-genome
sequences. Nature 475:493–496
Li WH, Sadler LA (1991) Low nucleotide diversity in man. Genetics 129:513–523
Lipson M, Szécsényi-Nagy A, Mallick S, Pósa A, Stégmár B et al (2017) Parallel palaeogenomic
transects reveal complex genetic history of early European farmers. Nature 551:368–372
Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M et al (2018) Ancient genomes
document multiple waves of migration in Southeast Asian prehistory. Science 361:92–95
Livingston RJ, von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, Rieder MJ,
Gowrisankar S, Aronow BJ, Weiss RB, Nickerson DA (2004) Pattern of sequence variation
across 213 environmental response genes. Genome Res 14:1821–1831
Lohmueller KE, Degenhardt JD, Keinan A (2010) Sex-averaged recombination and mutation rates
on the X chromosome: a comment on Labuda et al. Am J Hum Genet 86:978–980
Lu D, Xu S (2013) Principal component analysis reveals the 1000 genomes project does not
sufficiently cover the human genetic diversity in Asia. Front Genet 4:127
Luca F, Hudson RR, Witonsky DB, Di Rienzo A (2011) A reduced representation approach to
population genetic analyses and applications to human evolution. Genome Res 21:1087–1098
Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis
G, Cheng JY, Crawford JE et al (2016) A genomic history of Aboriginal Australia. Nature
538:207–214
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt
S, Tandon A, Skoglund P et al (2016) The Simons Genome Diversity Project: 300 genomes from
142 diverse populations. Nature 538:201–206
Malmstrom H, Gilbert MTP, Thomas MG, Brandstrom M, Stora J, Molnar P, Andersen PK,
Bendixen C, Holmlund G, Gotherstrom A et al (2009) Ancient DNA reveals lack of continuity
between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol 19:1758–1762
Marjoram P, Donnelly P (1994) Pairwise comparisons of mitochondrial DNA sequences in
subdivided populations and implications for early human evolution. Genetics 136:673–683
Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genomewide human variation data reveals signals of differential demographic history in three large
world populations. Genetics 166:351–372
McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T et al (2018) The prehistoric peopling of
Southeast Asia. Science 361:88–92
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de
Filippo C et al (2012) A high-coverage genome sequence from an archaic Denisovan individual.
Science 338:222–226
Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martinez I, Gracia A, Bermudez
de Castro JM, Carbonell E, Pääbo S (2014) A mitochondrial genome sequence of a hominin
from Sima de los Huesos. Nature 505:403–406
Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price
AL, Reich D (2011) The history of African gene flow into Southern Europeans, Levantines, and
Jews. PLoS Genet 7:e1001373