8 Inferring Human Demographic History from Genetic Data
203
Rightmire GP (2009) Out of Africa: modern human origins special feature: middle and later
Pleistocene hominins in Africa and Southwest Asia. Proc Natl Acad Sci USA 106:16046–16050
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise
genetic differences. Mol Biol Evol 9:552–569
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW
(2002) Genetic structure of human populations. Science 298:2381–2385
Sampietro ML, Lao O, Caramelli D, Lari M, Pou R, Marti M, Bertranpetit J, Lalueza-Fox C (2007)
Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe. Proc Biol Sci
274:2161–2167
Sankararaman S, Sridhar S, Kimmel G, Halperin E (2008) Estimating local ancestry in admixed
populations. Am J Hum Genet 82:290–303
Sankararaman S, Patterson N, Li H, Pääbo S, Reich D (2012) The date of interbreeding between
Neandertals and modern humans. PLoS Genet 8:e1002947
Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J et al (2014) The genomic landscape
of Neanderthal ancestry in present-da humans. Nature 507:354–357
Sankararaman S, Mallick S, Patterson N, Reich D (2016) The combined landscape of Denisovan
and Neanderthal ancestry in present-day humans. Curr Biol 26:1241–1247
Schiffels S, Durbin R (2014) Inferring human population size and separation history from multiple
genome sequences. Nat Genet 46:919–925
Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A et al (2014) Genomic
structure in Europeans dating back at least 36,200 years. Science 346:1113–1118
Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M,
Possnert G, Paabo S (2004) No evidence of Neandertal mtDNA contribution to early modern
humans. PLoS Biol 2:E57
Sheehan S, Harris K, Song YS (2013) Estimating variable effective population sizes from multiple
genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194:647–
662
Shinde V, Narasimhan V, Rohland N, Mallick S, Mah M et al (2019) An ancient Harappan genome
lacks ancestry from steppe pastoralists or Iranian farmers. Cell 179:729–735
Sjödin P, Sjöstrand AE, Jakobsson M, Blum MGB (2012) Resequencing data provide no evidence
for a human bottleneck in Africa during the penultimate glacial period. Mol Biol Evol 29:1851–
1860
Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P, Willerslev E, Gilbert MT, Gotherstrom
A, Jakobsson M (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in
Europe. Science 336:466–469
Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable
and exponentially growing populations. Genetics 129:555–562
Steinrücken M, Kamm J, Spence JP, Song YS (2019) Inference of complex population histories using whole-genome sequences from multiple populations. Proc Natl Acad Sci USA
116:17115–17120
Stringer CB, Andrews P (1988) Genetic and fossil evidence for the origin of modern humans.
Science 239:1263–1268
Takahata N (1993) Allelic genealogy and human evolution. Mol Biol Evol 10:2–22
Tellier LN (2009) Urban world history: an economic and geographical perspective. Presses de
l’Universite du Quebec, Montreal
Tennessen JA, Bigham AW, O’Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun
G et al (2012) Evolution and functional impact of rare coding variation from deep sequencing
of human exomes. Science 337:64–69
Terhorst J, Kamm JA, Song YS (2017) Robust and scalable inference of population history from
hundreds of unphased whole genomes. Nat Genet 49:303–309
Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, Cheung K, Bonne-Tamir B, SantachiaraBenerecetti AS, Moral P, Krings M (1996) Global patterns of linkage disequilibrium at the CD4
locus and modern human origins. Science 271:1380–1387
203
Rightmire GP (2009) Out of Africa: modern human origins special feature: middle and later
Pleistocene hominins in Africa and Southwest Asia. Proc Natl Acad Sci USA 106:16046–16050
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise
genetic differences. Mol Biol Evol 9:552–569
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW
(2002) Genetic structure of human populations. Science 298:2381–2385
Sampietro ML, Lao O, Caramelli D, Lari M, Pou R, Marti M, Bertranpetit J, Lalueza-Fox C (2007)
Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe. Proc Biol Sci
274:2161–2167
Sankararaman S, Sridhar S, Kimmel G, Halperin E (2008) Estimating local ancestry in admixed
populations. Am J Hum Genet 82:290–303
Sankararaman S, Patterson N, Li H, Pääbo S, Reich D (2012) The date of interbreeding between
Neandertals and modern humans. PLoS Genet 8:e1002947
Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J et al (2014) The genomic landscape
of Neanderthal ancestry in present-da humans. Nature 507:354–357
Sankararaman S, Mallick S, Patterson N, Reich D (2016) The combined landscape of Denisovan
and Neanderthal ancestry in present-day humans. Curr Biol 26:1241–1247
Schiffels S, Durbin R (2014) Inferring human population size and separation history from multiple
genome sequences. Nat Genet 46:919–925
Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A et al (2014) Genomic
structure in Europeans dating back at least 36,200 years. Science 346:1113–1118
Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M,
Possnert G, Paabo S (2004) No evidence of Neandertal mtDNA contribution to early modern
humans. PLoS Biol 2:E57
Sheehan S, Harris K, Song YS (2013) Estimating variable effective population sizes from multiple
genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194:647–
662
Shinde V, Narasimhan V, Rohland N, Mallick S, Mah M et al (2019) An ancient Harappan genome
lacks ancestry from steppe pastoralists or Iranian farmers. Cell 179:729–735
Sjödin P, Sjöstrand AE, Jakobsson M, Blum MGB (2012) Resequencing data provide no evidence
for a human bottleneck in Africa during the penultimate glacial period. Mol Biol Evol 29:1851–
1860
Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P, Willerslev E, Gilbert MT, Gotherstrom
A, Jakobsson M (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in
Europe. Science 336:466–469
Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable
and exponentially growing populations. Genetics 129:555–562
Steinrücken M, Kamm J, Spence JP, Song YS (2019) Inference of complex population histories using whole-genome sequences from multiple populations. Proc Natl Acad Sci USA
116:17115–17120
Stringer CB, Andrews P (1988) Genetic and fossil evidence for the origin of modern humans.
Science 239:1263–1268
Takahata N (1993) Allelic genealogy and human evolution. Mol Biol Evol 10:2–22
Tellier LN (2009) Urban world history: an economic and geographical perspective. Presses de
l’Universite du Quebec, Montreal
Tennessen JA, Bigham AW, O’Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun
G et al (2012) Evolution and functional impact of rare coding variation from deep sequencing
of human exomes. Science 337:64–69
Terhorst J, Kamm JA, Song YS (2017) Robust and scalable inference of population history from
hundreds of unphased whole genomes. Nat Genet 49:303–309
Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, Cheung K, Bonne-Tamir B, SantachiaraBenerecetti AS, Moral P, Krings M (1996) Global patterns of linkage disequilibrium at the CD4
locus and modern human origins. Science 271:1380–1387