Literature DB >> 21850041

Learning about human population history from ancient and modern genomes.

Mark Stoneking1, Johannes Krause.   

Abstract

Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of modern humans from Africa, followed by two archaic admixture events: one with Neanderthals somewhere outside Africa and a second with Denisovans that (so far) has only been detected in New Guinea. These new developments promise to reveal new stories about human population history, without having to resort to storytelling.

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Year:  2011        PMID: 21850041     DOI: 10.1038/nrg3029

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  92 in total

1.  A human genome diversity cell line panel.

Authors:  Howard M Cann; Claudia de Toma; Lucien Cazes; Marie-Fernande Legrand; Valerie Morel; Laurence Piouffre; Julia Bodmer; Walter F Bodmer; Batsheva Bonne-Tamir; Anne Cambon-Thomsen; Zhu Chen; J Chu; Carlo Carcassi; Licinio Contu; Ruofu Du; Laurent Excoffier; G B Ferrara; Jonathan S Friedlaender; Helena Groot; David Gurwitz; Trefor Jenkins; Rene J Herrera; Xiaoyi Huang; Judith Kidd; Kenneth K Kidd; Andre Langaney; Alice A Lin; S Qasim Mehdi; Peter Parham; Alberto Piazza; Maria Pia Pistillo; Yaping Qian; Qunfang Shu; Jiujin Xu; S Zhu; James L Weber; Henry T Greely; Marcus W Feldman; Gilles Thomas; Jean Dausset; L Luca Cavalli-Sforza
Journal:  Science       Date:  2002-04-12       Impact factor: 47.728

2.  South Asia, the Andamanese, and the genetic evidence for an "early" human dispersal out of Africa.

Authors:  Richard Cordaux; Mark Stoneking
Journal:  Am J Hum Genet       Date:  2003-06       Impact factor: 11.025

3.  High-throughput sequencing of complete human mtDNA genomes from the Philippines.

Authors:  Ellen D Gunnarsdóttir; Mingkun Li; Marc Bauchet; Knut Finstermeier; Mark Stoneking
Journal:  Genome Res       Date:  2010-12-08       Impact factor: 9.043

4.  Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians.

Authors:  Manfred Kayser; Oscar Lao; Kathrin Saar; Silke Brauer; Xingyu Wang; Peter Nürnberg; Ronald J Trent; Mark Stoneking
Journal:  Am J Hum Genet       Date:  2008-01       Impact factor: 11.025

5.  Mapping human genetic diversity in Asia.

Authors:  Mahmood Ameen Abdulla; Ikhlak Ahmed; Anunchai Assawamakin; Jong Bhak; Samir K Brahmachari; Gayvelline C Calacal; Amit Chaurasia; Chien-Hsiun Chen; Jieming Chen; Yuan-Tsong Chen; Jiayou Chu; Eva Maria C Cutiongco-de la Paz; Maria Corazon A De Ungria; Frederick C Delfin; Juli Edo; Suthat Fuchareon; Ho Ghang; Takashi Gojobori; Junsong Han; Sheng-Feng Ho; Boon Peng Hoh; Wei Huang; Hidetoshi Inoko; Pankaj Jha; Timothy A Jinam; Li Jin; Jongsun Jung; Daoroong Kangwanpong; Jatupol Kampuansai; Giulia C Kennedy; Preeti Khurana; Hyung-Lae Kim; Kwangjoong Kim; Sangsoo Kim; Woo-Yeon Kim; Kuchan Kimm; Ryosuke Kimura; Tomohiro Koike; Supasak Kulawonganunchai; Vikrant Kumar; Poh San Lai; Jong-Young Lee; Sunghoon Lee; Edison T Liu; Partha P Majumder; Kiran Kumar Mandapati; Sangkot Marzuki; Wayne Mitchell; Mitali Mukerji; Kenji Naritomi; Chumpol Ngamphiw; Norio Niikawa; Nao Nishida; Bermseok Oh; Sangho Oh; Jun Ohashi; Akira Oka; Rick Ong; Carmencita D Padilla; Prasit Palittapongarnpim; Henry B Perdigon; Maude Elvira Phipps; Eileen Png; Yoshiyuki Sakaki; Jazelyn M Salvador; Yuliana Sandraling; Vinod Scaria; Mark Seielstad; Mohd Ros Sidek; Amit Sinha; Metawee Srikummool; Herawati Sudoyo; Sumio Sugano; Helena Suryadi; Yoshiyuki Suzuki; Kristina A Tabbada; Adrian Tan; Katsushi Tokunaga; Sissades Tongsima; Lilian P Villamor; Eric Wang; Ying Wang; Haifeng Wang; Jer-Yuarn Wu; Huasheng Xiao; Shuhua Xu; Jin Ok Yang; Yin Yao Shugart; Hyang-Sook Yoo; Wentao Yuan; Guoping Zhao; Bin Alwi Zilfalil
Journal:  Science       Date:  2009-12-11       Impact factor: 47.728

6.  Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific.

Authors:  Manfred Kayser; Silke Brauer; Richard Cordaux; Amanda Casto; Oscar Lao; Lev A Zhivotovsky; Claire Moyse-Faurie; Robb B Rutledge; Wulf Schiefenhoevel; David Gil; Alice A Lin; Peter A Underhill; Peter J Oefner; Ronald J Trent; Mark Stoneking
Journal:  Mol Biol Evol       Date:  2006-08-21       Impact factor: 16.240

7.  Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.

Authors:  Tomislav Maricic; Mark Whitten; Svante Pääbo
Journal:  PLoS One       Date:  2010-11-16       Impact factor: 3.240

8.  Molecular cloning of Ancient Egyptian mummy DNA.

Authors:  S Pääbo
Journal:  Nature       Date:  1985 Apr 18-24       Impact factor: 49.962

9.  Sequencing the nuclear genome of the extinct woolly mammoth.

Authors:  Webb Miller; Daniela I Drautz; Aakrosh Ratan; Barbara Pusey; Ji Qi; Arthur M Lesk; Lynn P Tomsho; Michael D Packard; Fangqing Zhao; Andrei Sher; Alexei Tikhonov; Brian Raney; Nick Patterson; Kerstin Lindblad-Toh; Eric S Lander; James R Knight; Gerard P Irzyk; Karin M Fredrikson; Timothy T Harkins; Sharon Sheridan; Tom Pringle; Stephan C Schuster
Journal:  Nature       Date:  2008-11-20       Impact factor: 49.962

10.  Ancient DNA from European early neolithic farmers reveals their near eastern affinities.

Authors:  Wolfgang Haak; Oleg Balanovsky; Juan J Sanchez; Sergey Koshel; Valery Zaporozhchenko; Christina J Adler; Clio S I Der Sarkissian; Guido Brandt; Carolin Schwarz; Nicole Nicklisch; Veit Dresely; Barbara Fritsch; Elena Balanovska; Richard Villems; Harald Meller; Kurt W Alt; Alan Cooper
Journal:  PLoS Biol       Date:  2010-11-09       Impact factor: 8.029

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  48 in total

1.  Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion.

Authors:  Shuhua Xu; Irina Pugach; Mark Stoneking; Manfred Kayser; Li Jin
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-06       Impact factor: 11.205

Review 2.  Functional primate genomics--leveraging the medical potential.

Authors:  Wolfgang Enard
Journal:  J Mol Med (Berl)       Date:  2012-05-04       Impact factor: 4.599

Review 3.  Demographic events and evolutionary forces shaping European genetic diversity.

Authors:  Krishna R Veeramah; John Novembre
Journal:  Cold Spring Harb Perspect Biol       Date:  2014-07-24       Impact factor: 10.005

Review 4.  Fostering Responsible Research on Ancient DNA.

Authors:  Jennifer K Wagner; Chip Colwell; Katrina G Claw; Anne C Stone; Deborah A Bolnick; John Hawks; Kyle B Brothers; Nanibaa' A Garrison
Journal:  Am J Hum Genet       Date:  2020-08-06       Impact factor: 11.025

5.  Rethinking dog domestication by integrating genetics, archeology, and biogeography.

Authors:  Greger Larson; Elinor K Karlsson; Angela Perri; Matthew T Webster; Simon Y W Ho; Joris Peters; Peter W Stahl; Philip J Piper; Frode Lingaas; Merete Fredholm; Kenine E Comstock; Jaime F Modiano; Claude Schelling; Alexander I Agoulnik; Peter A Leegwater; Keith Dobney; Jean-Denis Vigne; Carles Vilà; Leif Andersson; Kerstin Lindblad-Toh
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-21       Impact factor: 11.205

6.  Archaic human ancestry in East Asia.

Authors:  Pontus Skoglund; Mattias Jakobsson
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-31       Impact factor: 11.205

Review 7.  Targeted capture in evolutionary and ecological genomics.

Authors:  Matthew R Jones; Jeffrey M Good
Journal:  Mol Ecol       Date:  2015-07-30       Impact factor: 6.185

8.  Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.

Authors:  Pontus Skoglund; Bernd H Northoff; Michael V Shunkov; Anatoli P Derevianko; Svante Pääbo; Johannes Krause; Mattias Jakobsson
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-27       Impact factor: 11.205

9.  A revised timescale for human evolution based on ancient mitochondrial genomes.

Authors:  Qiaomei Fu; Alissa Mittnik; Philip L F Johnson; Kirsten Bos; Martina Lari; Ruth Bollongino; Chengkai Sun; Liane Giemsch; Ralf Schmitz; Joachim Burger; Anna Maria Ronchitelli; Fabio Martini; Renata G Cremonesi; Jiří Svoboda; Peter Bauer; David Caramelli; Sergi Castellano; David Reich; Svante Pääbo; Johannes Krause
Journal:  Curr Biol       Date:  2013-03-21       Impact factor: 10.834

Review 10.  Toward a new history and geography of human genes informed by ancient DNA.

Authors:  Joseph K Pickrell; David Reich
Journal:  Trends Genet       Date:  2014-08-26       Impact factor: 11.639

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