john hawks weblog

paleoanthropology, genetics and evolution

Bibliography

Found 105 results
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2013
Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, et al. 2013. Identifying recent adaptations in large-scale genomic data. Cell 152:703-13.
2012
Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, and Pääbo S. 2012. Analysis of human accelerated DNA regions using archaic hominin genomes. PloS one 7:e32877.
Hünemeier T, Gómez-Valdés J, Ballesteros-Romero M, de Azevedo S, Martínez-Abadías N, Esparza M, Sjøvold T, Bonatto SL, Salzano FM, Bortolini MC, et al. 2012. Cultural diversification promotes rapid phenotypic evolution in Xavánte Indians. Proc Natl Acad Sci U S A 109:73-7.
Minucci A, Moradkhani K, Hwang MJ, Zuppi C, Giardina B, and Capoluongo E. 2012. Glucose-6-phosphate dehydrogenase (G6PD) mutations database: review of the "old" and update of the new mutations. Blood cells, molecules & diseases 48:154-65.
Visser M, Kayser M, and Palstra R-J. 2012. HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome research.
Courtiol A, Pettay JE, Jokela M, Rotkirch A, and Lummaa V. 2012. Natural and sexual selection in a monogamous historical human population. Proceedings of the National Academy of Sciences.
Suo C, Xu H, Khor C-C, Ong RT, Sim X, Chen J, Tay W-T, Sim K-S, Zeng Y-X, Zhang X, et al. 2012. Natural positive selection and north-south genetic diversity in East Asia. European journal of human genetics : EJHG 20:102-10.
Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, et al. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature communications 3:698.
Balter M. 2012. The Peopling of the Aleutians. Science 335:158 - 161.
Keinan A, and Clark AG. 2012. Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants. Science 336:740 - 743.
Belezal S, dos Santos AM, McEvoy B, Alves I, Martinho C, Cameron E, Shriver MD, Parra EJ, and Rocha J. 2012. The timing of pigmentation lightening in Europeans. Molecular Biology and Evolution.
Chen Q, Fabry ME, Rybicki AC, Suzuka SM, Balazs TC, Etzion Z, de Jong K, Akoto EK, Canterino JE, Kaul DK, et al. 2012. A transgenic mouse model expressing exclusively human hemoglobin E: indications of a mild oxidative stress. Blood cells, molecules & diseases 48:91-101.
2011
Hernandez RD, Kelley JL, Elyashiv E, Melton CS, Auton A, McVean G, Project G1000, Sella G, and Przeworski M. 2011. Classic Selective Sweeps Were Rare in Recent Human Evolution. Science [Internet] 331:920–924. Available from: http://dx.doi.org/10.1126/science.1198878
Wu DD, and Zhang YP. 2011. Different level of population differentiation among human genes. BMC Evolutionary Biology [Internet] 11:16+. Available from: http://dx.doi.org/10.1186/1471-2148-11-16
Ebenesersdóttir S\'ıðurS, Sigurðsson Á, Sánchez-Quinto F, Lalueza-Fox C, Stefánsson K, and Helgason A. 2011. A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact?. Am. J. Phys. Anthropol. [Internet] 144:92–99. Available from: http://dx.doi.org/10.1002/ajpa.21419
Li H. 2011. A New Test for Detecting Recent Positive Selection that is Free from the Confounding Impacts of Demography. Molecular Biology and Evolution [Internet] 28:365–375. Available from: http://dx.doi.org/10.1093/molbev/msq211
Deguilloux M-F, Soler L, Pemonge M-H, Scarre C, Joussaume R, and Laporte L. 2011. News from the west: Ancient DNA from a French megalithic burial chamber. Am. J. Phys. Anthropol. [Internet] 144:108–118. Available from: http://dx.doi.org/10.1002/ajpa.21376
Metspalu M, Romero IG, Yunusbayev B, Chaubey G, Mallick CB, Hudjashov G, Nelis M, Mägi R, Metspalu E, Remm M, et al. 2011. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. American journal of human genetics 89:731-44.
Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admettla A, Pattini L, and Nielsen R. 2011. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS genetics 7:e1002355.
Amos W, and Bryant C. 2011. Using human demographic history to infer natural selection reveals contrasting patterns on different families of immune genes. Proceedings of the Royal Society B: Biological Sciences [Internet] 278:1587-1594. Available from: http://dx.doi.org/10.1098/rspb.2010.2056
2010
Pritchard JK, and Di Rienzo A. 2010. Adaptation - not by sweeps alone. Nature reviews. Genetics [Internet] 11:665–667. Available from: http://dx.doi.org/10.1038/nrg2880
Estrada AM, Prat EA, Sikora M, Engelken J, Soriano AR, Calafell F, and Bosch E. 2010. African signatures of recent positive selection in human FOXI1. BMC Evolutionary Biology [Internet] 10:267+. Available from: http://dx.doi.org/10.1186/1471-2148-10-267
Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt H-J, Torroni A, and Richards MB. 2010. The Archaeogenetics of Europe. [Internet] 20:R174–R183. Available from: http://www.cell.com/current-biology/abstract/S0960-9822(09)02069-7
Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, et al. 2010. Association of Trypanolytic ApoL1 Variants with Kidney Disease in African Americans. Science [Internet] 329:841–845. Available from: http://dx.doi.org/10.1126/science.1193032
Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, et al. 2010. A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection. Science [Internet] 327:883–886. Available from: http://dx.doi.org/10.1126/science.1183863
Sezgin E, Drosdak A, McIntosh C, Kessing B, Lautenberger JA, Goedert JJ, Phair JP, Troyer JL, Smith MW, and O'Brien SJ. 2010. Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I. Journal of Human Genetics [Internet] 55:613–620. Available from: http://dx.doi.org/10.1038/jhg.2010.77
Melchior L, Lynnerup N, Siegismund HR, Kivisild T, and Dissing J. 2010. Genetic Diversity among Ancient Nordic Populations. PLoS ONE [Internet] 5:e11898+. Available from: http://dx.doi.org/10.1371/journal.pone.0011898
Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, et al. 2010. Genetic Evidence for High-Altitude Adaptation in Tibet. Science [Internet] 329:72–75. Available from: http://dx.doi.org/10.1126/science.1189406
Pritchard JK, Pickrell JK, and Coop G. 2010. The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation. Current Biology [Internet] 20:R208–R215. Available from: http://dx.doi.org/10.1016/j.cub.2009.11.055
Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, and Boehnke M. 2010. Genome-wide association studies in diverse populations. Nature Reviews Genetics [Internet] 11:356–366. Available from: http://dx.doi.org/10.1038/nrg2760
Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Sykes N, Pagnamenta AT, et al. 2010. A genome-wide scan for common alleles affecting risk for autism. Human Molecular Genetics [Internet] 19:4072–4082. Available from: http://dx.doi.org/10.1093/hmg/ddq307
Piel FB, Patil AP, Howes RE, Nyangiri OA, Gething PW, Williams TN, Weatherall DJ, and Hay SI. 2010. Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis. Nature Communications [Internet] 1:104+. Available from: http://dx.doi.org/10.1038/ncomms1104
Malmstrom H, Linderholm A, Liden K, Stora J, Molnar P, Holmlund G, Jakobsson M, and Gotherstrom A. 2010. High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe. BMC Evolutionary Biology [Internet] 10:89+. Available from: http://dx.doi.org/10.1186/1471-2148-10-89
Dehaene S, Pegado F, Braga LW, Ventura P, Nunes Filho G, Jobert A, Dehaene-Lambertz G, Kolinsky R, Morais J, and Cohen L. 2010. How learning to read changes the cortical networks for vision and language. Science (New York, N.Y.) [Internet] 330:1359–1364. Available from: http://dx.doi.org/10.1126/science.1194140
Keinan A, and Reich D. 2010. Human Population Differentiation Is Strongly Correlated with Local Recombination Rate. PLoS Genet [Internet] 6:e1000886+. Available from: http://dx.doi.org/10.1371/journal.pgen.1000886
Anon. 2010. Integrating common and rare genetic variation in diverse human populations. Nature [Internet] 467:52–58. Available from: http://dx.doi.org/10.1038/nature09298
Fumagalli M, Pozzoli U, Cagliani R, Comi G, Bresolin N, Clerici M, and Sironi M. 2010. The landscape of human genes involved in the immune response to parasitic worms. BMC Evolutionary Biology [Internet] 10:264+. Available from: http://dx.doi.org/10.1186/1471-2148-10-264
Stearns SC, Byars SG, Govindaraju DR, and Ewbank D. 2010. Measuring selection in contemporary human populations. Nature Reviews Genetics [Internet] 11:611–622. Available from: http://dx.doi.org/10.1038/nrg2831
Iskow RC, McCabe MT, Mills RE, Torene S, Pittard SW, Neuwald AF, Van Meir EG, Vertino PM, and Devine SE. 2010. Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons. Cell [Internet] 141:1253–1261. Available from: http://dx.doi.org/10.1016/j.cell.2010.05.020
Albrechtsen A, Moltke I, and Nielsen R. 2010. Natural Selection and the Distribution of Identity-by-Descent in the Human Genome. Genetics [Internet] 186:295–308. Available from: http://dx.doi.org/10.1534/genetics.110.113977
Byars SG, Ewbank D, Govindaraju DR, and Stearns SC. 2010. Natural selection in a contemporary human population. Proceedings of the National Academy of Sciences [Internet] 107:1787–1792. Available from: http://dx.doi.org/10.1073/pnas.0906199106
Beall CM, Cavalleri GL, Deng L, Elston RC, Gao Y, Knight J, Li C, Li JC, Liang Y, McCormack M, et al. 2010. Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders. Proceedings of the National Academy of Sciences [Internet] 107:11459–11464. Available from: http://dx.doi.org/10.1073/pnas.1002443107
Liu W, Li Y, Learn GH, Rudicell RS, Robertson JD, Keele BF, Ndjango J-BN, Sanz CM, Morgan DB, Locatelli S, et al. 2010. Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature [Internet] 467:420–425. Available from: http://dx.doi.org/10.1038/nature09442
Ralph P, and Coop G. 2010. Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?. Genetics [Internet] 186:647–668. Available from: http://dx.doi.org/10.1534/genetics.110.119594
Chen H, Patterson N, and Reich D. 2010. Population differentiation as a test for selective sweeps. Genome Research [Internet] 20:393–402. Available from: http://dx.doi.org/10.1101/gr.100545.109
Fumagalli M, Cagliani R, Riva S, Pozzoli U, Biasin M, Piacentini L, Comi GP, Bresolin N, Clerici M, and Sironi M. 2010. Population Genetics of IFIH1: Ancient Population Structure, Local Selection, and Implications for Susceptibility to Type 1 Diabetes. Molecular Biology and Evolution [Internet] 27:2555–2566. Available from: http://dx.doi.org/10.1093/molbev/msq141
Wu D-DD, and Zhang Y-PP. 2010. Positive selection drives population differentiation in the skeletal genes in modern humans. Human molecular genetics [Internet]. Available from: http://dx.doi.org/10.1093/hmg/ddq107
Balaresque P, Bowden GR, Adams SM, Leung H-Y, King TE, Rosser ZH, Goodwin J, Moisan J-P, Richard C, Millward A, et al. 2010. A Predominantly Neolithic Origin for European Paternal Lineages. PLoS Biol [Internet] 8:e1000285+. Available from: http://dx.doi.org/10.1371/journal.pbio.1000285
Pavlidis P, Jensen JD, and Stephan W. 2010. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics [Internet] 185:907–922. Available from: http://dx.doi.org/10.1534/genetics.110.116459
Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, et al. 2010. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude. Science [Internet] 329:75–78. Available from: http://dx.doi.org/10.1126/science.1190371

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About the bibliography

My bibliography database represents years of work by many people. The core of the database was compiled by Milford Wolpoff, with contributions from many students and coauthors. I have added substantially to the database during the last fifteen years, and since I have been blogging all new entries are linked by Digital Object Identifier numbers to their place of publication.

If you find the database useful, please take time to thank the people who worked hard to compile it. I know they will appreciate hearing it.

This database began as a flat text file of bibliographic entries, which I have over the years scripted into a computer-readable format. Many errors have slipped in, including typos from the initial data entry, script fragments from my BibTeX database, and some entries that began in a non-standard format and were scrambled by scripts. Please do not write me expecting that I will fix these errors. It would take me weeks of work to do this. Works will be fixed as I cite them or enter updated information for them.

There are also errors of omission. Most entries are here because they got cited, in Milford's books, in the many research articles by him or his students, or in my work. I mention this mainly because I know that some of you will look up your own names, and find many important papers missing from the database. If you're disappointed in the representation of your articles here, by all means contact me and I will work with you. This database is mirrored on CiteULike and Mendeley and I can import your bibliographic data from these sites, EndNote, BibTeX or other standard formats.

A fuller introduction to the bibliography is in my initial announcement.

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.