john hawks weblog

paleoanthropology, genetics and evolution

Bibliography

Found 121 results
Filters: Keyword is selection  [Clear All Filters]
2012
Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, and Oota H. 2012. Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Molecular biology and evolution.
Quintana-Murci L. 2012. Gene Losses in the Human Genome. Science 335:806 - 807.
Jin W, Xu S, Wang H, Yu Y, Shen Y, Wu B, and Jin L. 2012. Genome-wide detection of natural selection in African Americans pre- and post-admixture. Genome research 22:519-27.
Plantinga TS, Alonso S, Izagirre N, Hervella M, Fregel R, van der Meer JW, Netea MG, and de la Rúa C. 2012. Low prevalence of lactase persistence in Neolithic South-West Europe. European journal of human genetics : EJHG.
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
Moreau C, Bherer C, Vezina H, Jomphe M, Labuda D, and Excoffier L. 2011. Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front. Science.
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
Yu H-S, Shen Y-H, Yuan G-X, Hu Y-G, Xu H-E, Xiang Z-H, and Zhang Z. 2011. Evidence of selection at melanin synthesis pathway loci during silkworm domestication. Molecular Biology and Evolution [Internet]. Available from: http://dx.doi.org/10.1093/molbev/msr002
Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, and Kellis M. 2011. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome research.
Tranah GJ, Manini TM, Lohman KK, Nalls MA, Kritchevsky S, Newman AB, Harris TB, Miljkovic I, Biffi A, Cummings SR, et al. 2011. Mitochondrial DNA variation in human metabolic rate and energy expenditure. Mitochondrion 11:855-61.
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
Foote AD, Morin PA, Durban JW, Pitman RL, Wade P, Willerslev E, Gilbert TMP, and da Fonseca RR. 2011. Positive selection on the killer whale mitogenome. Biology letters 7:116-8.
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
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
Haygood R, Babbitt CC, Fedrigo O, and Wray GA. 2010. Contrasts between adaptive coding and noncoding changes during human evolution. Proceedings of the National Academy of Sciences [Internet] 107:7853–7857. Available from: http://dx.doi.org/10.1073/pnas.0911249107
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
Wilkens H. 2010. Genes, modules and the evolution of cave fish. Heredity [Internet] 105:413–422. Available from: http://dx.doi.org/10.1038/hdy.2009.184
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
Lambert CA, Connelly CF, Madeoy J, Qiu R, Olson MV, and Akey JM. 2010. Highly Punctuated Patterns of Population Structure on the X Chromosome and Implications for African Evolutionary History. The American Journal of Human Genetics [Internet] 86:34–44. Available from: http://dx.doi.org/10.1016/j.ajhg.2009.12.002
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
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
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
Bray SM, Mulle JG, Dodd AF, Pulver AE, Wooding S, and Warren ST. 2010. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population. Proceedings of the National Academy of Sciences of the United States of America [Internet] 107:16222–16227. Available from: http://dx.doi.org/10.1073/pnas.1004381107
Guinan KJ, Cunningham RT, Meenagh A, Gonzalez A, Dring MM, McGuinness BW, Middleton D, and Gardiner CM. 2010. Signatures of natural selection and coevolution between killer cell immunoglobulin-like receptors (KIR) and HLA class I genes. Genes and Immunity [Internet] 11:467–478. Available from: http://dx.doi.org/10.1038/gene.2010.9
Tennessen JA, Madeoy J, and Akey JM. 2010. Signatures of positive selection apparent in a small sample of human exomes. Genome research [Internet] 20:1327–1334. Available from: http://dx.doi.org/10.1101/gr.106161.110
Kim Y, and Gulisija D. 2010. Signatures of Recent Directional Selection Under Different Models of Population Expansion During Colonization of New Selective Environments. Genetics [Internet] 184:571–585. Available from: http://dx.doi.org/10.1534/genetics.109.109447
Bernal V, Perez SI, Gonzalez PN, Sardi ML, and Pucciarelli HM. 2010. Spatial patterns and evolutionary processes in southern South America: A study of dental morphometric variation. Am. J. Phys. Anthropol. [Internet] 142:95–104. Available from: http://dx.doi.org/10.1002/ajpa.21206
Park C, Carrel L, and Makova KD. 2010. Strong Purifying Selection at Genes Escaping X Chromosome Inactivation. Molecular Biology and Evolution [Internet] 27:2446–2450. Available from: http://dx.doi.org/10.1093/molbev/msq143
Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, et al. 2010. Targeted investigation of the Neandertal genome by array-based sequence capture. Science (New York, N.Y.) [Internet] 328:723–725. Available from: http://dx.doi.org/10.1126/science.1188046

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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.