Difference between revisions of "Publications"

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[[Altrock et al. 2012|Altrock, P. M., A. Traulsen, and F. A. Reed. (2011) Stability Properties of Underdominance in Finite Subdivided Populations.]] [[PLoS Computational Biology]] 7: e1002260. doi:10.1371/journal.pcbi.1002260
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[[Allaby et al. 2010|Allaby, R. G., F. R. Friedlaender, F. A. Reed, K. K. Kidd, J. R. Kidd, et al. (2010) Prehistoric Pacific Population Movements.]] pp. 143-157 in [[The Global Origins and Developments of Seafaring]]. A. Anderson, J. H. Barrett & K. V. Boyle, Eds., ISBN: 978-1-902937-52-6, McDonald Institute for Archaeological Research, Cambridge, UK.
 +
 
 +
[[Altrock et al. 2010|Altrock, P. M., A. Traulsen, R. G. Reeves, and F. A. Reed. (2010) Using underdominance to bi-stably transform local populations.]] [[Journal of Theoretical Biology]] 267: 62-75. doi:10.1016/j.jtbi.2010.08.004
 +
 
 +
[[Altrock et al. 2011|Altrock, P. M., A. Traulsen, and F. A. Reed. (2011) Stability Properties of Underdominance in Finite Subdivided Populations.]] [[PLoS Computational Biology]] 7: e1002260. doi:10.1371/journal.pcbi.1002260
 +
 
 +
[[Aquadro et al. 2001|Aquadro, C. F., V. L. Bauer DuMont and F. A. Reed. (2001) Genome-wide variation in the human and fruitfly: a comparison.]] [[Current Opinion in Genetics & Development]] 11: 627-634. doi:10.1016/S0959-437X(00)00245-8
  
 
[[Bryk et al. 2017|Bryk, J., Reeves, R. G., Reed, F. A., & Denton, J. A. (2017). Transcriptional effects of a positive feedback circuit in ''Drosophila melanogaster'']]. ''[[BMC Genomics]]'', 18(1), 990; https://doi.org/10.1186/s12864-017-4385-z
 
[[Bryk et al. 2017|Bryk, J., Reeves, R. G., Reed, F. A., & Denton, J. A. (2017). Transcriptional effects of a positive feedback circuit in ''Drosophila melanogaster'']]. ''[[BMC Genomics]]'', 18(1), 990; https://doi.org/10.1186/s12864-017-4385-z
 +
 +
[[Friedlaender et al. 2008|Friedlaender, J. S., F. R. Friedlaender, F. A. Reed, K. K. Kidd, J. R. Kidd, et al. (2008) The Genetic Structure of Pacific Islanders.]] [[PLoS Genetics]] 4: e19. doi:10.1371/journal.pgen.0040019
  
 
[[Gokhale et al. 2014|Gokhale, C., R. G. Reeves, and F. A. Reed. (2014) Dynamics of a combined medea-underdominant population transformation system.]]  [[BMC Evolutionary Biology]] 14: 90.  doi:10.1186/1471-2148-14-98
 
[[Gokhale et al. 2014|Gokhale, C., R. G. Reeves, and F. A. Reed. (2014) Dynamics of a combined medea-underdominant population transformation system.]]  [[BMC Evolutionary Biology]] 14: 90.  doi:10.1186/1471-2148-14-98
  
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[[Láruson et al. 2018|Láruson, Á. J., Coppard, S. E., Pespeni, M. H., & Reed, F. A. (2018). Gene expression across tissues, sex, and life stages in the sea urchin ''Tripneustes gratilla'' [Toxopneustidae, Odontophora, Camarodonta]]]. ''[[bioRxiv]]'', 284224; doi: https://doi.org/10.1101/284224
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[[Gonder et al. 2007|Gonder, M. K., H. M. Mortensen, F. A. Reed, A. de Sousa and S. A. Tishkoff. (2007) Whole mtDNA Genome Sequence Analysis of Ancient African Lineages.]] [[Molecular Biology and Evolution]] 24: 757-768. doi:10.1093/molbev/msl209
 +
 
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[[Haubold et al. 2011|Haubold, B., F. A. Reed and P. Pfaffelhuber. (2011) Alignment-free estimation of nucleotide diversity.]] [[Bioinformatics]] 27: 449-455. doi:10.1093/bioinformatics/btq689
 +
 
 +
[[Kontanis and Reed 2006|Kontanis, E. J. and F. A. Reed. (2006) Evaluation of real-time PCR amplification effciencies to detect inhibitors.]] [[Journal of Forensic Sciences]] 51: 795-804. doi:10.1111/j.1556-4029.2006.00182.x
  
 
[[Láruson 2017|Láruson, Á. J. (2017). Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora]]. ''[[Ecology and Evolution]]'', 7(13), 4543-4551. https://doi.org/10.1002/ece3.3042
 
[[Láruson 2017|Láruson, Á. J. (2017). Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora]]. ''[[Ecology and Evolution]]'', 7(13), 4543-4551. https://doi.org/10.1002/ece3.3042
  
 
[[Láruson & Reed 2016|Láruson, Á. J., & Reed, F. A. (2016). Stability of underdominant genetic polymorphisms in population networks]]. ''[[Journal of Theoretical Biology]]'', 390, 156-163; https://doi.org/10.1016/j.jtbi.2015.11.023
 
[[Láruson & Reed 2016|Láruson, Á. J., & Reed, F. A. (2016). Stability of underdominant genetic polymorphisms in population networks]]. ''[[Journal of Theoretical Biology]]'', 390, 156-163; https://doi.org/10.1016/j.jtbi.2015.11.023
 +
 +
[[Láruson et al. 2018|Láruson, Á. J., Coppard, S. E., Pespeni, M. H., & Reed, F. A. (2018). Gene expression across tissues, sex, and life stages in the sea urchin ''Tripneustes gratilla'' [Toxopneustidae, Odontophora, Camarodonta]]]. ''[[bioRxiv]]'', 284224; doi: https://doi.org/10.1101/284224
 +
 +
[[Milinski et al. 2008|Milinski, M., R. Sommerfeld, H.-J. Krambeck, F. A. Reed and J. Marotzke. (2008) The collective risk social dilemma, and the prevention of simulated dangerous climate change.]] [[Proceedings of the National Academy of Sciences USA]] 105: 2291-2294. doi:10.1073/pnas.0709546105
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[[Reed 2004|Reed, F. A. (2004) Characterizing Diversity Reducing Selection in Humans and Fruitflies.]] Ph.D. Dissertation, Cornell University, Ithaca, NY. http://wwwlib.umi.com/dissertations/fullcit/3149436
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[[Reed 2007|Reed, F. A. (2007) Two-locus epistasis with sexually antagonistic selection: A genetic Parrondo’s paradox.]] [[Genetics]] 176: 1923-1929. doi:10.1534/genetics.106.069997
 +
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[[Reed 2008|Reed, F. A. (2008) Are Humans Still Evolving?]] In [[Encyclopedia of Life Sciences: Handbook of Human Molecular Evolution]], D. N. Cooper & H. Kehrer-Sawatzki, Eds., John Wiley & Sons, Ltd., Chichester, UK. http://www.els.net doi:10.1002/9780470015902.a0020794
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[[Reed 2012|Reed, F. A. (2012). Modern Human Migrations: The First 200,000 Years]]. In ''[[Migrations: Interdisciplinary Perspectives]]'' (pp. 315-326). Springer, Vienna.
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[[Reed and Aquadro 2006|Reed, F. A. and C. F. Aquadro. (2006) Mutation, selection and the future of human evolution.]] [[Trends in Genetics]] 22: 479-484. doi:10.1016/j.tig.2006.07.005
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[[Reed and Tishkoff 2006a|Reed, F. A. and S. A. Tishkoff. (2006) Positive selection can create false hotspots of recombination.]] [[Genetics]] 172: 2011-2014. doi:10.1534/genetics.105.052183
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[[Reed and Tishkoff 2006b|Reed, F. A. and S. A. Tishkoff. (2006) African human diversity, origins and migrations.]] [[Current Opinion in Genetics & Development]] 16: 597-605. doi:10.1016/j.gde.2006.10.008
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[[Reed et al. 2003|Reed, F. A., E. J. Kontanis, K. A. R. Kennedy and C. F. Aquadro. (2003) Ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern.]] [[American Journal of Physical Anthropology]] 121: 112-116. doi:10.1002/ajpa.10211
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[[Reed et al. 2005a|Reed, F. A., J. M. Akey and C. F. Aquadro. (2005) Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes.]] [[Genome Research]] 15: 1211-1221. doi:10.1101/gr.3413205
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[[Reed et al. 2005b|Reed, F. A., R. G. Reeves and C. F. Aquadro. (2005) Evidence of susceptibility and resistance to cryptic X-linked meiotic drive in natural populations of Drosophila melanogaster.]] [[Evolution]] 59: 1280-1291. doi:10.1111/j.0014-3820.2005.tb01778.x
  
 
[[Reed et al. 2013|Reed, F. A., A. Traulsen, P. M. Altrock (2013) Underdominance.]] In “[[Encyclopedia of Genetics]]” S. Brenner & J. H. Miller Eds., Elsevier Science Inc. doi:10.1016/B978-0-12-374984-0.01601-6
 
[[Reed et al. 2013|Reed, F. A., A. Traulsen, P. M. Altrock (2013) Underdominance.]] In “[[Encyclopedia of Genetics]]” S. Brenner & J. H. Miller Eds., Elsevier Science Inc. doi:10.1016/B978-0-12-374984-0.01601-6
  
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[[Reed 2012|Reed, F. A. (2012). Modern Human Migrations: The First 200,000 Years]]. In ''[[Migrations: Interdisciplinary Perspectives]]'' (pp. 315-326). Springer, Vienna.
+
[[Reeves et al. 2012|Reeves, R. G., J. Denton, F. Santucci, J. Bryk, and F. A. Reed. (2012) Scientific Standards and the Regulation of Genetically Modified Insects.]] [[PLoS Neglected Tropical Diseases]] 6: e1502. doi:10.1371/journal.pntd.0001502
  
 
[[Reeves et al. 2014|Reeves, R. G., J. Bryk, P. M. Altrock, J. Denton, and F. A. Reed. (2014) First Steps towards Underdominant Genetic Transformation of Insect Populations.]]  [[PLoS ONE]] 9: e97557.  doi:10.1371/journal.pone.0097557
 
[[Reeves et al. 2014|Reeves, R. G., J. Bryk, P. M. Altrock, J. Denton, and F. A. Reed. (2014) First Steps towards Underdominant Genetic Transformation of Insect Populations.]]  [[PLoS ONE]] 9: e97557.  doi:10.1371/journal.pone.0097557
  
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[[Reeves et al. 2012|Reeves, R. G., J. Denton, F. Santucci, J. Bryk, and F. A. Reed. (2012) Scientific Standards and the Regulation of Genetically Modified Insects.]] [[PLoS Neglected Tropical Diseases]] 6: e1502. doi:10.1371/journal.pntd.0001502
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[[Shafer et al. 2015|Shafer, A. B. A., J. B. W. Wolf, P. C. Alves, L. Bergström, M. W. Bruford, I. Brännström, et al. (2015) Genomics and the challenging translation into conservation practice.]] [[Trends in Ecology & Evolution]] 30 (2), 78-87. doi:10.1016/j.tree.2014.11.009
  
 
[[Shafer et al. 2016|Shafer, A., JBW Wolf, PC Alves, L Bergström, G Colling, L Dalén, et al. (2016) Reply to Garner et al.]] [[Trends in Ecology & Evolution]] 31 (2), 83-84. doi:10.1016/j.tree.2015.11.010
 
[[Shafer et al. 2016|Shafer, A., JBW Wolf, PC Alves, L Bergström, G Colling, L Dalén, et al. (2016) Reply to Garner et al.]] [[Trends in Ecology & Evolution]] 31 (2), 83-84. doi:10.1016/j.tree.2015.11.010
  
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[[Shafer et al. 2015|Shafer, A. B. A., J. B. W. Wolf, P. C. Alves, L. Bergström, M. W. Bruford, I. Brännström, et al. (2015) Genomics and the challenging translation into conservation practice.]] [[Trends in Ecology & Evolution]] 30 (2), 78-87. doi:10.1016/j.tree.2014.11.009
+
[[Stemshorn et al. 2011|Stemshorn, K. C., F. A. Reed, A. W. Nolte, and D. Tautz. (2011) Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.).]] [[Molecular Ecology]] 20: 1475-1491. doi:10.1111/j.1365-294X.2010.04997.x
  
 
[[Tabios et al. 2014|Tabios, M., L. Boell, and F. A. Reed. (2014) A new mutation of PDA synthase, sepia, isolated from wild Drosophila melanogaster.]] [[Drosophila Information Service]] 97: 176-177.
 
[[Tabios et al. 2014|Tabios, M., L. Boell, and F. A. Reed. (2014) A new mutation of PDA synthase, sepia, isolated from wild Drosophila melanogaster.]] [[Drosophila Information Service]] 97: 176-177.
 
http://www.ou.edu/journals/dis/DIS97/Tabios%20176.pdf
 
http://www.ou.edu/journals/dis/DIS97/Tabios%20176.pdf
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[[Tishkoff et al. 2007|Tishkoff, S. A., F. A. Reed, A. Ranciaro, B. F. Voight, C. C. Babbitt, et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe.]] [[Nature Genetics]] 39: 31-40. doi:10.1038/ng1946
 +
 +
[[Tishkoff et al. 2008|Tishkoff, S. A., M. K. Gonder, B. M. Henn, H. M. Mortensen, N. Fernandopulle, et al. (2007) History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation.]] [[Molecular Biology and Evolution]] 24: 2180-2195. doi:10.1093/molbev/msm155
 +
 +
[[Tishkoff et al. 2009|Tishkoff, S. A., F. A. Reed, F. R. Friedlaender, C. Ehret, A. Ranciaro, et al. (2009) The Genetic Structure and History of Africans and African Americans.]] [[Science]] 324: 1035-1044. doi:10.1126/science.1172257
  
 
[[Traulsen and Reed 2012|Traulsen, A. and F. A. Reed. (2012) From genes to games: Cooperation and cyclic dominance of meiotic drive alleles.]] [[Journal of Theoretical Biology]] 299: 120-125. doi:10.1016/j.jtbi.2011.04.032
 
[[Traulsen and Reed 2012|Traulsen, A. and F. A. Reed. (2012) From genes to games: Cooperation and cyclic dominance of meiotic drive alleles.]] [[Journal of Theoretical Biology]] 299: 120-125. doi:10.1016/j.jtbi.2011.04.032

Revision as of 10:36, 26 July 2018

Allaby, R. G., F. R. Friedlaender, F. A. Reed, K. K. Kidd, J. R. Kidd, et al. (2010) Prehistoric Pacific Population Movements. pp. 143-157 in The Global Origins and Developments of Seafaring. A. Anderson, J. H. Barrett & K. V. Boyle, Eds., ISBN: 978-1-902937-52-6, McDonald Institute for Archaeological Research, Cambridge, UK.

Altrock, P. M., A. Traulsen, R. G. Reeves, and F. A. Reed. (2010) Using underdominance to bi-stably transform local populations. Journal of Theoretical Biology 267: 62-75. doi:10.1016/j.jtbi.2010.08.004

Altrock, P. M., A. Traulsen, and F. A. Reed. (2011) Stability Properties of Underdominance in Finite Subdivided Populations. PLoS Computational Biology 7: e1002260. doi:10.1371/journal.pcbi.1002260

Aquadro, C. F., V. L. Bauer DuMont and F. A. Reed. (2001) Genome-wide variation in the human and fruitfly: a comparison. Current Opinion in Genetics & Development 11: 627-634. doi:10.1016/S0959-437X(00)00245-8

Bryk, J., Reeves, R. G., Reed, F. A., & Denton, J. A. (2017). Transcriptional effects of a positive feedback circuit in Drosophila melanogaster. BMC Genomics, 18(1), 990; https://doi.org/10.1186/s12864-017-4385-z

Friedlaender, J. S., F. R. Friedlaender, F. A. Reed, K. K. Kidd, J. R. Kidd, et al. (2008) The Genetic Structure of Pacific Islanders. PLoS Genetics 4: e19. doi:10.1371/journal.pgen.0040019

Gokhale, C., R. G. Reeves, and F. A. Reed. (2014) Dynamics of a combined medea-underdominant population transformation system. BMC Evolutionary Biology 14: 90. doi:10.1186/1471-2148-14-98

Gonder, M. K., H. M. Mortensen, F. A. Reed, A. de Sousa and S. A. Tishkoff. (2007) Whole mtDNA Genome Sequence Analysis of Ancient African Lineages. Molecular Biology and Evolution 24: 757-768. doi:10.1093/molbev/msl209

Haubold, B., F. A. Reed and P. Pfaffelhuber. (2011) Alignment-free estimation of nucleotide diversity. Bioinformatics 27: 449-455. doi:10.1093/bioinformatics/btq689

Kontanis, E. J. and F. A. Reed. (2006) Evaluation of real-time PCR amplification effciencies to detect inhibitors. Journal of Forensic Sciences 51: 795-804. doi:10.1111/j.1556-4029.2006.00182.x

Láruson, Á. J. (2017). Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora. Ecology and Evolution, 7(13), 4543-4551. https://doi.org/10.1002/ece3.3042

Láruson, Á. J., & Reed, F. A. (2016). Stability of underdominant genetic polymorphisms in population networks. Journal of Theoretical Biology, 390, 156-163; https://doi.org/10.1016/j.jtbi.2015.11.023

Láruson, Á. J., Coppard, S. E., Pespeni, M. H., & Reed, F. A. (2018). Gene expression across tissues, sex, and life stages in the sea urchin Tripneustes gratilla [Toxopneustidae, Odontophora, Camarodonta]. bioRxiv, 284224; doi: https://doi.org/10.1101/284224

Milinski, M., R. Sommerfeld, H.-J. Krambeck, F. A. Reed and J. Marotzke. (2008) The collective risk social dilemma, and the prevention of simulated dangerous climate change. Proceedings of the National Academy of Sciences USA 105: 2291-2294. doi:10.1073/pnas.0709546105

Reed, F. A. (2004) Characterizing Diversity Reducing Selection in Humans and Fruitflies. Ph.D. Dissertation, Cornell University, Ithaca, NY. http://wwwlib.umi.com/dissertations/fullcit/3149436

Reed, F. A. (2007) Two-locus epistasis with sexually antagonistic selection: A genetic Parrondo’s paradox. Genetics 176: 1923-1929. doi:10.1534/genetics.106.069997

Reed, F. A. (2008) Are Humans Still Evolving? In Encyclopedia of Life Sciences: Handbook of Human Molecular Evolution, D. N. Cooper & H. Kehrer-Sawatzki, Eds., John Wiley & Sons, Ltd., Chichester, UK. http://www.els.net doi:10.1002/9780470015902.a0020794

Reed, F. A. (2012). Modern Human Migrations: The First 200,000 Years. In Migrations: Interdisciplinary Perspectives (pp. 315-326). Springer, Vienna.

Reed, F. A. and C. F. Aquadro. (2006) Mutation, selection and the future of human evolution. Trends in Genetics 22: 479-484. doi:10.1016/j.tig.2006.07.005

Reed, F. A. and S. A. Tishkoff. (2006) Positive selection can create false hotspots of recombination. Genetics 172: 2011-2014. doi:10.1534/genetics.105.052183

Reed, F. A. and S. A. Tishkoff. (2006) African human diversity, origins and migrations. Current Opinion in Genetics & Development 16: 597-605. doi:10.1016/j.gde.2006.10.008

Reed, F. A., E. J. Kontanis, K. A. R. Kennedy and C. F. Aquadro. (2003) Ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern. American Journal of Physical Anthropology 121: 112-116. doi:10.1002/ajpa.10211

Reed, F. A., J. M. Akey and C. F. Aquadro. (2005) Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes. Genome Research 15: 1211-1221. doi:10.1101/gr.3413205

Reed, F. A., R. G. Reeves and C. F. Aquadro. (2005) Evidence of susceptibility and resistance to cryptic X-linked meiotic drive in natural populations of Drosophila melanogaster. Evolution 59: 1280-1291. doi:10.1111/j.0014-3820.2005.tb01778.x

Reed, F. A., A. Traulsen, P. M. Altrock (2013) Underdominance. In “Encyclopedia of Genetics” S. Brenner & J. H. Miller Eds., Elsevier Science Inc. doi:10.1016/B978-0-12-374984-0.01601-6

Reeves, R. G., J. Denton, F. Santucci, J. Bryk, and F. A. Reed. (2012) Scientific Standards and the Regulation of Genetically Modified Insects. PLoS Neglected Tropical Diseases 6: e1502. doi:10.1371/journal.pntd.0001502

Reeves, R. G., J. Bryk, P. M. Altrock, J. Denton, and F. A. Reed. (2014) First Steps towards Underdominant Genetic Transformation of Insect Populations. PLoS ONE 9: e97557. doi:10.1371/journal.pone.0097557

Shafer, A. B. A., J. B. W. Wolf, P. C. Alves, L. Bergström, M. W. Bruford, I. Brännström, et al. (2015) Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution 30 (2), 78-87. doi:10.1016/j.tree.2014.11.009

Shafer, A., JBW Wolf, PC Alves, L Bergström, G Colling, L Dalén, et al. (2016) Reply to Garner et al. Trends in Ecology & Evolution 31 (2), 83-84. doi:10.1016/j.tree.2015.11.010

Stemshorn, K. C., F. A. Reed, A. W. Nolte, and D. Tautz. (2011) Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.). Molecular Ecology 20: 1475-1491. doi:10.1111/j.1365-294X.2010.04997.x

Tabios, M., L. Boell, and F. A. Reed. (2014) A new mutation of PDA synthase, sepia, isolated from wild Drosophila melanogaster. Drosophila Information Service 97: 176-177. http://www.ou.edu/journals/dis/DIS97/Tabios%20176.pdf

Tishkoff, S. A., F. A. Reed, A. Ranciaro, B. F. Voight, C. C. Babbitt, et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics 39: 31-40. doi:10.1038/ng1946

Tishkoff, S. A., M. K. Gonder, B. M. Henn, H. M. Mortensen, N. Fernandopulle, et al. (2007) History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation. Molecular Biology and Evolution 24: 2180-2195. doi:10.1093/molbev/msm155

Tishkoff, S. A., F. A. Reed, F. R. Friedlaender, C. Ehret, A. Ranciaro, et al. (2009) The Genetic Structure and History of Africans and African Americans. Science 324: 1035-1044. doi:10.1126/science.1172257

Traulsen, A. and F. A. Reed. (2012) From genes to games: Cooperation and cyclic dominance of meiotic drive alleles. Journal of Theoretical Biology 299: 120-125. doi:10.1016/j.jtbi.2011.04.032

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