Difference between revisions of "Population Genetics"

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=Topics=
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*[[Population Division]]
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*[[Fluctuating Population Size and Genetic Drift]]
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*[[Coalescence]]
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*[[Mutation-Drift Equilibrium]]
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*[[Probability of fixation]]
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*[[Selection]]
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*[[Genetic Load]]
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*[[Selective Sweeps]]
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**https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607448/
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*[[ABBA BABA Test]]
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**http://evomics.org/learning/population-and-speciation-genomics/2018-population-and-speciation-genomics/abba-baba-statistics/
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**http://coleoguy.blogspot.com/2013/05/abba-baba.html
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**https://academic.oup.com/mbe/article/32/1/244/2925550
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**https://www.nature.com/articles/nrg3446
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*Detecting Selection
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**https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000304
  
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=ABBA BABA Test=
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=Notes=
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*https://onlinelibrary.wiley.com/doi/full/10.1046/j.1420-9101.2001.00303.x
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*https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894624/
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*https://www.biorxiv.org/content/early/2017/09/25/193425
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*https://www.jstor.org/stable/4621318
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*https://onlinelibrary.wiley.com/doi/full/10.1111/j.1558-5646.2007.00052.x
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*https://link.springer.com/article/10.1023/A:1024029432658
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*http://www.pnas.org/content/112/6/1662
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*https://academic.oup.com/biolinnean/article/98/3/501/2532218
  
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http://evomics.org/learning/population-and-speciation-genomics/2018-population-and-speciation-genomics/abba-baba-statistics/
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http://www.genetics.org/content/205/3/1003
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http://coleoguy.blogspot.com/2013/05/abba-baba.html
 
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https://academic.oup.com/mbe/article/32/1/244/2925550
 
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https://www.nature.com/articles/nrg3446
 
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=Reading=
 
  
 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448894/
 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448894/
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https://www.nature.com/subjects/population-genetics
 
https://www.nature.com/subjects/population-genetics
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https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00223-7
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Dobzhansky, T. (1955, January). A review of some fundamental concepts and problems of population genetics. In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 20, pp. 1-15). Cold Spring Harbor Laboratory Press.
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Chakravarti, A. (1999). Population genetics—making sense out of sequence. Nature genetics, 21(1s), 56.
 +
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Lanfear, R., Kokko, H., & Eyre-Walker, A. (2014). Population size and the rate of evolution. Trends in ecology & evolution, 29(1), 33-41.
 +
 +
Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285.
 +
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Charlesworth, B., & Charlesworth, D. (2017). Population genetics from 1966 to 2016. Heredity, 118(1), 2.
 +
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Casillas, S., & Barbadilla, A. (2017). Molecular population genetics. Genetics, 205(3), 1003-1035.
 +
 +
Schrider, D. R., & Kern, A. D. (2018). Supervised machine learning for population genetics: a new paradigm. Trends in Genetics.
 +
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Habel, J. C., Zachos, F. E., Dapporto, L., Roedder, D., Radespiel, U., Tellier, A., & Schmitt, T. (2015). Population genetics revisited–towards a multidisciplinary research field. Biological Journal of the Linnean Society, 115(1), 1-12. [https://watermark.silverchair.com/bij12481.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAa4wggGqBgkqhkiG9w0BBwagggGbMIIBlwIBADCCAZAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM1hcOBNja5dG7G4PhAgEQgIIBYd8I4ZJ_kSqRhYHFfa8W642UhMnoSA9fD3V8hPupYWWgGpsv85ZSz0zO3vq6fbesHLsJTrbrKGwN9OMFd5VZlY8DyEfhrje4MrNoRyq7VZVqQyRZSgSrysC9r1H506pX6B59qibMaZC5hOmJPA5lzg9kqeGHdnywvJWRCmW-c6xYdZFCO5oLAi4dIi5QHPk7Gkn-RvUoXJVThAwegq-emBVzhjM8hB2jvfbtzyCwrBIrhsUr1dz7a1m1C93nZi-fzC0rY437oeKc3uaZtSberz9y-r7jxVB9peT3GEiJV2lU0FMWl_vXbULMkHCaVew9H8rkwg0waLZzKtY8_ruS3rBARxWQ0SdebIV0Y76kOw2UF7qy2CYHFNGiQW6Y_HPrx70fRtPfoPMVWJXQhNj2Ojq-NA3sjqaMthNI7BgxLwgoLeBrKglwtrzzTiQUH5gGE70Wiw0-Cs2Z-pdbA3RmixLv]
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Dlugosch, K. M., Anderson, S. R., Braasch, J., Cang, F. A., & Gillette, H. D. (2015). The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Molecular ecology, 24(9), 2095-2111.
 +
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Cvijović, I., Ba, A. N. N., & Desai, M. M. (2018). Experimental Studies of Evolutionary Dynamics in Microbes. Trends in Genetics.
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[[Hardy 1908|Hardy, G. H. (1908) Mendelian Proportions in a mixed population. Science 28(706): 49-50.]]
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[[Haldane 1937|Haldane, J. B. S. (1937). The effect of variation of fitness. The American Naturalist, 71(735), 337-349.]]
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Under neutrality are small spikes of high diversity that contribute more to PC loading and tend to be shared between populations expected from older coalescent regions (and the high variance of the coalescent process) because there is more time for both mutation (high diversity), recombination (small regions), and gene flow or shared ancestry (found across populations)?
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https://www.quantamagazine.org/neutral-theory-of-evolution-challenged-by-evidence-for-dna-selection-20181108/
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=What Links Here=
 +
{{Special:WhatLinksHere/{{FULLPAGENAME}}}}

Latest revision as of 17:09, 9 November 2018

Topics

Notes

http://www.genetics.org/content/205/3/1003

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448894/

https://www.nature.com/articles/hdy201655

https://academic.oup.com/aobpla/article/doi/10.1093/aobpla/plv026/200461

https://onlinelibrary.wiley.com/doi/full/10.1111/mam.12052

https://www.nature.com/subjects/population-genetics

https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00223-7

Dobzhansky, T. (1955, January). A review of some fundamental concepts and problems of population genetics. In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 20, pp. 1-15). Cold Spring Harbor Laboratory Press.

Chakravarti, A. (1999). Population genetics—making sense out of sequence. Nature genetics, 21(1s), 56.

Lanfear, R., Kokko, H., & Eyre-Walker, A. (2014). Population size and the rate of evolution. Trends in ecology & evolution, 29(1), 33-41.

Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285.

Charlesworth, B., & Charlesworth, D. (2017). Population genetics from 1966 to 2016. Heredity, 118(1), 2.

Casillas, S., & Barbadilla, A. (2017). Molecular population genetics. Genetics, 205(3), 1003-1035.

Schrider, D. R., & Kern, A. D. (2018). Supervised machine learning for population genetics: a new paradigm. Trends in Genetics.

Habel, J. C., Zachos, F. E., Dapporto, L., Roedder, D., Radespiel, U., Tellier, A., & Schmitt, T. (2015). Population genetics revisited–towards a multidisciplinary research field. Biological Journal of the Linnean Society, 115(1), 1-12. [1]

Dlugosch, K. M., Anderson, S. R., Braasch, J., Cang, F. A., & Gillette, H. D. (2015). The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Molecular ecology, 24(9), 2095-2111.

Cvijović, I., Ba, A. N. N., & Desai, M. M. (2018). Experimental Studies of Evolutionary Dynamics in Microbes. Trends in Genetics.

Hardy, G. H. (1908) Mendelian Proportions in a mixed population. Science 28(706): 49-50.

Haldane, J. B. S. (1937). The effect of variation of fitness. The American Naturalist, 71(735), 337-349.

Under neutrality are small spikes of high diversity that contribute more to PC loading and tend to be shared between populations expected from older coalescent regions (and the high variance of the coalescent process) because there is more time for both mutation (high diversity), recombination (small regions), and gene flow or shared ancestry (found across populations)?

https://www.quantamagazine.org/neutral-theory-of-evolution-challenged-by-evidence-for-dna-selection-20181108/

What Links Here

Retrieved from "http://hawaiireedlab.com/labwiki/index.php?title=Population_Genetics&oldid=1798"