Evolutionary determinants of genome-wide nucleotide composition

Hongan Long; Way Sung; Sibel Kucukyildirim; Emily Williams; Samuel F. Miller; Wanfeng Guo; Caitlyn Patterson; Colin Gregory; Chloe Strauss; Casey Stone; Cécile Berne; David Kysela; William R. Shoemaker; Mario E. Muscarella; Haiwei Luo; Jay T. Lennon; Yves V. Brun; Michael Lynch

doi:10.1038/s41559-017-0425-y

Evolutionary determinants of genome-wide nucleotide composition

Hongan Long, Way Sung, Sibel Kucukyildirim, Emily Williams, Samuel F. Miller, Wanfeng Guo, Caitlyn Patterson, Colin Gregory, Chloe Strauss, Casey Stone, Cécile Berne, David Kysela, William R. Shoemaker, Mario E. Muscarella, Haiwei Luo, Jay T. Lennon, Yves V. Brun, Michael Lynch

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Abstract

One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G + C versus A + T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. We demonstrate that although genomic G + C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G + C composition at fourfold redundant sites is consistently elevated above the neutral expectation - more so than for any other class of sites.

Original language	English (US)
Pages (from-to)	237-240
Number of pages	4
Journal	Nature Ecology and Evolution
Volume	2
Issue number	2
DOIs	https://doi.org/10.1038/s41559-017-0425-y
State	Published - Feb 1 2018

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Ecology

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Long, H., Sung, W., Kucukyildirim, S., Williams, E., Miller, S. F., Guo, W., Patterson, C., Gregory, C., Strauss, C., Stone, C., Berne, C., Kysela, D., Shoemaker, W. R., Muscarella, M. E., Luo, H., Lennon, J. T., Brun, Y. V., & Lynch, M. (2018). Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology and Evolution, 2(2), 237-240. https://doi.org/10.1038/s41559-017-0425-y

Long, H, Sung, W, Kucukyildirim, S, Williams, E, Miller, SF, Guo, W, Patterson, C, Gregory, C, Strauss, C, Stone, C, Berne, C, Kysela, D, Shoemaker, WR, Muscarella, ME, Luo, H, Lennon, JT, Brun, YV & Lynch, M 2018, 'Evolutionary determinants of genome-wide nucleotide composition', Nature Ecology and Evolution, vol. 2, no. 2, pp. 237-240. https://doi.org/10.1038/s41559-017-0425-y

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abstract = "One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G + C versus A + T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. We demonstrate that although genomic G + C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G + C composition at fourfold redundant sites is consistently elevated above the neutral expectation - more so than for any other class of sites.",

author = "Hongan Long and Way Sung and Sibel Kucukyildirim and Emily Williams and Miller, {Samuel F.} and Wanfeng Guo and Caitlyn Patterson and Colin Gregory and Chloe Strauss and Casey Stone and C{\'e}cile Berne and David Kysela and Shoemaker, {William R.} and Muscarella, {Mario E.} and Haiwei Luo and Lennon, {Jay T.} and Brun, {Yves V.} and Michael Lynch",

note = "Funding Information: Support was provided by the Multidisciplinary University Research Initiative awards W911NF-09-1-0444 and W911NF-14-1-0411 from the US Army Research Office to M.L., National Institutes of Health awards R01-GM036827 and R35-GM122566 to M.L., National Natural Science Foundation of China 31741071 to H.L., R01-GM51986 and R35-GM122556 to Y.V.B., F32-GM083581 to D.T.K. and National Science Foundation grant DOB 1442246 to J.T.L. We thank T. G. Doak, P. Keightley, K. Morris, R. Ness, I. Ruiz-Trillo, S. Simpson, W. K. Thomas, A. Uchimura and Z. Ye for providing strains and/ or technical help in data acquisition. We thank L. Duret for helpful comments. Publisher Copyright: {\textcopyright} 2017 The Author(s).",

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AU - Sung, Way

AU - Kucukyildirim, Sibel

AU - Williams, Emily

AU - Miller, Samuel F.

AU - Guo, Wanfeng

AU - Patterson, Caitlyn

AU - Gregory, Colin

AU - Strauss, Chloe

AU - Stone, Casey

AU - Berne, Cécile

AU - Kysela, David

AU - Shoemaker, William R.

AU - Muscarella, Mario E.

AU - Luo, Haiwei

AU - Lennon, Jay T.

AU - Brun, Yves V.

AU - Lynch, Michael

N1 - Funding Information: Support was provided by the Multidisciplinary University Research Initiative awards W911NF-09-1-0444 and W911NF-14-1-0411 from the US Army Research Office to M.L., National Institutes of Health awards R01-GM036827 and R35-GM122566 to M.L., National Natural Science Foundation of China 31741071 to H.L., R01-GM51986 and R35-GM122556 to Y.V.B., F32-GM083581 to D.T.K. and National Science Foundation grant DOB 1442246 to J.T.L. We thank T. G. Doak, P. Keightley, K. Morris, R. Ness, I. Ruiz-Trillo, S. Simpson, W. K. Thomas, A. Uchimura and Z. Ye for providing strains and/ or technical help in data acquisition. We thank L. Duret for helpful comments. Publisher Copyright: © 2017 The Author(s).

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Evolutionary determinants of genome-wide nucleotide composition

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