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How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome.

Nery MF, González DJ, Opazo JC.

PLoS One. 2013 Jun 19;8(6):e65491. Print 2013.


Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins.

Sun YB, Zhou WP, Liu HQ, Irwin DM, Shen YY, Zhang YP.

Genome Biol Evol. 2013;5(1):130-9. doi: 10.1093/gbe/evs123.


Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown.

McGowen MR, Grossman LI, Wildman DE.

Proc Biol Sci. 2012 Sep 22;279(1743):3643-51. doi: 10.1098/rspb.2012.0869. Epub 2012 Jun 27.


Adaptive evolution of the osmoregulation-related genes in cetaceans during secondary aquatic adaptation.

Xu S, Yang Y, Zhou X, Xu J, Zhou K, Yang G.

BMC Evol Biol. 2013 Sep 9;13:189. doi: 10.1186/1471-2148-13-189.


Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

Shen T, Xu S, Wang X, Yu W, Zhou K, Yang G.

BMC Evol Biol. 2012 Mar 24;12:39. doi: 10.1186/1471-2148-12-39.


Positive selection on the H3 hemagglutinin gene of human influenza virus A.

Bush RM, Fitch WM, Bender CA, Cox NJ.

Mol Biol Evol. 1999 Nov;16(11):1457-65.


The molecular signature of selection underlying human adaptations.

Harris EE, Meyer D.

Am J Phys Anthropol. 2006;Suppl 43:89-130. Review.


Natural selection on functional modules, a genome-wide analysis.

Serra F, Arbiza L, Dopazo J, Dopazo H.

PLoS Comput Biol. 2011 Mar;7(3):e1001093. doi: 10.1371/journal.pcbi.1001093. Epub 2011 Mar 3.


Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.

Arbiza L, Dopazo J, Dopazo H.

PLoS Comput Biol. 2006 Apr;2(4):e38. Epub 2006 Apr 28.


Adaptive evolution of 5'HoxD genes in the origin and diversification of the cetacean flipper.

Wang Z, Yuan L, Rossiter SJ, Zuo X, Ru B, Zhong H, Han N, Jones G, Jepson PD, Zhang S.

Mol Biol Evol. 2009 Mar;26(3):613-22. doi: 10.1093/molbev/msn282. Epub 2008 Dec 10.


Genome-wide scan for bats and dolphin to detect their genetic basis for new locomotive styles.

Shen YY, Zhou WP, Zhou TC, Zeng YN, Li GM, Irwin DM, Zhang YP.

PLoS One. 2012;7(11):e46455. doi: 10.1371/journal.pone.0046455. Epub 2012 Nov 6.


Codon-substitution models for heterogeneous selection pressure at amino acid sites.

Yang Z, Nielsen R, Goldman N, Pedersen AM.

Genetics. 2000 May;155(1):431-49.


Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.

Campanaro S, Treu L, Valle G.

BMC Evol Biol. 2008 Nov 13;8:313. doi: 10.1186/1471-2148-8-313.


Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter.

Lefébure T, Stanhope MJ.

Genome Res. 2009 Jul;19(7):1224-32. doi: 10.1101/gr.089250.108. Epub 2009 Mar 20.


Range-wide Yangtze freshwater dolphin expedition: The last chance to see Baiji?

Wang K, Wang D, Zhang X, Pfluger A, Barrett L.

Environ Sci Pollut Res Int. 2006 Oct;13(6):418-24.


Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.

Zhang J, Nielsen R, Yang Z.

Mol Biol Evol. 2005 Dec;22(12):2472-9. Epub 2005 Aug 17.


Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites.

Anisimova M, Yang Z.

Mol Biol Evol. 2007 May;24(5):1219-28. Epub 2007 Mar 5.


Detecting positive selection within genomes: the problem of biased gene conversion.

Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT.

Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2571-80. doi: 10.1098/rstb.2010.0007.

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