Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes).
Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae)). Gene evolutionary analyses indicated that MC1R in loaches was under purifying selection pressure, with various sites having different dN/dS values. Both Botiidae and Cobitidae had lower dN/dS values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoridae and Nemacheilidae, both had larger dN/dS values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MC1R gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. tangqy@ihb.ac.cn.
Qiong-Ying
QY
Tang
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;University of Chinese Academy of Sciences, Beijing 100049, China.
Li-Xia
LX
Shi
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
Fei
F
Liu
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
Dan
D
Yu
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. tangqy@ihb.ac.cn;hzliu@ihb.ac.cn.
Huan-Zhang
HZ
Liu
D000818:Animals; D003531:Cypriniformes / Q000235:genetics*; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics*; D010802:Phylogeny; D044102:Receptor, Melanocortin, Type 1 / Q000235:genetics*
D029941:Fish Proteins; D044102:Receptor, Melanocortin, Type 1
Cobitoidea; Gene evolution; Melanocortin 1 receptor gene; Molecular phylogeny
Proc Biol Sci. 2006 Jul 7;273(1594):1613-8
16769631
BMC Evol Biol. 2007 Mar 20;7:44
17374158
Cell Mol Life Sci. 2010 Aug;67(15):2591-603
20229234
Curr Biol. 2003 Dec 16;13(24):R947-50
14680649
Mol Phylogenet Evol. 2006 May;39(2):529-41
16337410
J Hered. 2012 May-Jun;103(3):322-9
22351934
Mol Phylogenet Evol. 2013 Jun;67(3):621-5
23499612
Front Genet. 2013 Jan 25;4:6
23355846
Bioinformatics. 2003 Aug 12;19(12):1572-4
12912839
Proc Biol Sci. 2005 Aug 22;272(1573):1633-40
16087416
Trends Genet. 2010 May;26(5):231-9
20381892
Mol Biol Evol. 2013 Dec;30(12):2725-9
24132122
Mol Biol Evol. 2007 Aug;24(8):1586-91
17483113
J Fish Biol. 2009 Dec;75(9):2197-208
20738682
Mol Biol Evol. 2005 Apr;22(4):1107-18
15689528
J Mol Evol. 2010 May;70(5):405-12
20449580
Gene. 2013 Jan 25;513(2):282-6
23116942
Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
9396791
Gene. 2012 Oct 15;508(1):60-72
22868207
Bioinformatics. 2014 May 1;30(9):1312-3
24451623
Syst Biol. 2003 Oct;52(5):696-704
14530136
Mol Phylogenet Evol. 2009 Jun;51(3):500-14
19141325
PLoS Genet. 2009 Jan;5(1):e1000326
19119422
Mol Phylogenet Evol. 2006 May;39(2):347-57
16213167
Genet Mol Biol. 2012 Jan;35(1):81-7
22481878
Gene. 2007 Oct 15;401(1-2):114-22
17707598
Mol Phylogenet Evol. 2011 Dec;61(3):739-49
21708276
Mol Biol Evol. 2013 Jul;30(7):1720-8
23564938
Nucleic Acids Res. 1997 Nov 15;25(22):4692-3
9358185
Mol Phylogenet Evol. 2009 Aug;52(2):550-7
19303453
J Evol Biol. 2011 Oct;24(10):2289-98
21812853
Evolution. 2004 Aug;58(8):1794-808
15446431
Nat Methods. 2012 Jul 30;9(8):772
22847109
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
Mol Phylogenet Evol. 2007 Sep;44(3):1358-65
17433724
Comput Appl Biosci. 1996 Dec;12(6):543-8
9021275