I have used the codeml, Paml to calculate the dn/ds for CCR genes from eurosids I and eurosid II. Branch model was used to detected the dn/ds for eurosid I and eurosid II. My tree file is as followed:
eurosid I was labeled:
((((((((((GMCCR3:0.02582438,GMCCR4:0.02675515):1.0000:0.05577668,(LJCCR:0.12328497,MTCCR1:0.08238538):0.5600:0.02113965):0.4440:0.02082863,(MTCCR2:0.16763916,(GMCCR1:0.03579333,GMCCR2:0.02407780):1.0000:0.06137924):0.8080:0.04503114):1.0000:0.10174445,(CLCCR6:0.14157313,(CLCCR3:0.02017909,(CLCCR2:0.02541275,(CLCCR4:0.04626749,CLCCR5:0.03035711):0.5280:0.00751061):0.3820:0.00278782):0.9980:0.07102660):1.0000:0.14319834):0.6100:0.03483046,(((MECCR1:0.14586705,MECCR2:0.04392616):0.6080:0.01391169,RCCCR:0.06862493):0.8520:0.03921974,(PTCCR6:0.05558522,((PTCCR4:0.00221847,PTCCR5:0.00434989):0.9480:0.01007720,(PTCCR2:0.01542710,(PTCCR1:0.00252632,PTCCR3:0.00073382):0.8960:0.00837029):0.9980:0.02960551):0.9980:0.03946824):0.9940:0.04163838):0.7700:0.02494774):0.4380:0.01384928,(CPCCR:0.18585226,CSCCR:0.09556386):0.1460:0.00824786):0.1220:0.00935932,((MDCCR1:0.01346009,MDCCR2:0.04686282):1.0000:0.04564256,(PPECCR1:0.07772828,PPECCR2:0.02653864):1.0000:0.05468761):0.9300:0.04860845):0.3600:0.01812053,FVCCR:0.13690345)#1:0.4260:0.01616605,(((((BRCCR3:0.03658894,TPCCR2:0.02700440):0.4060:0.00212783,BRCCR1:0.04196917):0.9760:0.03214981,ATCCR2:0.03327158):0.4040:0.00370350,CRUCCR2:0.03499411):1.0000:0.11075167,(CRUCCR1:0.04888622,((ALCCR:0.01975692,ATCCR1:0.02858721):0.8840:0.01990057,(TPCCR1:0.01910029,(BRCCR2:0.04227218,BRCCR4:0.03024930):0.6280:0.00899337):0.6520:0.00798847):0.6620:0.01263573):0.9840:0.04930956):1.0000:0.14029092):0.4700:0.01371471,(CLCCR1:0.02812017,CMCCR:0.03148548):1.0000:0.12771266,(ZMCCR2:0.34876751,(OSCCR1:0.08236509,(OSCCR2:0.04618675,ZMCCR1:0.07821228):0.6300:0.02162819):0.9480:0.10456098):1.0000:0.12396680);
eurosid II was labeled:
((((((((((GMCCR3:0.02582438,GMCCR4:0.02675515):1.0000:0.05577668,(LJCCR:0.12328497,MTCCR1:0.08238538):0.5600:0.02113965):0.4440:0.02082863,(MTCCR2:0.16763916,(GMCCR1:0.03579333,GMCCR2:0.02407780):1.0000:0.06137924):0.8080:0.04503114):1.0000:0.10174445,(CLCCR6:0.14157313,(CLCCR3:0.02017909,(CLCCR2:0.02541275,(CLCCR4:0.04626749,CLCCR5:0.03035711):0.5280:0.00751061):0.3820:0.00278782):0.9980:0.07102660):1.0000:0.14319834):0.6100:0.03483046,(((MECCR1:0.14586705,MECCR2:0.04392616):0.6080:0.01391169,RCCCR:0.06862493):0.8520:0.03921974,(PTCCR6:0.05558522,((PTCCR4:0.00221847,PTCCR5:0.00434989):0.9480:0.01007720,(PTCCR2:0.01542710,(PTCCR1:0.00252632,PTCCR3:0.00073382):0.8960:0.00837029):0.9980:0.02960551):0.9980:0.03946824):0.9940:0.04163838):0.7700:0.02494774):0.4380:0.01384928,(CPCCR:0.18585226,CSCCR:0.09556386):0.1460:0.00824786):0.1220:0.00935932,((MDCCR1:0.01346009,MDCCR2:0.04686282):1.0000:0.04564256,(PPECCR1:0.07772828,PPECCR2:0.02653864):1.0000:0.05468761):0.9300:0.04860845):0.3600:0.01812053,FVCCR:0.13690345):0.4260:0.01616605,(((((BRCCR3:0.03658894,TPCCR2:0.02700440):0.4060:0.00212783,BRCCR1:0.04196917):0.9760:0.03214981,ATCCR2:0.03327158):0.4040:0.00370350,CRUCCR2:0.03499411):1.0000:0.11075167,(CRUCCR1:0.04888622,((ALCCR:0.01975692,ATCCR1:0.02858721):0.8840:0.01990057,(TPCCR1:0.01910029,(BRCCR2:0.04227218,BRCCR4:0.03024930):0.6280:0.00899337):0.6520:0.00798847):0.6620:0.01263573):0.9840:0.04930956)#1:1.0000:0.14029092):0.4700:0.01371471,(CLCCR1:0.02812017,CMCCR:0.03148548):1.0000:0.12771266,(ZMCCR2:0.34876751,(OSCCR1:0.08236509,(OSCCR2:0.04618675,ZMCCR1:0.07821228):0.6300:0.02162819):0.9480:0.10456098):1.0000:0.12396680);
Results are shown in attached file.
I wonder how to interpret the results?it seems that eurosid II and I experience different selective pressure since p
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