#NEXUS
begin mrbayes;

	set autoclose=yes nowarn=yes;
	
	execute Data_matrix_AV_CODING.nex;

	taxset fossils = Armadilleon_morticina Armadilleon_petrorum Armadilleon_petrorum Biamosa_barachek Crusopimpla_tadushiensis Crusopimpla_rediviva Crusopimpla_weltii Ebriosa_flava Eclytus_lutatus Madma_oisella Marjorietta_minor Palaeometopius_eocenicus Pappous_trichomatius Pherhombus_antennalis Pherhombus_brischkei Pherhombus_kraxtepellensis PHY_spnov1 PHY_spnov2 Rasnitsynites_tarsalis Thymaris_senilis Tobiasites_striatus Townesites_mandibularis Triclistus_bibori Zagryphus_tilloyi PHY_NHMD_876130 RHY_NHMB_2811 MET_DO_3441 TRY_NHMD_876111;
	taxset fossils_of_interest =  NHMD_876130 NHMB_2811 DO_3441 NHMD_876111;
	taxset fossils_except_cruso = Armadilleon_morticina Armadilleon_petrorum Armadilleon_petrorum Biamosa_barachek Ebriosa_flava Eclytus_lutatus Madma_oisella Marjorietta_minor Palaeometopius_eocenicus Pappous_trichomatius Pherhombus_antennalis Pherhombus_brischkei Pherhombus_kraxtepellensis PHY_spnov1 PHY_spnov2 Rasnitsynites_tarsalis Thymaris_senilis Tobiasites_striatus Townesites_mandibularis Triclistus_bibori Zagryphus_tilloyi PHY_NHMD_876130 RHY_NHMB_2811 MET_DO_3441 TRY_NHMD_876111;


[### partitions as copied from the PartionFinder results]

	charset Subset1 = 1-1249 5606-6280\3;						[#28S, H4RJC_1] 
	charset Subset2 = 1250-2042\3;								[#CO1_1 ]
	charset Subset3 = 1251-2042\3;								[#CO1_2 ]
	charset Subset4 = 1252-2042\3;								[#CO1_3 ]
	charset Subset5 = 2043-2599\3 5184-5605\3 3912-4276\3 3459-3910\3 5607-6280\3 4278-4732\3 4734-5182\3; [#CAD_1, G46_2, NSNS5_2, RC8_2, H4RJC_2, G23_2, G45_2]
	charset Subset6 = 4735-5182\3 2044-2599\3 2602-3073\3;		[#G45_3, CAD_2, 8DK_3 ]
	charset Subset7 = 2045-2599\3 4733-5182\3 4277-4732\3;		[#CAD_3, G45_1, G23_1 ]
	charset Subset8 = 2600-3073\3 5183-5605\3;  				[#8DK_1, G46_1 ]
	charset Subset9 = 2601-3073\3;								[#8DK_2 ]
	charset Subset10 = 3911-4276\3 3074-3457\3 3458-3910\3;		[#NSNS5_1, 161TS_1, RC8_1]
	charset Subset11 = 3075-3457\3;								[#161TS_2]
	charset Subset12 = 3076-3457\3 3460-3910\3 4279-4732\3;		[#161TS_3, RC8_3, G23_3 ]
	charset Subset13 = 3913-4276\3;								[#NSNS5_3]
	charset Subset14 = 5185-5605\3;								[#G46_3 ]
	charset Subset15 = 5608-6280\3;								[#H4RJC_3]
	charset morpho = 6281-6506;

[## 16 Partitions in total: 15 from PartitionFinder, plus 1 morphology]	
	partition all = 16:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7, Subset8, Subset9, Subset10, Subset11, Subset12, Subset13, Subset14, Subset15, morpho;
	set partition = all;


[### ordered characters:]				
	charset morpho_ordered =  6281 6282 6283 6284 6285 6286 6287 6288 6289 6290 6291 6292 6293 6294 6295 6296 6297 6298 6299 6300 6301 6302 6303 6304 6305 6306 6307 6308 6309 6310 6311 6312 6313 6314 6315 6316 6317 6318 6319 6320 6321 6322 6323 6324 6325 6326 6327 6328 6329 6330 6331 6332 6333 6334 6335 6336 6337 6338;
	ctype ordered : morpho_ordered;
	
	lset applyto=(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15) nst=mixed rates=invgamma;	
	lset applyto=(16) coding=variable rates=gamma;								
		
	prset applyto=(all) ratepr=variable;                                            
	unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);

[### running mcmc]
	mcmcp temp=0.05 nchain=4 samplefreq=1000 printfr=1000 checkfr=1000 nruns=4;  [### sets mcmc; 4 runs]
	mcmc ngen=20000000; [append=yes;] 	[mcmcp ngen=20000000; append=yes; ]
	
	sump burninfr=0.5;   		
	sumt burninfr=0.5 contype=halfcompat outputname = Comb_WITH_Fossils_halfcompat;  
	sumt burninfr=0.5 contype=allcompat outputname = Comb_WITH_Fossils_allcompat; 
 	
	delete fossils_of_interest 	[### deletes the 4 new fossils]
	sumt burninfr=0.5 contype=halfcompat outputname = Comb_without_4_Fossils_halfcompat;  
	sumt burninfr=0.5 contype=allcompat outputname = Comb_without_4_Fossils_allcompat;  
	
	delete fossils_except_cruso; [### deletes all fossils except Crusopimpla]
	sumt burninfr=0.5 contype=halfcompat outputname = Comb_without_Fossils_butCruso_halfcompat;  
	sumt burninfr=0.5 contype=allcompat outputname = Comb_without_Fossils_butCruso_allcompat; 
	
	delete fossils;				[### deletes all fossils]
	sumt burninfr=0.5 contype=halfcompat outputname = Comb_without_ALL_Fossils_halfcompat;  
	sumt burninfr=0.5 contype=allcompat outputname = Comb_without_ALL_Fossils_allcompat;
	
	end;