#NEXUS
BEGIN TAXA;
	DIMENSIONS NTAX=32;
	TAXLABELS
		Porifera Placozoa Xenacoelomorpha Echinodermata Enteropneusta Vertebrata Bryozoa Brachiopoda Phoronida Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Gastrotricha Gnathostomulida Micrognathozoa Chaetognatha Rotifera Nemertea Onychophora Arthropoda Tardigrada Nematoda Nematomorpha Priapulida Kinorhyncha Loricifera Ctenophora Anthozoa Medusozoa Saccorhytus
	;
END;
BEGIN CHARACTERS;
	DIMENSIONS NCHAR=134;
	FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="012345" INTERLEAVE=YES;
MATRIX
Porifera	1(01)0010(01)0--000-0000--0----000-0--00000-0--00000-----00-00-010(01)00000-?0-00000000000000000-0000(01)00000000000---0---00000------1---0000--0-
Placozoa	1?001000--100-1000--0-0--000-0--00000-0--00000-----00-00?100000000-?0-0000000000000000000111001000000000---0---00000------1---0000--0-
Xenacoelomorpha  	100?1?(01)111111110000-0-0-0000-0?000000-0-0000000000011000-100000000-00-0000100000000000001001111001000000---0---00000-----010-?0000--0-
Echinodermata 	11001111101011100010110-00000000000001111000110000011000-100000000-00-0000000010000000001001111000000000---0---00000-----0100-00001010
Enteropneusta 	11011111101011100010110-00000010000001111101110000011000-100000000-00-0000000010000000001001111000000000---0---00000-----0100000001010
Vertebrata	10111111101011100010110-00000000000001(01)11110001111111000-100000000-00-0000000010000000001001111000000000---0---00000-----0100-00001010
Bryozoa  	11011111101011100011100-00000000000000000000000000011000-100000000-00-0000000010000?000010011110000000111001---0011110110-110-00011011
Brachiopoda	110111111010111000(01)11(01)0-00000000000000010000000000011000-100000000-00-00000000(01)0000?000010011110000000111010---0011111111-101-00011110
Phoronida 	11011111101011110011100-00000000000000010000000000011000-100000000-00-0001000010000?00001001111000000000---0---0001111111-101-00011110
Annelida  	110111111010111100101(012)0-00000110000100000000000000011000-100000000-00-00010000110011000010011110010101111010---00110-----1110100011111
Sipuncula	110111111010111100111?0-0000?010000100000000000000011000-100000000-00-0001000011001100001001111000010110---0---00110-----1110000011111
Mollusca 	110111111010111100101(012)(01)000000010000100000000000000011000-100000000-00-00010000110011000010011110011100110(01)01---11110-----1110100011010
Entoprocta	1101111110101111001110100000-0000001000-0000000000011000-100000000-00-0001000010000100001001111001110010---0---00010-----111--00010-11
Platyhelminthes 	1101111110101111000-000-0000-0100001000-0000000000011000-100000000-00-000000000000010000100111100101-000---0---00000-----111-100010-11
Gastrotricha	11011111101011100010100-0000-0100000000-0000000000011000-100000000-00-0001000010100100001001111001000000---0---00000-----111-100010-0-
Gnathostomulida	110111111010111100101?0-0000-0100000000-0000000000011000-100000000-00-0000000010000100001001111001001000---111100000-----110-110010-0-
Micrognathozoa	1??????1?0?0111?00101?0-0000-01000000??-0000000000011000-100000000-00-000000001?000100001001111?010?1000---1?1100000-----11?-111110-??
Chaetognatha	11011111101011100010110-00000010000001000000000000011000-100000000-00-0001000010000100001001111110000000---100000000-----110010000100-
Rotifera	1101111110101110001?1?0-000000100001000-0000000000011000-100000000-00-0000000010000100001001111110001?10---111100000-----110-111110-0-
Nemertea	110111111010111100101(01)0-00000010000100000000000000011000-100000000-00-0000000010000100001001111001010000---0-??00000-----1110100011011
Onychophora	11011111101011100010121111111010001010000000000000011000-100000000-00-0001110010110011101001111---000000---0-??00000-----00--10000100-
Arthropoda	111111111010111000101(01)11100(01)1110001010000000000000011000-100000000-00-0001110010110011101001111---000000---0-??00000-----00--10000100-
Tardigrada 	11011111101011100010101111001010001000000000000000011000-100000000-00-0001110010110011101001111---000000---0-??00000-----00-010000100-
Nematoda	1101111110101110001010101000-0111010000-0000000000011000-100000000-00-0001110010110010111001111---000000---0-??00000-----00--000000-0-
Nematomorpha	1101111110101110001011101000-0101010000-0000000000011000-100000000-00-0001110010110010111001111---000000---0-??00000-----00--000000-0-
Priapulida	1101111110101110001011111000-0111110000-0000000000011000-100000000-00-000111101011?010101001111---000000---0-??00000-----00--000000-0-
Kinorhyncha 	110111111010111000101?101000-0111110000-0000000000011000-100000000-00-000111101011?010101001111---000?00---0-??00000-----00--000000-0-
Loricifera	110111111010111000101?101000-0111110000-0000000000011000-100000000-00-000111111011?010101001111---000?00---0-??00000-----00--100000-0-
Ctenophora	100111111100101011100-0-0000-00000000-0-00000000000??1111100000000-00-00000000?0000000001001111000000000---0---00000------0---00000-10
Anthozoa	1101111101101010010-0-0-0000-00000000-0-0000000000011(01)101101011001(01)1100(01)(01)0000000000000001001111000000000---0---00000------1---00000-10
Medusozoa	1101111101101010010-0-0-0000-00000000-0-0000000000000210(01)101100111(01)1111000000000000000001001111000000000---0---00000------1---00000-10
Saccorhytus	1?????11????1?0???0??????0?0?0??00??????0??????????110???????????????????11-0-0????01???1???1110000????0---?---??000??????00??????????;
End;
begin mrbayes;
	set autoclose = yes nowarn = yes;
	lset nst = 6 rates = invgamma;
	unlink statefreq = ( all ) revmat = ( all ) shape = ( all ) pinvar = ( all );
	prset applyto = ( all ) ratepr = variable;
	outgroup Porifera;
	constraint one = Brachiopoda Phoronida;
	constraint two = Brachiopoda Phoronida Bryozoa;
	constraint three = Annelida Sipuncula;
	constraint four = Annelida Sipuncula Mollusca;
	constraint five = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca;
	constraint six = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta;
	constraint seven = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes;
	constraint eight = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea;
	constraint nine = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha;
	constraint ten = Micrognathozoa Rotifera;
	constraint eleven = Micrognathozoa Rotifera Gnathostomulida;
	constraint twelve = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida;
	constraint thirteen = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha;
	constraint fourteen = Kinorhyncha Loricifera;
	constraint fourteentwo = Priapulida Kinorhyncha Loricifera;
	constraint fifteen = Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha;
	constraint sixteen = Onychophora Arthropoda;
	constraint seventeen = Onychophora Arthropoda Tardigrada;
	constraint eighteen = Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada;
	constraint nineteen = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada;
	constraint twenty = Echinodermata Enteropneusta;
	constraint twentyone = Echinodermata Enteropneusta Vertebrata;
	constraint twentytwo = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada Echinodermata Enteropneusta Vertebrata;
	constraint twentythree = Anthozoa Medusozoa;
	constraint twentyfour = Anthozoa Medusozoa Saccorhytus Ctenophora;
	constraint twentyfive = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada Echinodermata Enteropneusta Vertebrata Anthozoa Medusozoa Saccorhytus Ctenophora;
	constraint twentysix = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada Echinodermata Enteropneusta Vertebrata Anthozoa Medusozoa Saccorhytus Ctenophora Xenacoelomorpha;
	constraint twentyseven = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada Echinodermata Enteropneusta Vertebrata Anthozoa Medusozoa Saccorhytus Ctenophora Xenacoelomorpha Placozoa;
	constraint twentyeight = Brachiopoda Phoronida Bryozoa Annelida Sipuncula Mollusca Entoprocta Platyhelminthes Nemertea Gastrotricha Micrognathozoa Rotifera Gnathostomulida Chaetognatha Priapulida Kinorhyncha Loricifera Nematoda Nematomorpha Onychophora Arthropoda Tardigrada Echinodermata Enteropneusta Vertebrata Anthozoa Medusozoa Saccorhytus Ctenophora Xenacoelomorpha Placozoa Porifera;
	prset topologypr=constraints(one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fourteentwo, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, twentyone, twentytwo, twentythree, twentyfour, twentyfive, twentysix, twentyseven, twentyeight);
	mcmcp ngen = 100000 relburnin = yes burninfrac = 0.25 printfreq = 1000 samplefreq = 1000 nchains = 4 savebrlens = yes filename= ss_saccoel_mcmc;
	mcmc;
      	ssp alpha=0.4 nsteps=100 ngen=50000000 relburnin = yes burninfrac = 0.25 filename= ss_saccoel append=no;
	ss;
END;
sumt;
sump;


