Supplementary File S2
Presence/absence (1/0) data matrices for 367 and 470 retrotransposon datasets


#NEXUS 

Begin data;
	Dimensions ntax=7 nchar=367;
	Format datatype=standard;
	Matrix
Car 1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111110111010000000000000000000000000000000000000000000000011001010010111000111000111110110011111100101111001000001100000010010010111000001010001011111111111111111111111111111011111110000010
Pho 11111?11111110111?111?1?1111?1111111111?1011?11111?11111111111111111111111111111111111111111111111111?111111111111?1111111111111111111111111111111111111111111111111?111111??1111111111011101000000000000?0001?000000?000000000000000000?000?10010100101?100?111000111110?100111?110010111?0010000011100000100?00101110?0001010001011111111111111111111111111111011111110000010
Cet 1111111111111111111100000000000001111111111111111111111110000000000000111111111111111111111111111111111111111111111111111111111111111000100001111001111101111000000001111011111111100011111111111111111111111111111111111111111100000000000000000000000000000000000101111111111110000111000111000001111100000000000110100000000011110000111111111111111111111011111111111000000
Per 0000000000000000000011001011110111101110010111100001010111111111111111111111111111111110111111111111111111111011111111111111101111111111011001110111111010000000001001110111111111101110000101011011111101111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111011100100100101101011111111111111111111100111101110110000
Chi 0000010000000000000000110110001010010001001000011110101001111111111111111111101111111111111101011111111011111110111111111111111111111111000100011111111110000101010110101011111111100101100000011111011011101100000000000001000010111111111000100111101000111000111000000000000000011000000001111000010010101101101000111111111111111111111111111111111111111111111111110001101
Eul 0000000000000000000000000000000000000000100000000000000000000000000000000000010000000001000010100000000100000101000000000000010000000110000010000000000010000010100000000100000000010010000000100100111000000000000000000000000001000000000100010000000000000000000000001000100001101101000000000110000001000000000001100010001110000010100000000000000000000100000010001111111
Out 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
	;
End;





#NEXUS 

Begin data;
	Dimensions ntax=7 nchar=470;
	Format datatype=standard;
	Matrix
Car 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111101110100000000000000000000000000000000000000000000000110010100101110001110001111101100111111001011110010000011000000100100101110000010100010111111111111111111111111111110111111100000100000111111111111111111111100000000000111111111111110000000000111111100000001111111111111111000101111000
Pho 11111?11111110111?111?1?1111?1111111111?1011?11111?11111111111111111111111111111111111111111111111111?111111111111?1111111111111111111111111111111111111111111111111?111111??1111111111011101000000000000?0001?000000?000000000000000000?000?10010100101?100?111000111110?100111?110010111?0010000011100000100?00101110?0001010001011111111111111111111111111111011111110000010?000111?111111?111111111110000000000?1?111?11111?1100000000001?1111?0000?0?11?11111111?1111000101111?00
Cet 11111111111111111111000000000000011111111111111111111111100000000000001111111111111111111111111111111111111111111111111111111111111110001000011110011111011110000000011110111111111000111111111111111111111111111111111111111111000000000000000000000000000000000001011111111111100001110001110000011111000000000001101000000000111100001111111111111111111110111111111110000001111000000011111111100000000001111111111000000111111111111111000100000000011111110001111111111001111111
Per 00000000000000000000110010111101111011100101111000010101111111111111111111111111111111101111111111111111111110111111111111111011111111110110011101111110100000000010011101111111111011100001010110111111011111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111110111001001001011010111111111111111111111001111011101100000000000000000000000011111111111111111000111111111111111111000000011111111110000001111111111111110011111
Chi 00000100000000000000001101100010100100010010000111101010011111111111111111111011111111111111010111111110111111101111111111111111111111110001000111111111100001010101101010111111111001011000000111110110111011000000000000010000101111111110001001111010001110001110000000000000000110000000011110000100101011011010001111111111111111111111111111111111111111111111111100011011111111111100000000000000011110000000111111111000001111111111111000011111101111111110000000111011100111
Eul 00000000000000000000000000000000000000001000000000000000000000000000000000000100000000010000101000000001000001010000000000000100000001100000100000000000100000101000000001000000000100100000001001001110000000000000000000000000010000000001000100000000000000000000000010001000011011010000000001100000010000000000011000100011100000101000000000000000000001000000100011111110000000000000000000000000000000000000000000000000000000000????????????????????????????????????111111111
Out 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
	;
End;