Appendix 1. Input file structure and output from DANRAN.EXE. Numbers in the second line of input are #hosts, #parasites and #nodes in parasites' phylogeney (i.e., characters in the first matrix). Input file 'Rosen fish - area relationships' 10 17 32 one 10000000010000001--------------- two 01000000010000001--------------- thr 00100000001000011--------------- fou 00010000001000011--------------- fiv 00001000000000111--------------- six 00000100000001111--------------- sev 00000010000011111--------------- eig 00000001000111111--------------- nin 00000000100111111--------------- etn -----------------100000000000001 ntn -----------------010000000000011 twt -----------------001000000000111 teo -----------------000100000001111 tet -----------------000010000011111 teh -----------------000001000111111 tef -----------------000000101111111 tev -----------------000000011111111 one 11110000001000000 two 00000000100000001 thr 00001000000000001 fou 00000100000010000 fiv 00000100000010000 six 00000100010000000 sev 00000000000000100 eig 00000001000000010 nin 00000010000100000 ten 00000010000001000 'Hafner and Nadler - lice on gophers' 8 10 19 Tward 0000000001000100001 Tmino 0000000010000100001 Gthom 0000000100000010011 Gactu 0000001000001010011 Gewin 0000010000001010011 Gchap 0000100000000000111 Gpana 0001000000010001111 Gsetz 0010000000010001111 Gcher 0100000000100001111 Gcost 1000000000100001111 Ttal 1010000000 Tbot 0101000000 Gbur 0000100000 Ohis 0000010000 Ocav 0000001000 Ound 0000000100 Oche 0000000110 Ohet 0000000001 'Liolopids & Verts - Brooks & McLennan' 11 6 10 one 1000000001 two 0100000011 thr 0010000011 for 0001000111 fiv 0000101111 six 0000011111 A 000000 B 000000 C 100000 D 000000 E 010000 F 001000 G 000000 H 000100 I 000000 J 000010 K 000001 Output Phylogenetic Covariance Probability for: 'Rosen fish - area relationships Using: ie; 1 at 47 steps 4 at 46 steps 25 at 45 steps 83 at 44 steps 141 at 43 steps 184 at 42 steps 232 at 41 steps 177 at 40 steps <<<<<<< OBSERVED LENGTH 92 at 39 steps 37 at 38 steps 23 at 37 steps 1 at 36 steps 0 at 35 steps 0 at 34 steps 0 at 33 steps 0 at 32 steps Your p-value is: 0.330669 Phylogenetic Covariance Probability for: 'Hafner and Nadler - lice on gophers Using: tread (0((1 2)((3(4 5))(6(7 8))))); 7 at 35 steps 25 at 34 steps 60 at 33 steps 120 at 32 steps 155 at 31 steps 168 at 30 steps 177 at 29 steps 134 at 28 steps 75 at 27 steps 47 at 26 steps <<<<<<< OBSERVED LENGTH 19 at 25 steps 9 at 24 steps 3 at 23 steps 1 at 22 steps 0 at 21 steps Your p-value is: 0.079920 Phylogenetic Covariance Probability for: 'Liolopids & Verts - Brooks & McLennan Using: tread (0(1((2 3 4)(5 6 ((7 8)(9(10 11))))))); 210 at 14 steps 288 at 13 steps 299 at 12 steps 147 at 11 steps 56 at 10 steps <<<<<<< OBSERVED LENGTH Your p-value is: 0.056943 'stingray paras & areas - 1st 23' 6 13 23 one 1000111---------------- two 0100111---------------- thr 0010011---------------- fou 0001001---------------- eig -------10011----------- nin -------01011----------- ten -------00101----------- tht ------------10000000111 fot ------------01000000111 fit ------------00100000011 sit ------------00010001001 set ------------00001011001 eit ------------00000111001 upar 0001000000100 mana 0000000000010 leti 0010001001000 orin 0100011010101 mara 1000001010000 magd 1000100100000 'stingray paras & areas - all 33' 6 23 33 one 1000111-------------------------- two 0100111-------------------------- thr 0010011-------------------------- fou 0001001-------------------------- eig -------10011--------------------- nin -------01011--------------------- ten -------00101--------------------- tht ------------10000000111---------- fot ------------01000000111---------- fit ------------00100000011---------- sit ------------00010001001---------- set ------------00001011001---------- eit ------------00000111001---------- tfo -----------------------1--------- tfi ------------------------1-------- tsi -------------------------1------- tse --------------------------1------ tei ---------------------------1----- tni ----------------------------1---- tht -----------------------------1--- tho ------------------------------1-- thu -------------------------------1- tht --------------------------------1 upar 00010000001001100000011 mana 00000000000101100000000 leti 00100010010000011100000 orin 01000110101011100101100 mara 10000010100000000000000 magd 10001001000000000010000 Phylogenetic Covariance Probability for: 'stingray paras & areas - 1st 23 Using: ie; 6 at 33 steps 49 at 32 steps 173 at 31 steps 269 at 30 steps 251 at 29 steps <<<<<<< OBSERVED LENGTH 162 at 28 steps 65 at 27 steps 21 at 26 steps 4 at 25 steps 0 at 24 steps 0 at 23 steps Your p-value is: 0.503497 Phylogenetic Covariance Probability for: 'stingray paras & areas - all 33 Using: ie; 6 at 45 steps 26 at 44 steps 76 at 43 steps 209 at 42 steps 241 at 41 steps <<<<<<< OBSERVED LENGTH 218 at 40 steps 139 at 39 steps 62 at 38 steps 16 at 37 steps 7 at 36 steps 0 at 35 steps 0 at 34 steps 0 at 33 steps Your p-value is: 0.683317 'stingray paras - composite areas' 10 23 33 one 1000111-------------------------- two 0100111-------------------------- thr 0010011-------------------------- fou 0001001-------------------------- eig -------10011--------------------- nin -------01011--------------------- ten -------00101--------------------- tht ------------10000000111---------- fot ------------01000000111---------- fit ------------00100000011---------- sit ------------00010001001---------- set ------------00001011001---------- eit ------------00000111001---------- tfo -----------------------1--------- tfi ------------------------1-------- tsi -------------------------1------- tse --------------------------1------ tei ---------------------------1----- tni ----------------------------1---- tht -----------------------------1--- tho ------------------------------1-- thu -------------------------------1- tht --------------------------------1 upar 00010000001001100000011 mana 00000000000101100000000 leti 00100010010000011100000 orin1 01000110100000000001100 orin2 00000000001011100000000 orin3 00000010000000000100000 mara1 00000010000000000000000 mara2 10000000000000000000000 mara3 00000000100000000000000 magd 10001001000000000010000 'Brooks & Glen - Worms on primates' 5 10 18 worm1 10000000001------- worm2 01000000011------- worm3 00100000111------- worm4 00010001111------- worm5 00001011111------- worm6 00000111111------- worm12 -----------1000001 worm13 -----------0100011 worm14 -----------0010111 worm15 -----------0001111 Hyalo 1110001000 Pongo 0010000100 Homo 0000101000 Pan 0000100010 Gorril 0000100001 Phylogenetic Covariance Probability for: 'stingray paras - composite areas Using: ie; 3 at 47 steps 6 at 46 steps 30 at 45 steps 53 at 44 steps 140 at 43 steps 231 at 42 steps 205 at 41 steps 183 at 40 steps 89 at 39 steps 44 at 38 steps 14 at 37 steps <<<<<<< OBSERVED LENGTH 2 at 36 steps 0 at 35 steps 0 at 34 steps 0 at 33 steps Your p-value is: 0.016983 Phylogenetic Covariance Probability for: 'Brooks & Glen - Worms on primates Using: ie; 78 at 21 steps 219 at 20 steps 371 at 19 steps 248 at 18 steps <<<<<<< OBSERVED LENGTH 79 at 17 steps 5 at 16 steps Your p-value is: 0.332667