TESTOUT.DOC EXAMPLE OUTPUT FROM TEST.DAT THE FIRST TABLE IS THE ET PROFILES AND THE NUMBER OF ISOLATES (n) FOR EACH ET. ETDIV: Multilocus Diversity Analysis plant data source 1/26/90 No. of isolates = 52 No. of loci = 20 No. of populations = 5 28 Electrophoretic Types (ETs) ________________________________________________________________________________ Reference PGI ACO PE2 MDH M1P BGA MPI IPO NSP SKD ET isolate n IDH G3P AK PGD GOT ADH G6P CAK TDH GLU ________________________________________________________________________________ 1 AB 32 1 7 7 7 2 4 2 2 8 5 3 5 6 3 2 2 4 2 3 5 2 2 AC 33 1 7 7 8 2 4 2 2 6 5 3 5 6 3 2 2 4 2 3 5 2 3 AD 21 1 7 0 7 2 4 2 2 6 5 3 0 6 3 2 2 0 2 3 3 2 4 AE 44 1 5 5 7 2 4 4 2 6 6 3 3 6 3 2 2 4 2 3 3 2 5 BA 14 4 7 5 7 2 4 4 2 6 5 3 7 6 6 4 2 4 2 4 6 2 6 BB 28 2 7 5 6 2 4 4 2 10 5 3 3 6 6 2 2 4 2 4 6 2 7 BC 48 1 7 5 6 2 4 4 2 6 5 3 2 6 6 2 2 4 2 4 6 2 8 BD 31 2 5 5 5 2 4 4 2 6 5 3 5 6 6 2 2 4 2 4 6 2 9 BE 2 1 7 5 7 2 4 4 2 6 5 3 5 6 6 2 2 4 2 4 6 2 10 BF 12 1 5 5 8 2 4 4 2 6 25 3 7 0 6 2 2 4 2 4 6 2 11 CA 7 9 5 5 6 2 2 4 2 8 2 3 2 6 6 2 2 4 2 4 5 2 12 CB 34 1 5 3 6 2 2 4 2 8 2 3 2 6 6 2 2 4 2 4 5 2 13 CC 1 2 5 5 6 2 2 4 2 5 2 3 2 6 6 2 2 4 2 4 5 2 14 CD 5 6 5 5 6 2 2 4 2 6 2 3 2 6 6 2 2 4 2 4 5 2 15 CE 51 1 5 5 6 2 2 4 2 6 2 3 2 6 6 4 2 4 2 4 5 2 16 CF 50 1 4 5 6 2 2 4 2 6 2 3 2 6 6 2 2 4 2 4 5 2 17 CG 10 1 5 5 8 2 2 4 2 2 25 3 2 6 3 2 2 4 2 4 5 2 18 DA 20 3 4 5 7 2 6 4 2 6 5 3 0 0 3 2 2 4 2 4 2 2 19 DB 26 1 3 5 7 2 6 4 2 6 5 3 3 0 3 2 2 4 2 4 2 4 20 DC 24 1 5 5 8 2 6 4 2 6 3 3 3 0 3 2 2 4 2 4 2 2 21 DD 27 1 5 5 7 2 6 4 2 6 3 3 3 4 3 2 2 4 2 4 2 2 22 DE 4 1 5 5 8 2 6 4 2 6 3 3 5 0 3 2 2 4 2 4 2 2 23 DF 13 1 5 5 8 2 4 4 2 6 3 3 5 4 3 2 2 4 2 4 2 2 24 DG 22 1 5 0 8 2 4 4 2 6 3 3 5 0 3 1 2 4 2 4 2 2 25 DH 23 1 5 5 8 0 4 4 2 7 3 3 5 4 3 2 2 4 2 0 2 2 26 EA 15 4 7 5 8 2 4 4 6 8 3 3 5 4 3 2 2 4 2 4 3 4 27 FA 6 1 8 5 7 2 1 6 2 6 2 5 2 7 3 2 2 4 2 4 8 2 28 HA 3 1 9 4 2 0 4 4 2 6 5 0 5 2 6 2 2 0 2 1 6 2 ________________________________________________________________________________ THIS IS A LIST OF THE ISOLATES FOR EACH ET WITH n >1. IN THIS EXAMPLE NULLS ARE SCORED AS ZEROS AND ISOLATES THAT DIFFER ONLY BY NULL ALLELES ARE POOLED TO THE MOST COMMON ETS. __________________________ ETs with multiple isolates __________________________ ET- 5 4 isolates BA 11 BA 14 BA 30 BA 35 ET- 6 2 isolates BB 28 BB 29 ET- 8 2 isolates BD 31 BD 43 ET- 11 9 isolates CA 7 CA 8 CA 9 CA 36 CA 37 CA 38 CA 40 CA 41 CA 42 ET- 13 2 isolates CC 1 CC 17 ET- 14 6 isolates CD 5 CD 39 CD 45 CD 46 CD 47 CD 49 ET- 18 3 isolates DA 18 DA 20 DA 52 ET- 26 4 isolates EA 15 EA 16 EA 19 EA 25 ET DIVERSITY WITHIN EACH POPULATION. POPULATIONS ARE DEFINED IN THE GENERAL SENSE AND CAN REPRESENT GEOGRAPHICAL POPULATIONS, SEROTYPES, HOSTS, ETC. IN THIS CASE, ISOLATES WERE COLLECTED FROM DIFFERENT TISSUES (AIRSACS, LUNGS, HEARTS, LIVER, AND OTHER). ET DIVERSITY ESTIMATES THE PROBABILITY THAT TWO ISOLATES CHOSEN AT RANDOM FROM WITHIN A POPULATION ARE DIFFERENT ETS. (SEE WHITTAM 1989, Antonie van Leeuwenhoek 55:23-32) _____________________________________________ Population No. ETs No. isolates ET div _____________________________________________ air 7 9 .944 lun 7 9 .917 hea 11 15 .933 liv 12 16 .958 oth 2 3 .667 total 28 52 .948 _____________________________________________ THIS TABLE IS A LIST OF THE NUMBER OF ISOLATES OF EACH ET FROM THE POPULATIONS. ______________________________________ Frequency of isolation in populations ______________________________________ ET Total air lun hea liv oth 1 1 0 0 0 1 0 2 1 0 0 0 1 0 3 1 0 1 0 0 0 4 1 0 0 1 0 0 5 4 1 0 0 1 2 6 2 0 0 1 1 0 7 1 0 1 0 0 0 8 2 0 1 1 0 0 9 1 1 0 0 0 0 10 1 0 0 1 0 0 11 9 0 3 4 2 0 12 1 0 0 0 1 0 13 2 1 0 1 0 0 14 6 2 0 1 3 0 15 1 0 1 0 0 0 16 1 0 0 0 0 1 17 1 0 0 0 1 0 18 3 1 0 2 0 0 19 1 0 0 0 1 0 20 1 0 0 1 0 0 21 1 0 0 0 1 0 22 1 0 0 1 0 0 23 1 0 0 0 1 0 24 1 0 1 0 0 0 25 1 0 0 1 0 0 26 4 2 0 0 2 0 27 1 1 0 0 0 0 28 1 0 1 0 0 0 THESE TWO TABLES SUMMARIZE THE OCCURRENCE OF ETS IN PAIRS OF POPULATIONS. THE TOP TABLE IS FOR ALL ETS AND THE BOTTOM TABLE IS FOR ONLY THE ETS WITH MULTIPLE ISOLATES. FOR EACH TABLE, THE UPPER TRIANGULAR MATRIX IS THE PROPORTION OF ETS SHARED BETWEEN A PAIR OF POPULATIONS. THE LOWER TRIANGULAR MATRIX IS THE PROBABILITY THAT TWO ISOLATES SELECTED AT RANDOM FROM THE TWO POPULATIONS ARE DIFFERENT ETS. ______________________________________ ET overlap - prop. shared / prob same ______________________________________ All ETs ETs air lun hea liv oth air 7 0.000 0.000 0.200 0.188 0.125 lun 7 0.000 0.000 0.125 0.056 0.000 hea 11 0.037 0.096 0.000 0.150 0.000 liv 12 0.076 0.042 0.050 0.000 0.077 oth 2 0.074 0.000 0.000 0.042 0.000 Only ETs with multiple isolates ETs air lun hea liv oth air 5 0.000 0.000 0.375 0.429 0.200 lun 2 0.000 0.000 0.333 0.167 0.000 hea 6 0.071 0.325 0.000 0.375 0.000 liv 5 0.175 0.167 0.133 0.000 0.200 oth 1 0.143 0.000 0.000 0.111 0.000 THE NEXT SET OF LISTS ARE THE ALLELE FREQUENCIES IN POPULATIONS FOR EACH LOCUS SEPARATELY. ROWS ARE POPULATIONS AND COLUMNS ARE ALLELES. THE SINGLE LOCUS DIVERSITY, h, IS ALSO GIVEN. ____________________ Allele frequencies ____________________ PGI h 7 5 4 3 8 9 air 0.810 0.429 0.286 0.143 0.000 0.143 0.000 lun 0.667 0.286 0.571 0.000 0.000 0.000 0.143 hea 0.345 0.091 0.818 0.091 0.000 0.000 0.000 liv 0.621 0.417 0.500 0.000 0.083 0.000 0.000 oth 1.000 0.500 0.000 0.500 0.000 0.000 0.000 mean 0.693 0.344 0.435 0.147 0.017 0.029 0.029 IDH h 7 0 5 3 4 air 0.000 0.000 0.000 1.000 0.000 0.000 lun 0.667 0.000 0.286 0.571 0.000 0.143 hea 0.000 0.000 0.000 1.000 0.000 0.000 liv 0.439 0.167 0.000 0.750 0.083 0.000 oth 0.000 0.000 0.000 1.000 0.000 0.000 mean 0.257 0.033 0.057 0.864 0.017 0.029 ACO h 7 8 6 5 2 air 0.667 0.571 0.143 0.286 0.000 0.000 lun 0.857 0.143 0.143 0.429 0.143 0.143 hea 0.764 0.182 0.364 0.364 0.091 0.000 liv 0.727 0.333 0.333 0.333 0.000 0.000 oth 1.000 0.500 0.000 0.500 0.000 0.000 mean 0.718 0.346 0.197 0.382 0.047 0.029 G3P h 2 0 air 0.000 1.000 0.000 lun 0.286 0.857 0.143 hea 0.182 0.909 0.091 liv 0.000 1.000 0.000 oth 0.000 1.000 0.000 mean 0.092 0.953 0.047 PE2 h 4 2 6 1 air 0.810 0.429 0.286 0.143 0.143 lun 0.476 0.714 0.286 0.000 0.000 hea 0.709 0.455 0.273 0.273 0.000 liv 0.667 0.500 0.333 0.167 0.000 oth 1.000 0.500 0.500 0.000 0.000 mean 0.626 0.519 0.335 0.116 0.029 AK h 2 4 6 air 0.286 0.000 0.857 0.143 lun 0.286 0.143 0.857 0.000 hea 0.000 0.000 1.000 0.000 liv 0.303 0.167 0.833 0.000 oth 0.000 0.000 1.000 0.000 mean 0.174 0.062 0.910 0.029 MDH h 2 6 air 0.286 0.857 0.143 lun 0.000 1.000 0.000 hea 0.000 1.000 0.000 liv 0.167 0.917 0.083 oth 0.000 1.000 0.000 mean 0.090 0.955 0.045 PGD h 8 6 10 5 2 7 air 0.524 0.143 0.714 0.000 0.143 0.000 0.000 lun 0.286 0.143 0.857 0.000 0.000 0.000 0.000 hea 0.618 0.091 0.636 0.091 0.091 0.000 0.091 liv 0.682 0.333 0.500 0.083 0.000 0.083 0.000 oth 0.000 0.000 1.000 0.000 0.000 0.000 0.000 mean 0.442 0.142 0.742 0.035 0.047 0.017 0.018 M1P h 5 6 25 2 3 air 0.714 0.429 0.000 0.000 0.429 0.143 lun 0.667 0.571 0.000 0.000 0.286 0.143 hea 0.836 0.273 0.091 0.091 0.273 0.273 liv 0.758 0.417 0.000 0.083 0.250 0.250 oth 1.000 0.500 0.000 0.000 0.500 0.000 mean 0.684 0.438 0.018 0.035 0.347 0.162 GOT h 3 5 0 air 0.286 0.857 0.143 0.000 lun 0.286 0.857 0.000 0.143 hea 0.000 1.000 0.000 0.000 liv 0.000 1.000 0.000 0.000 oth 0.000 1.000 0.000 0.000 mean 0.113 0.943 0.029 0.029 BGA h 5 0 3 7 2 air 0.810 0.286 0.143 0.000 0.143 0.429 lun 0.714 0.429 0.143 0.000 0.000 0.429 hea 0.836 0.273 0.091 0.273 0.091 0.273 liv 0.773 0.333 0.000 0.250 0.083 0.333 oth 1.000 0.000 0.000 0.000 0.500 0.500 mean 0.760 0.264 0.075 0.105 0.163 0.393 ADH h 6 0 4 7 2 air 0.714 0.571 0.143 0.143 0.143 0.000 lun 0.524 0.714 0.143 0.000 0.000 0.143 hea 0.618 0.545 0.364 0.091 0.000 0.000 liv 0.530 0.667 0.083 0.250 0.000 0.000 oth 0.000 1.000 0.000 0.000 0.000 0.000 mean 0.496 0.700 0.147 0.097 0.029 0.029 MPI h 3 6 air 0.571 0.429 0.571 lun 0.476 0.286 0.714 hea 0.545 0.455 0.545 liv 0.530 0.583 0.417 oth 0.000 0.000 1.000 mean 0.472 0.350 0.650 G6P h 2 4 1 air 0.286 0.857 0.143 0.000 lun 0.524 0.714 0.143 0.143 hea 0.000 1.000 0.000 0.000 liv 0.167 0.917 0.083 0.000 oth 1.000 0.500 0.500 0.000 mean 0.345 0.798 0.174 0.029 IPO h 2 air 0.000 1.000 lun 0.000 1.000 hea 0.000 1.000 liv 0.000 1.000 oth 0.000 1.000 mean 0.000 1.000 CAK h 4 0 air 0.000 1.000 0.000 lun 0.476 0.714 0.286 hea 0.000 1.000 0.000 liv 0.000 1.000 0.000 oth 0.000 1.000 0.000 mean 0.112 0.943 0.057 NSP h 2 air 0.000 1.000 lun 0.000 1.000 hea 0.000 1.000 liv 0.000 1.000 oth 0.000 1.000 mean 0.000 1.000 TDH h 3 4 0 1 air 0.000 0.000 1.000 0.000 0.000 lun 0.524 0.143 0.714 0.000 0.143 hea 0.345 0.091 0.818 0.091 0.000 liv 0.303 0.167 0.833 0.000 0.000 oth 0.000 0.000 1.000 0.000 0.000 mean 0.239 0.080 0.873 0.018 0.029 SKD h 5 3 6 2 8 air 0.905 0.286 0.143 0.286 0.143 0.143 lun 0.810 0.286 0.143 0.429 0.143 0.000 hea 0.782 0.273 0.091 0.273 0.364 0.000 liv 0.712 0.500 0.083 0.167 0.250 0.000 oth 1.000 0.500 0.000 0.500 0.000 0.000 mean 0.739 0.369 0.092 0.331 0.180 0.029 GLU h 2 4 air 0.286 0.857 0.143 lun 0.000 1.000 0.000 hea 0.000 1.000 0.000 liv 0.303 0.833 0.167 oth 0.000 1.000 0.000 mean 0.120 0.938 0.062 THIS TABLE GIVES THE COMPONENTS OF GENETIC DIVERSITY. Hs IS THE WITHIN POPULATION DIVERSITY, Ht IS THE DIVERSITY IN THE TOTAL POPULATION AND Gst IS NEI'S COEFFICIENT OF GENETIC DIFFERENTIATION. (SEE WHITTAM ET AL. 1989, Epidem. Inf. 102:37-46 for an example) Summary table __________________________________________________ Locus #alleles Hs Ht Gst __________________________________________________ PGI 6 0.689 0.693 0.007 IDH 5 0.221 0.257 0.138 ACO 5 0.803 0.718 0.000 G3P 2 0.094 0.092 0.000 PE2 4 0.732 0.626 0.000 AK 3 0.175 0.174 0.000 MDH 2 0.090 0.090 0.000 PGD 6 0.422 0.442 0.045 M1P 5 0.795 0.684 0.000 GOT 3 0.114 0.113 0.000 BGA 5 0.827 0.760 0.000 ADH 5 0.477 0.496 0.037 MPI 2 0.425 0.472 0.100 G6P 3 0.395 0.345 0.000 IPO 1 0.000 0.000 0.000 CAK 2 0.095 0.112 0.148 NSP 1 0.000 0.000 0.000 TDH 4 0.234 0.239 0.017 SKD 5 0.842 0.739 0.000 GLU 2 0.118 0.120 0.022 Total 3.5 0.377 0.359 0.000 __________________________________________________ THIS TABLE SUMMARIZES GENETIC VARIATION WITHIN EACH POPULATION AND INCLUDES THE PROPORTION OF POLYMORPHIC LOCI, AND THE MEAN AND STANDARD ERRORS OF SINGLE LOCUS DIVERSITY (h) WITHIN EACH POPULATION ACROSS ETS AND ISOLATES. ________________________________________ Genetic diversity within populations ________________________________________ No. of Polymor- Mean no. ETs Isolates Population ETs phic loci alleles H SE(H) H SE(H) ________________________________________________________________________ air 7 .70 2.40 .398 .074 .390 .072 lun 7 .80 2.40 .426 .061 .382 .055 hea 11 .55 2.40 .329 .077 .311 .074 liv 12 .75 2.40 .384 .066 .359 .062 oth 2 .35 1.35 .350 .109 .233 .073 ________________________________________________________________________