1. Measures of Character Fit Measures of Character Fit

2. Measures of Character Fit Parsimony programme utilizes a number of different statistics to assess the ‘quality’ of cladograms. Standard measures are cladogram length, the consistency index and the retention index.

3. Cladogram length The cladogram length is the minimum number of steps (changes) needed in building the cladogram for the given data. Therefore, the larger the dataset (number of characters) the longer the cladogram length. The possible minimum length of a cladogram (L) is given below: C = total number of characters wj = weight on character j lj = number of changes in character j (number of states of the character, i.e. j – 1)

4. Cladogram length ‘+’ is gain and ‘-’ is loss of character Cladogram length = ?

5. Cladogram length ‘+’ is gain and ‘-’ is loss of character Cladogram length = 1 + 1 + 1 + 1 + 2 + 2 = 8 1 2 3 4 5 6 Character

6. Fit of Character The fit of a character depends on the occurrence of the character on the cladogram. When a character fits a cladogram perfectly (for binary character, to one node with one step), it can be considered 100% consistent with that particular cladogram. When a character does not fit a cladogram perfectly (to more than one node with more than one step), it is less than 100% consistent. Such character exhibits homoplasy.

7. ‘+’ is gain and ‘-’ is loss of character Which character(s) are perfect and which character(s) are not perfect? Fit of Character

8. Fit of character Homoplasy is discordance with a particular cladogram and can be measured by various indices: consistency index (ci) homoplasy index (hi) retention index (ri) rescaled consistency (rc)

9. Consistency index Character consistency (ci) is defined as: ci = m/s m is the minimum number of steps of a character can show on a cladogram s is the minimum number of steps of a character shows on a cladogram

10. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1s1 m1m1 ci1 ci = m/s

11. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s11s11 m11m11 ci11 ci = m/s

12. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s111s111 m111m111 ci111 ci = m/s

13. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111s1111 m1111m1111 ci1111 ci = m/s

14. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s11112s11112 m11111m11111 ci11110.5 ci = m/s

15. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s111122s111122 m111111m111111 ci11110.505 ci = m/s

16. Consistency index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ci = m/s CI = M/S CI = 6/8 = 0.75

17. Homoplasy index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- Homoplasy index (hi) explains the level of homoplasy of a character. hi = 1 - ci HI = 1 - CI hi00000.50.5-

18. Problems with CI or HI The inclusion of uninformative characters (autapomorphies) in calculation will inflate CI values. As the number of taxa increases, value of CI are observed to decrease. CI values can never reach zero.

19. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- Retention index (ri) is defined as: ri = (g – s) / (g – m) g is the fewest number of variables of a character hi00000.50.5-

20. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ri = (g – s) / (g – m) hi00000.50.5- g2g2 ri1 2 e.g. character 1 has two variables which are “1” and “0”. Variable “1” appears two times and variable “0” appears 4 times. Therefore, the g value for character 1 is 2.

21. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ri = (g – s) / (g – m) hi00000.50.5- g23g23 ri11

22. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ri = (g – s) / (g – m) hi00000.50.5- g232g232 ri111

23. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ri = (g – s) / (g – m) hi00000.50.5- g2321g2321 ri111∞

24. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ri = (g – s) / (g – m) hi00000.50.5- g23212g23212 ri111∞0

25. Retention index Characters 123456123456 X000000-X000000- A000111-A000111- B001111-B001111- C011101-C011101- D111100-D111100- E111100-E111100- s1111228s1111228 m1111116m1111116 ci11110.50.5- ri = (g – s) / (g – m) RI = (G – S) / (G – M) = (13 – 8) / (13 – 6) = 5/7 = 0.71 CI = S/M = 8/6 = 0.75 hi00000.50.5- g23212313 ri111∞00.5-

26. Rescaled Consistency Index In rescaled consistency index (RC), RI value is used to rescaled CI value. RC = CI x RI = 0.75 x 0.71 = 0.53