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Table 1 Statistics based on a Maximum Parsimony Ratchet analysis showing the retention index as a measure of homoplasy.

From: Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae)

  

total characters (with indels)

Trees found (with indels)

Steps (with indels)

RI (with indels)

agt1 full sampling

coding

1088 (1088)

1253 (N/A)

405 (N/A)

0.827 (N/A)

 

non-coding

1009 (1192)

1721 (1539)

978 (1205)

0.799 (0.794)

 

total

2097 (2280)

232 (362)

1395 (1622)

0.802 (0.798)

agt1 reduced sampling

coding

1088 (1088)

206 (N/A)

260 (N/A)

0.742 (N/A)

 

non-coding

856 (971)

323 (55)

613 (746)

0.636 (0.628)

 

total

1944 (2059)

50 (64)

876 (1010)

0.667 (0.658)

matK-trnK-psbA full sampling

coding

1609 (1621)

158 (172)

448 (461)

0.882 (0.883)

 

non-coding

1475 (1554)

39 (85)

422 (518)

0.879 (0.877)

 

total

3085 (3174)

1007 (1356)

881 (990)

0.874 (0.873)

matK-trnK-psbA reduced sampling

coding

1606 (1614)

18 (15)

303 (312)

0.840 (0.383)

 

non-coding

1310 (1361)

9 (28)

287 (343)

0.837 (0.831)

 

total

2916 (2974)

12 (21)

587 (651)

0.832 (0.828)

ndhF-rpl32-trnL reduced sampling

coding

362 (367)

2 (2)

58 (63)

0.962 (0.964)

 

non-coding

1668 (1783)

10 (8)

246 (382)

0.822 (0.823)

 

total

2030 (2150)

1 (65)

305 (448)

0.847 (0.836)

psbA-trnH reduced sampling

coding

29 (29)

1 (N/A)

2 (N/A)

1.000 (N/A)

 

non-coding

324 (370)

810 (28)

46 (100)

0.727 (0.714)

 

total

353 (399)

1044 (38)

49 (103)

0.696 (0.700)