Table 4

Analysis of congruence between the chromosomal inversion plus per gene phylogeny and CHC data.

PARSIMONY METHODS

TEST FOR SERIAL INDEPENDENCY (TFSI)


Linear Parsimony (LP)

Squared Change Parsimony Gradual (SCPG)

Squared Change Parsimony Punctuated (SCPP)





Characters

Reference Tree

Random Trees

P

Reference Tree

Random Trees

P

Reference Tree

Random Trees

P

Observed Mean C-Statistics

P


Female CV1

26.91

37.14

0.0012

37.17

78.63

0.0921

105.88

166.56

0.0026

0.3615

0.0020

Female CV2

32.17

32.75

0.3317

94.71

75.49

0.7182

228.03

158.34

0.9553

-0.3217

0.0090

Female CV3

27.47

30.34

0.1287

26.10

39.20

0.1756

69.06

82.77

0.1976

0.1094

0.2460

Female CV4

26.61

29.81

0.0931

31.77

42.13

0.3025

66.29

89.39

0.0683

0.1593

0.2210

Female CV5

26.31

37.30

0.0040

23.43

51.03

0.0306

59.80

108.28

0.0223

0.2981

0.0480

Male CV1

16.24

23.37

0.0004

11.88

28.88

0.0002

32.43

61.08

0.0004

0.447

0.0010

Male CV2

32.43

32.13

0.4783

83.85

69.03

0.6803

197.64

146.13

0.9652

-0.2548

0.0490

Male CV3

29.20

30.75

0.2032

35.84

47.76

0.2850

91.14

101.18

0.2689

0.0579

0.2930

Male CV4

28.92

31.11

0.1142

53.11

56.40

0.4929

99.37

119.68

0.1340

0.0761

0.3000

Male CV5

27.39

36.75

0.0080

43.49

51.24

0.8830

75.87

108.81

0.0699

0.1669

0.1590


The reconstructed phylogeny used in the character evolution analysis represents the first out of six most parsimonious trees and was based on 13 populations/species of the D. buzzatii cluster (see Table 1) plus three species of the D. mojavensis cluster. CDF analysis was based on 21 CHC peaks to generate the canonical variates (CVs). Three different parsimony methods were used in Mesquite [57]: linear parsimony (LP), squared-change parsimony assuming a gradual model of evolution (SCPG), and squared-change parsimony with a punctuated model of evolution (SCPP). In all three models, presence of phylogenetic signal for each character (i.e. female and male CVs) was assessed by comparing the mean parsimony character steps from the reference tree (as shown on Figure 6) with those of a population of random trees. Terminal taxa were reshuffled 10,000 times to generate the random trees. Phylogenetic signal was positive when the mean parsimony character steps for the reference tree were significantly smaller than the mean parsimony character steps for the random trees. See Additional File 2: Figure S2 for details. The detection of phylogenetic signal was also examined with the test for serial independence (TFSI) run with 1,000 replicates using the program Phylogenetic Independence 2.0 [69]. P-values in bold represent significant values after false discovery rate (FDR) analysis. See Additional File 12: Table S8 for FDR calculations.

Oliveira et al. BMC Evolutionary Biology 2011 11:179   doi:10.1186/1471-2148-11-179

Open Data