Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila

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.

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