Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

Table 1 Comparison of parallel changes in internal and terminal branches of nematodes, insects and deuterostomes

	Branches where parallel changes were analyzed
	N_Io	N_In	N_Ag	N_Aa
#RGC_CAMs (%)	6 (67)	1 (11)	0 (0)	2 (22)
Relative branch length	0.201	0.169	0.365	0.265
Normalized #parallel changes	29.9	5.9	0.	7.5
#RGC_CAs (%)	45 (45)	22 (22)	15 (15)	19 (19)
Relative branch length	0.205	0.205	0.340	0.250
Normalized #parallel changes	219.5	107.3	44.1	76.
	N_Do	N_Dn	N_Hs	N_Mm
#RGC_CAMs (%)	0 (0)	2 (100)	0 (0)	0 (0)
Relative branch length	0.094	0.621	0.109	0.176
Normalized #parallel changes	0.	3.2	0.	0.
#RGC_CAs (%)	28 (33)	51 (60)	3 (3.5)	3 (3.5)
Relative branch length	0.121	0.581	0.139	0.159
Normalized #parallel changes	231.4	82.1	21.6	18.9
	Io_Do	Io_Dn	Io_Hs	Io_Mm
#RGC_CAMs (%)	1 (50)	1 (50)	0 (0)	0 (0)
Relative branch length	0.094	0.621	0.109	0.176
Normalized #parallel changes	10.6	1.6	0	0
#RGC_CAs (%)	21 (45)	24 (51)	1 (2)	1 (2)
Branch length	0.121	0.581	0.139	0.159
Normalized #parallel changes	173.6	41.3	7.2	6.3
	In_Do	In_Dn	In_Hs	In_Mm
#RGC_CAMs (%)	0 (0)	0 (0)	0 (0)	0 (0)
Relative branch length	0.094	0.621	0.109	0.176
#RGC_CAs (%)	5 (23)	16 (72)	0 (0)	1 (5)
Relative branch length	0.121	0.581	0.139	0.159
Normalized #parallel changes	41.3	27.5	0.	6.3

N is the internal nematode branch, Io is the "old" internal insect branch, In is the "new" internal insect branch, Do is the "old" internal deutrostome branch, Dn is the "new" internal deutrostome branch, Ag indicates the terminal branch leading to Anopheles gambiae, Aa indicates the terminal branch leading to Aedes aegypti, Hs indicates the terminal branch leading to human, Mm indicates the terminal branch leading to mouse. The relative branch length was calculated as the ratio of the length of the analyzed branch to the total length of all involved branches averaged over 255 sampling experiments. Normalized number of parallel changes is the number of parallel changes divided by the branch length.

ISSN: 1745-6150