Table 2

The data partitions used for phylogenetic analysis
Dataset Num. Alignment length Nuc. Sub. MP MP
Genes Full Gblocks Model Const. Inform.
Mitochondrial
12S 1 917 879 TN93 - -
16S 1 1,566 1,509 TVM - -
ATPase6 1 693 683 GTRG - -
ATPase8 1 180 164 HKY85I - -
CytB 1 1,142 1,142 TIMG - -
COI 1 1,554 1,554 GTRG - -
COII 1 690 690 TRNG - -
ND1 1 972 972 F81 - -
ND2 1 1,067 1,057 GTRIG - -
ND3 1 351 309 GTR - -
ND4 1 1,395 1,377 GTR - -
ND4L 1 300 294 GTRIG - -
ND6 1 508 471 TRNIG - -
MA 13 n/a 10,656 FR 6,826 2,158
M4 11 1,075 - FR 131 644
Nuclear
N4N 2301 297,856 - FR 229,627 42,176
N4S 879 163,484 - FR 126,801 22,984
N4A 3180 461,340 - FR 356,428 65,160

The alignment length prior to Gblocks (Full), the resulting alignment size of conserved sites (Gblocks), the maximum parsimony constant (MP Const.) and informative (MP Inform.) sites are listed. Datasets including multiple genes include all Mitochondrial genes (MA), fourfold degenerate sites (4ds) of mitochondrial genes (M4), 4ds site of nuclear genes with no evidence of positive selection (N4N), 4ds sites of nuclear genes having evidence of positive selection (N4S) and 4ds sites of all nuclear genes (N4A). The nucleotide substitution models (Nuc. Sub. Model) are listed including the free rates mixture model implemented in PhyML (FR).

Kober and Bernardi

Kober and Bernardi BMC Evolutionary Biology 2013 13:88   doi:10.1186/1471-2148-13-88

Open Data