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Table 2 The data partitions used for phylogenetic analysis

From: Phylogenomics of strongylocentrotid sea urchins

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

  1. 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).