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Table 1 Genetic diversity indices from two mitochondrial and eleven nuclear loci examined in this study

From: Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus) uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily

Name

Locus

Nucleotides (bp)

Variable sites

Parsimony-informative sites

p-distance

SE

Model of evolution

Nuclear

Combined

7276

690

412

0.017

0.001

TVM+G

D2

Flanking region of the microsatellite loci D2

393

55

34

0.028

0.004

TIM3+G

D8

Flanking region of the microsatellite loci D8

516

59

37

0.019

0.003

TPM2uf+G

T36

Flanking region of the microsatellite loci T36

394

45

33

0.024

0.004

HKY

X-src

Tyrosine kinase

520

66

45

0.024

0.003

TVM+I

Rag1

Recombination activating gene

1574

64

40

0.007

0.001

TIM3+G

GNG13

Guanine nucleotide binding protein (G protein) subunit gamma 13 (1st intron)

531

46

33

0.017

0.003

TPM2uf

G6PD

Glucose-6-phosphate dehydrogenase (6th intron)

526

48

27

0.018

0.003

HKY+G

UNG

Uracil-DNA-glycosylase (4th intron)

277

18

10

0.011

0.003

JC+G

POLB

DNA polymerase beta (7th to 11th intron)

672

43

22

0.01

0.002

TPM3uf+G

FEN1

Flap structure-specific endonuclease 1 (3rd intron)

827

123

63

0.021

0.003

TPM3uf+G

TP53

Tumor protein p53 (4th intron)

1046

123

68

0.024

0.003

TPM1uf+G

mtDNA

Combined

1239

291

192

0.051

0.003

TPM1uf+I+G

cytb

Cytochrome b

360

112

67

0.059

0.006

TPM1uf+I+G

D-loop

Control region

879

179

125

0.047

0.004

TIM2+I+G

  1. Nucleotide diversity (the average of p-distance between all the species) and standard error (SE) estimate were calculated using MEGA 4.0 [69]. Nucleotide diversity indicates estimates of average sequence divergence across all sequence-pairs. SE was estimated by a bootstrap procedure (1000 replicates). The best-fit evolutionary model was selected for each gene as well as for combined entire sequences of mitochondrial and nuclear genes using jModeltest under the Akaike Information Criterion [70].