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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].