order · mtDNA statistics

Caudata

27 species in 7 families. Every region of their mitochondrial genomes, side by side.

Group

species

36.4%

mean GC, whole genome

SD 2.9, range 31.7–41.8%

16,456

median genome length, bp

Range 16,294–20,001 bp

families

Regions

GC content of each region across Caudata, % of A + C + G + T

Parameter

Chart

GC % of every region
Region
Whole genome	27	36.43%	2.90	0.080	31.66%Onychodactylus fischeri	36.16%	41.83%Proteus anguinus	0.22	0.28
Protein-coding	27	36.43%	3.38	0.093	31.05%Onychodactylus fischeri	35.65%	42.58%Proteus anguinus	0.21	0.3
All rRNA	27	36.54%	2.11	0.058	33.15%Onychodactylus fischeri	36.86%	39.76%Gyrinophilus porphyriticus	0.25	0.2
All tRNA	27	36.30%	2.11	0.058	32.12%Ambystoma tigrinum	36.31%	40.65%Proteus anguinus	0.23	0.25
12S rRNA	27	39.58%	2.32	0.059	36.06%Onychodactylus fischeri	39.47%	43.91%Proteus anguinus	0.27	0.17
16S rRNA	27	34.74%	2.21	0.064	31.00%Afghanodon mustersi	34.62%	38.96%Gyrinophilus palleucus	0.22	0.28
D-loop	26	35.40%	1.85	0.052	28.57%Hemidactylium scutatum	35.78%	37.58%Ambystoma tigrinum	0.20	0.33
ND1	27	35.62%	3.05	0.086	30.75%Ambystoma mexicanum	35.39%	40.74%Triturus cristatus	0.19	0.33
ND2	27	33.67%	4.23	0.125	27.86%Onychodactylus fischeri	32.53%	42.42%Triturus cristatus	0.23	0.24
COX1	27	39.59%	3.39	0.086	33.72%Onychodactylus fischeri	38.81%	46.03%Proteus anguinus	0.19	0.35
COX2	27	37.11%	3.07	0.083	31.88%Onychodactylus fischeri	36.79%	42.44%Triturus carnifex	0.22	0.28
ATP8	27	29.55%	3.29	0.111	24.40%Ambystoma tigrinum	29.17%	36.31%Triturus cristatus	0.15	0.47
ATP6	27	35.56%	4.15	0.117	29.09%Onychodactylus fischeri	34.36%	44.01%Triturus carnifex	0.27	0.17
COX3	27	39.81%	3.34	0.084	35.29%Onychodactylus fischeri	38.98%	46.68%Tylototriton verrucosus	0.11	0.59
ND3	27	36.82%	4.42	0.120	28.49%Onychodactylus fischeri	36.18%	45.40%Triturus carnifex	0.22	0.28
ND4L	27	36.11%	3.91	0.108	31.31%Ambystoma mexicanum	34.68%	45.45%Proteus anguinus	0.31	0.11
ND4	27	35.96%	3.96	0.110	29.83%Onychodactylus fischeri	34.67%	43.61%Proteus anguinus	0.22	0.26
ND5	27	34.25%	3.13	0.091	29.09%Onychodactylus fischeri	33.83%	40.45%Proteus anguinus	0.23	0.25
ND6	27	36.95%	4.01	0.108	30.81%Ambystoma texanum	35.88%	45.09%Triturus carnifex	0.08	0.68
CYTB	27	37.73%	3.57	0.095	31.99%Onychodactylus fischeri	37.04%	43.73%Triturus cristatus	0.12	0.55

Families of Caudata

GC content of the whole genome, % of A + C + G + T

Region

Parameter

Chart

Families of Caudata

Plethodontidae	7	36.34%	1.33	0.037	33.71%Phaeognathus hubrichti	36.47%	37.77%Gyrinophilus palleucus	−0.08	0.86
Salamandridae	7	39.83%	1.73	0.043	37.59%Notophthalmus perstriatus	40.66%	41.70%Triturus cristatus	0.62	0.14
Hynobiidae	5	33.76%	1.22	0.036	31.66%Onychodactylus fischeri	34.18%	34.80%Salamandrella keyserlingii	−0.68	0.21
Ambystomatidae	4	33.67%	0.66	0.020	33.06%Ambystoma tigrinum	33.55%	34.53%Ambystoma talpoideum	–	–
Cryptobranchidae	2	35.47%	0.06	0.002	35.42%Andrias japonicus	35.47%	35.51%Andrias davidianus	–	–
Proteidae	1	41.83%	–	–	41.83%Proteus anguinus	41.83%	41.83%Proteus anguinus	–	–
Sirenidae	1	34.14%	–	–	34.14%Siren lacertina	34.14%	34.14%Siren lacertina	–	–

Codon usage

Share of each codon in all 13 protein-coding genes, across Caudata

Gene

Loading codon usage…

Every species, region by region

Each region's page lists the value of every species, with the same statistics by class, order or family and a CSV download.

Whole genome Protein-coding All rRNA All tRNA 12S rRNA 16S rRNA D-loop ND1 ND2 COX1 COX2 ATP8 ATP6 COX3 ND3 ND4L ND4 ND5 ND6 CYTB

Caudata taxon page Plot GC content against GC skew All data downloads

The charts

Each chart draws the rows of the table under it, in the table's order: sort a column to reorder the chart.Chart sets its axis.
Distribution: the range (line), mean ± SD (bar), median (tick) and mean (dot). Lengths of the regions are on a log scale.
Variation: the coefficient of variation, or the SD for the skews, which vary around zero.
Lifespan r: r with its 95% confidence interval (Fisher z). Lifespan map: r of every parameter in every region at once, bold where the Benjamini–Hochberg q-value over the map is below 0.05.

What the numbers are

Species: species with the region annotated. SD is the sample standard deviation, CV = SD / mean.
Base percentages are over A + C + G + T, so GC % + AT % = 100. Skews are on the L strand as deposited in RefSeq: GC skew = (G − C) / (G + C), AT skew = (A − T) / (A + T).
Min and Max name the species with the extreme value.

Lifespan columns

r is the Pearson correlation of the parameter with log₁₀ maximum lifespan within the group (5 or more species), and p its two-tailed p-value, as on the original MitoAge. They are not corrected for multiple testing or for shared ancestry: the plot shows Benjamini–Hochberg q-values and phylogenetic contrasts.

The original site labelled the base columns with their complements, so its skews have the opposite sign. Seemethods.