family · mtDNA statistics

Plethodontidae

7 species in 5 genera. Every region of their mitochondrial genomes, side by side.

Group

species

36.3%

mean GC, whole genome

SD 1.3, range 33.7–37.8%

16,778

median genome length, bp

Range 16,294–20,001 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	7	36.34%	1.33	0.037	33.71%Phaeognathus hubrichti	36.47%	37.77%Gyrinophilus palleucus	−0.08	0.86
Protein-coding	7	36.11%	1.57	0.043	33.07%Phaeognathus hubrichti	36.19%	37.49%Gyrinophilus palleucus	0.06	0.89
All rRNA	7	37.90%	1.73	0.046	34.56%Phaeognathus hubrichti	38.04%	39.76%Gyrinophilus porphyriticus	0.07	0.89
All tRNA	7	36.91%	1.51	0.041	34.77%Plethodon cinereus	37.08%	38.95%Gyrinophilus palleucus	−0.20	0.67
12S rRNA	7	39.73%	1.53	0.038	36.69%Phaeognathus hubrichti	40.11%	41.32%Gyrinophilus porphyriticus	−0.36	0.42
16S rRNA	7	36.82%	1.97	0.054	33.29%Phaeognathus hubrichti	37.19%	38.96%Gyrinophilus palleucus	0.26	0.58
D-loop	7	34.24%	2.67	0.078	28.57%Hemidactylium scutatum	34.91%	36.79%Plethodon elongatus	0.61	0.14
ND1	7	36.27%	1.47	0.041	34.81%Plethodon elongatus	36.46%	39.01%Plethodon cinereus	0.68	0.1
ND2	7	33.98%	2.02	0.060	30.15%Phaeognathus hubrichti	34.58%	35.54%Gyrinophilus porphyriticus	−0.31	0.5
COX1	7	39.20%	2.19	0.056	35.43%Phaeognathus hubrichti	40.06%	41.47%Plethodon cinereus	−0.06	0.89
COX2	7	37.35%	1.41	0.038	34.59%Phaeognathus hubrichti	37.35%	39.28%Plethodon cinereus	0.17	0.72
ATP8	7	29.71%	2.16	0.073	27.27%Phaeognathus hubrichti	29.09%	33.95%Hemidactylium scutatum	−0.72	0.07
ATP6	7	35.09%	2.20	0.063	31.29%Phaeognathus hubrichti	35.38%	37.72%Gyrinophilus palleucus	0.19	0.68
COX3	7	39.18%	1.76	0.045	36.10%Phaeognathus hubrichti	39.41%	40.69%Gyrinophilus palleucus	0.17	0.71
ND3	7	36.51%	2.38	0.065	31.90%Phaeognathus hubrichti	36.89%	39.08%Gyrinophilus porphyriticus	−0.20	0.67
ND4L	7	36.50%	2.10	0.057	34.12%Hemidactylium scutatum	36.70%	39.19%Gyrinophilus porphyriticus	0.32	0.49
ND4	7	35.49%	2.01	0.057	32.00%Phaeognathus hubrichti	35.49%	37.63%Plethodon cinereus	0.28	0.54
ND5	7	34.07%	1.80	0.053	30.41%Phaeognathus hubrichti	34.37%	35.86%Gyrinophilus porphyriticus	0.02	0.96
ND6	7	36.54%	2.48	0.068	33.72%Hemidactylium scutatum	36.26%	39.92%Gyrinophilus palleucus	0.40	0.37
CYTB	7	35.80%	0.95	0.026	34.62%Plethodon cinereus	35.78%	37.07%Hemidactylium scutatum	−0.72	0.07

Genera of Plethodontidae

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

Region

Parameter

Chart

Genera of Plethodontidae

Gyrinophilus	2	37.68%	0.13	0.003	37.59%Gyrinophilus porphyriticus	37.68%	37.77%Gyrinophilus palleucus	–	–
Plethodon	2	36.33%	0.18	0.005	36.20%Plethodon elongatus	36.33%	36.47%Plethodon cinereus	–	–
Hemidactylium	1	36.51%	–	–	36.51%Hemidactylium scutatum	36.51%	36.51%Hemidactylium scutatum	–	–
Phaeognathus	1	33.71%	–	–	33.71%Phaeognathus hubrichti	33.71%	33.71%Phaeognathus hubrichti	–	–
Pseudotriton	1	36.16%	–	–	36.16%Pseudotriton ruber	36.16%	36.16%Pseudotriton ruber	–	–

Codon usage

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

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

Plethodontidae taxon page 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.