class · mtDNA statistics

Chondrichthyes

Sharks and rays: 87 species in 11 orders. Every region of their mitochondrial genomes, side by side.

Group

species

38.9%

mean GC, whole genome

SD 2.2, range 33.7–43.2%

16,751

median genome length, bp

Range 16,613–20,201 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	87	38.94%	2.20	0.056	33.65%Bathyraja maculata	38.97%	43.23%Isurus oxyrinchus	−0.02	0.88
Protein-coding	87	39.55%	2.69	0.068	32.66%Callorhinchus milii	39.47%	44.82%Isurus oxyrinchus	−0.02	0.88
All rRNA	87	39.07%	1.19	0.030	36.06%Torpedo marmorata	39.22%	41.42%Aetobatus flagellum	−0.03	0.8
All tRNA	87	38.56%	1.44	0.037	33.22%Callorhinchus capensis	38.96%	40.70%Triakis semifasciata	0.05	0.66
12S rRNA	87	41.72%	1.35	0.032	37.59%Torpedo marmorata	41.93%	44.01%Hemitriakis japanica	0.04	0.72
16S rRNA	87	37.55%	1.33	0.036	34.19%Rhizoprionodon acutus	37.45%	40.33%Okamejei kenojei	−0.06	0.59
D-loop	73	34.89%	8.02	0.230	27.31%Bathyraja albomaculata	33.93%	100.00%Galeorhinus galeus	0.17	0.14
ND1	87	40.50%	2.98	0.074	32.41%Bathyraja parmifera	40.51%	45.44%Okamejei kenojei	−0.03	0.79
ND2	87	39.56%	3.17	0.080	31.48%Callorhinchus milii	39.77%	46.12%Isurus oxyrinchus	0.03	0.8
COX1	87	39.93%	2.63	0.066	35.39%Bathyraja parmifera	39.88%	46.01%Isurus oxyrinchus	−0.07	0.55
COX2	87	38.16%	2.05	0.054	32.27%Bathyraja interrupta	38.35%	43.42%Isurus oxyrinchus	0.10	0.35
ATP8	87	31.97%	4.00	0.125	23.64%Callorhinchus milii	31.55%	39.29%Dipturus trachyderma	−0.05	0.64
ATP6	87	37.57%	3.28	0.087	30.41%Bathyraja interrupta	36.99%	44.15%Beringraja binoculata	−0.03	0.8
COX3	87	42.47%	2.86	0.067	35.62%Callorhinchus milii	41.86%	47.96%Leucoraja naevus	−0.07	0.55
ND3	87	42.07%	3.46	0.082	32.66%Callorhinchus capensis	42.12%	47.85%Beringraja binoculata	−0.08	0.46
ND4L	87	41.74%	3.14	0.075	33.33%Callorhinchus milii	42.09%	46.80%Isurus oxyrinchus	−0.06	0.55
ND4	87	39.16%	2.99	0.076	31.98%Callorhinchus milii	39.10%	45.11%Isurus oxyrinchus	−0.04	0.72
ND5	87	38.36%	2.94	0.077	29.06%Callorhinchus milii	38.74%	43.77%Isurus oxyrinchus	0.00	0.98
ND6	87	38.23%	2.31	0.060	30.46%Callorhinchus milii	38.34%	43.87%Aetobatus flagellum	0.19	0.08
CYTB	87	40.67%	2.92	0.072	33.07%Bathyraja taranetzi	40.61%	45.93%Okamejei kenojei	−0.02	0.87

Orders of Chondrichthyes

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

Region

Parameter

Chart

Orders of Chondrichthyes

Carcharhiniformes	31	38.33%	0.81	0.021	36.80%Galeus melastomus	38.41%	40.04%Hemitriakis japanica	0.05	0.8
Rajiformes	24	39.63%	3.14	0.079	33.65%Bathyraja maculata	41.11%	42.39%Okamejei kenojei	−0.22	0.29
Lamniformes	10	40.05%	1.99	0.050	36.83%Pseudocarcharias kamoharai	40.06%	43.23%Isurus oxyrinchus	0.38	0.29
Myliobatiformes	6	40.05%	0.74	0.019	38.92%Mobula alfredi	40.20%	40.87%Aetobatus flagellum	−0.24	0.65
Rhinopristiformes	4	39.93%	0.21	0.005	39.69%Pristis pristis	39.96%	40.13%Acroteriobatus annulatus	–	–
Chimaeriformes	3	35.45%	2.70	0.076	33.73%Callorhinchus milii	34.05%	38.56%Chimaera monstrosa	–	–
Orectolobiformes	3	37.18%	0.25	0.007	36.95%Ginglymostoma cirratum	37.14%	37.44%Chiloscyllium plagiosum	–	–
Squaliformes	3	39.05%	0.25	0.006	38.78%Squalus acanthias	39.11%	39.26%Somniosus microcephalus	–	–
Heterodontiformes	1	39.86%	–	–	39.86%Heterodontus francisci	39.86%	39.86%Heterodontus francisci	–	–
Hexanchiformes	1	38.23%	–	–	38.23%Notorynchus cepedianus	38.23%	38.23%Notorynchus cepedianus	–	–
Torpediniformes	1	34.32%	–	–	34.32%Torpedo marmorata	34.32%	34.32%Torpedo marmorata	–	–

Codon usage

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

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

Chondrichthyes 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.