order · mtDNA statistics

Testudines

51 species in 11 families. Every region of their mitochondrial genomes, side by side.

Group

species

38.9%

mean GC, whole genome

SD 1.1, range 35.8–41.5%

16,661

median genome length, bp

Range 16,439–19,438 bp

families

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	51	38.91%	1.09	0.028	35.81%Kinosternon leucostomum	38.79%	41.52%Trionyx triunguis	0.04	0.78
Protein-coding	51	39.69%	1.18	0.030	35.69%Kinosternon leucostomum	39.68%	42.77%Trionyx triunguis	0.06	0.67
All rRNA	51	39.71%	0.93	0.023	36.57%Kinosternon leucostomum	39.69%	41.05%Mauremys sinensis	−0.04	0.76
All tRNA	51	38.34%	0.69	0.018	37.03%Kinosternon leucostomum	38.20%	39.94%Geoclemys hamiltonii	0.24	0.09
12S rRNA	51	41.34%	0.95	0.023	38.65%Kinosternon leucostomum	41.37%	43.46%Pelusios castaneus	0.22	0.12
16S rRNA	51	38.72%	1.11	0.029	35.32%Kinosternon leucostomum	38.64%	40.74%Mauremys sinensis	−0.17	0.23
D-loop	50	31.30%	3.51	0.112	25.27%Mauremys caspica	31.65%	46.36%Stigmochelys pardalis	0.08	0.58
ND1	51	39.60%	1.61	0.041	36.36%Sternotherus carinatus	39.46%	44.70%Geochelone elegans	0.16	0.28
ND2	51	38.57%	1.47	0.038	33.78%Kinosternon leucostomum	38.70%	41.39%Geochelone elegans	−0.06	0.68
COX1	51	41.26%	1.06	0.026	37.96%Kinosternon leucostomum	41.34%	43.47%Trionyx triunguis	−0.03	0.81
COX2	51	38.19%	1.60	0.042	34.50%Chelydra serpentina	38.26%	41.63%Trionyx triunguis	0.10	0.5
ATP8	51	34.85%	2.66	0.076	28.40%Emydura macquarii	35.12%	41.07%Mauremys annamensis	0.07	0.6
ATP6	51	38.23%	1.61	0.042	35.53%Kinosternon leucostomum	38.01%	42.98%Trionyx triunguis	0.13	0.36
COX3	51	42.12%	1.31	0.031	39.16%Kinosternon leucostomum	42.04%	46.68%Trionyx triunguis	0.19	0.17
ND3	51	38.61%	2.19	0.057	33.81%Cyclemys dentata	38.68%	43.42%Pelusios castaneus	0.33	0.02
ND4L	51	40.00%	1.95	0.049	35.02%Kinosternon leucostomum	40.07%	44.11%Trionyx triunguis	−0.07	0.64
ND4	51	38.75%	1.61	0.042	35.01%Kinosternon leucostomum	38.88%	43.30%Trionyx triunguis	−0.18	0.22
ND5	51	39.03%	1.28	0.033	34.55%Kinosternon leucostomum	39.29%	42.17%Geochelone elegans	0.07	0.64
ND6	51	38.55%	2.29	0.059	29.90%Kinosternon leucostomum	38.45%	44.64%Pelusios castaneus	0.22	0.13
CYTB	51	42.14%	1.46	0.035	37.69%Kinosternon leucostomum	42.11%	45.47%Pelusios castaneus	0.03	0.82

Families of Testudines

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

Region

Parameter

Chart

Families of Testudines

Geoemydidae	16	38.93%	0.86	0.022	37.50%Notochelys platynota	39.01%	40.56%Geoclemys hamiltonii	0.18	0.5
Testudinidae	10	39.18%	1.37	0.035	37.29%Testudo graeca	38.72%	41.27%Geochelone elegans	−0.18	0.61
Chelidae	6	38.91%	0.83	0.021	37.78%Chelodina longicollis	38.80%	40.11%Platemys platycephala	−0.71	0.12
Trionychidae	5	39.35%	1.24	0.031	38.58%Lissemys punctata	38.81%	41.52%Trionyx triunguis	0.68	0.2
Emydidae	4	38.84%	0.10	0.003	38.73%Trachemys scripta	38.82%	38.97%Terrapene carolina	–	–
Cheloniidae	2	39.08%	0.52	0.013	38.71%Caretta caretta	39.08%	39.45%Chelonia mydas	–	–
Chelydridae	2	37.81%	0.14	0.004	37.71%Chelydra serpentina	37.81%	37.91%Macrochelys temminckii	–	–
Kinosternidae	2	36.34%	0.76	0.021	35.81%Kinosternon leucostomum	36.34%	36.87%Sternotherus carinatus	–	–
Pelomedusidae	2	39.57%	1.23	0.031	38.70%Pelomedusa subrufa	39.57%	40.44%Pelusios castaneus	–	–
Carettochelyidae	1	39.86%	–	–	39.86%Carettochelys insculpta	39.86%	39.86%Carettochelys insculpta	–	–
Platysternidae	1	38.60%	–	–	38.60%Platysternon megacephalum	38.60%	38.60%Platysternon megacephalum	–	–

Codon usage

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

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

Testudines 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.