family · mtDNA statistics

Testudinidae

10 species in 8 genera. Every region of their mitochondrial genomes, side by side.

Group

species

39.2%

mean GC, whole genome

SD 1.4, range 37.3–41.3%

17,311

median genome length, bp

Range 16,446–19,438 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	10	39.18%	1.37	0.035	37.29%Testudo graeca	38.72%	41.27%Geochelone elegans	−0.18	0.61
Protein-coding	10	40.07%	0.98	0.025	39.27%Malacochersus tornieri	39.80%	42.39%Geochelone elegans	−0.12	0.74
All rRNA	10	40.17%	0.61	0.015	38.95%Testudo graeca	40.30%	40.96%Geochelone elegans	−0.35	0.33
All tRNA	10	38.94%	0.53	0.014	37.96%Stigmochelys pardalis	38.91%	39.75%Geochelone elegans	0.20	0.58
12S rRNA	10	41.80%	0.75	0.018	40.00%Testudo graeca	42.00%	42.67%Chelonoidis carbonarius	−0.19	0.6
16S rRNA	10	39.19%	0.69	0.018	38.31%Testudo graeca	39.06%	40.31%Geochelone elegans	−0.37	0.29
D-loop	9	32.90%	5.30	0.161	28.60%Indotestudo forstenii	31.65%	46.36%Stigmochelys pardalis	−0.09	0.81
ND1	10	41.06%	1.46	0.036	38.93%Malacochersus tornieri	40.97%	44.70%Geochelone elegans	−0.06	0.86
ND2	10	39.13%	1.11	0.028	37.44%Chelonoidis carbonarius	39.15%	41.39%Geochelone elegans	−0.00	0.99
COX1	10	41.34%	0.52	0.013	40.89%Chelonoidis carbonarius	41.25%	42.51%Geochelone elegans	−0.32	0.37
COX2	10	38.72%	1.18	0.030	36.68%Indotestudo forstenii	38.57%	40.90%Aldabrachelys gigantea	0.24	0.51
ATP8	10	36.67%	1.34	0.037	35.12%Manouria emys	36.83%	38.51%Testudo marginata	−0.33	0.36
ATP6	10	37.95%	1.50	0.039	36.26%Testudo marginata	37.43%	40.68%Manouria emys	−0.22	0.54
COX3	10	42.39%	1.05	0.025	40.89%Chelonoidis carbonarius	42.22%	44.13%Manouria emys	−0.03	0.94
ND3	10	40.07%	1.37	0.034	37.89%Testudo kleinmanni	39.86%	42.69%Geochelone elegans	−0.22	0.54
ND4L	10	40.20%	1.28	0.032	37.71%Chelonoidis carbonarius	40.40%	41.75%Geochelone elegans	−0.08	0.82
ND4	10	38.61%	1.67	0.043	35.85%Testudo graeca	38.28%	41.65%Geochelone elegans	−0.26	0.46
ND5	10	39.59%	1.13	0.029	38.41%Stigmochelys pardalis	39.55%	42.17%Geochelone elegans	−0.03	0.94
ND6	10	38.84%	1.54	0.040	37.14%Malacochersus tornieri	38.57%	42.48%Geochelone elegans	−0.21	0.57
CYTB	10	42.16%	0.91	0.022	41.17%Indotestudo forstenii	41.91%	44.14%Geochelone elegans	0.09	0.79

Genera of Testudinidae

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

Region

Parameter

Chart

Genera of Testudinidae

Testudo	3	38.14%	0.79	0.021	37.29%Testudo graeca	38.28%	38.85%Testudo kleinmanni	–	–
Indotestudo	1	38.40%	–	–	38.40%Indotestudo forstenii	38.40%	38.40%Indotestudo forstenii	–	–
Malacochersus	1	37.83%	–	–	37.83%Malacochersus tornieri	37.83%	37.83%Malacochersus tornieri	–	–
Manouria	1	40.03%	–	–	40.03%Manouria emys	40.03%	40.03%Manouria emys	–	–
Chelonoidis	1	38.59%	–	–	38.59%Chelonoidis carbonarius	38.59%	38.59%Chelonoidis carbonarius	–	–
Aldabrachelys	1	40.13%	–	–	40.13%Aldabrachelys gigantea	40.13%	40.13%Aldabrachelys gigantea	–	–
Geochelone	1	41.27%	–	–	41.27%Geochelone elegans	41.27%	41.27%Geochelone elegans	–	–
Stigmochelys	1	41.09%	–	–	41.09%Stigmochelys pardalis	41.09%	41.09%Stigmochelys pardalis	–	–

Codon usage

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

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

Testudinidae 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.