family · mtDNA statistics

Leuciscidae

61 species in 39 genera. Every region of their mitochondrial genomes, side by side.

Group

species

44.4%

mean GC, whole genome

SD 1.2, range 41.3–46.5%

16,645

median genome length, bp

Range 16,545–17,859 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	61	44.41%	1.21	0.027	41.27%Macrhybopsis aestivalis	44.47%	46.51%Notropis buccata	0.17	0.2
Protein-coding	61	44.50%	1.51	0.034	40.44%Macrhybopsis aestivalis	44.76%	47.22%Alburnus mossulensis	0.22	0.08
All rRNA	61	46.56%	0.71	0.015	45.07%Ptychocheilus lucius	46.66%	48.05%Notropis stramineus	−0.09	0.48
All tRNA	61	45.36%	0.73	0.016	43.89%Nocomis biguttatus	45.30%	47.25%Notropis buccata	−0.23	0.08
12S rRNA	61	49.75%	0.59	0.012	48.34%Phenacobius mirabilis	49.79%	51.15%Cyprinella spiloptera	−0.07	0.6
16S rRNA	61	44.75%	0.89	0.020	42.85%Ptychocheilus lucius	44.88%	46.70%Notropis stramineus	−0.08	0.52
D-loop	56	35.61%	4.96	0.139	0.00%Iberochondrostoma almacai	36.41%	37.86%Paranotropis volucellus	0.01	0.97
ND1	61	46.60%	2.39	0.051	40.72%Macrhybopsis aestivalis	46.87%	51.18%Alburnus mossulensis	0.13	0.3
ND2	61	47.63%	2.34	0.049	42.01%Macrhybopsis aestivalis	48.23%	52.82%Notropis buccata	0.18	0.17
COX1	61	43.62%	1.15	0.026	41.26%Macrhybopsis aestivalis	43.65%	46.16%Pseudaspius hakonensis	0.34	0.008
COX2	61	42.19%	1.28	0.030	38.93%Macrhybopsis storeriana	42.11%	44.57%Pseudochondrostoma polylepis	0.46	1.8 × 10⁻⁴
ATP8	61	39.91%	2.27	0.057	35.15%Nocomis biguttatus	40.00%	45.68%Semotilus corporalis	0.41	0.001
ATP6	61	42.26%	1.77	0.042	37.72%Macrhybopsis storeriana	42.54%	46.12%Pseudaspius leptocephalus	0.21	0.1
COX3	61	45.69%	1.31	0.029	42.86%Pimephales notatus	45.79%	48.72%Alburnus mossulensis	0.12	0.35
ND3	61	44.21%	2.31	0.052	36.10%Macrhybopsis aestivalis	44.41%	48.71%Oreoleuciscus potanini	0.19	0.14
ND4L	61	45.29%	1.87	0.041	40.74%Pimephales promelas	45.45%	49.83%Notropis buccata	0.20	0.12
ND4	61	43.91%	1.72	0.039	38.52%Macrhybopsis aestivalis	43.99%	46.96%Notropis buccata	0.21	0.1
ND5	61	43.39%	1.79	0.041	38.78%Macrhybopsis aestivalis	43.74%	46.20%Cyprinella spiloptera	0.18	0.17
ND6	61	47.17%	2.43	0.051	41.95%Phenacobius mirabilis	47.32%	52.30%Rhinichthys atratulus	0.18	0.16
CYTB	61	44.35%	1.73	0.039	40.75%Macrhybopsis storeriana	44.52%	48.29%Notropis buccata	−0.00	1

Genera of Leuciscidae

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

Region

Parameter

Chart

Genera of Leuciscidae

Notropis	7	44.79%	1.45	0.032	42.95%Notropis texanus	44.31%	46.51%Notropis buccata	0.41	0.36
Cyprinella	3	45.48%	0.66	0.015	45.06%Cyprinella lutrensis	45.12%	46.24%Cyprinella spiloptera	–	–
Luxilus	3	44.83%	0.09	0.002	44.76%Luxilus chrysocephalus	44.79%	44.93%Luxilus cornutus	–	–
Pseudaspius	3	45.73%	0.32	0.007	45.53%Pseudaspius hakonensis	45.57%	46.10%Pseudaspius leptocephalus	–	–
Chrosomus	2	43.87%	0.45	0.010	43.55%Chrosomus eos	43.87%	44.19%Chrosomus erythrogaster	–	–
Gila	2	44.00%	0.08	0.002	43.95%Gila robusta	44.00%	44.06%Gila alutacea	–	–
Pimephales	2	42.87%	0.10	0.002	42.80%Pimephales notatus	42.87%	42.94%Pimephales promelas	–	–
Alburnus	2	46.10%	0.55	0.012	45.72%Alburnus alburnus	46.10%	46.49%Alburnus mossulensis	–	–
Rhinichthys	2	45.66%	0.18	0.004	45.53%Rhinichthys cataractae	45.66%	45.79%Rhinichthys atratulus	–	–
Semotilus	2	43.98%	0.44	0.010	43.67%Semotilus atromaculatus	43.98%	44.29%Semotilus corporalis	–	–
Leuciscus	2	45.48%	0.84	0.018	44.89%Leuciscus idus	45.48%	46.07%Leuciscus baicalensis	–	–
Ptychocheilus	2	43.37%	0.17	0.004	43.25%Ptychocheilus lucius	43.37%	43.49%Ptychocheilus oregonensis	–	–
Macrhybopsis	2	41.51%	0.33	0.008	41.27%Macrhybopsis aestivalis	41.51%	41.74%Macrhybopsis storeriana	–	–
Nocomis	2	43.11%	0.66	0.015	42.64%Nocomis biguttatus	43.11%	43.58%Nocomis micropogon	–	–
Abramis	1	43.04%	–	–	43.04%Abramis brama	43.04%	43.04%Abramis brama	–	–

Codon usage

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

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

Leuciscidae 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.