Table 3

Substitution rate of Human mtDNA obtained in this study and in other studies using different methods (for a more extensive list see Santos et al [37]).

Reference

Region

Method

Human-chimpanzee divergence time (Myr)

Substitution rate as expressed by authors

Standardized substitution rate mutations/site/Myra


Horai et al. [27]

Synonymous positions

Phylogenetic

4.9

3.89 × 10-8 mut/site/year

0.0389

Kivisild et al. [29]

4212 synonymous positions

Phylogenetic

6

3.5 × 10-8 transversions/site/year

0.035

Kivisild et al. [29]

Synonymous positions

Phylogenetic

6

2.1 × 10-9 transversions/site/year

0.0021

Kivisild et al. [29]

rRNA positions

Phylogenetic

6

4.1 × 10-10 transversions/site/year

0.00041

Cann et al. [19]

Complete mtDNA

Phylogenetic

-

0.01–0.02 mut/site/Myr

0.01–0.02

Torroni et al. [26]

Complete mtDNA

Phylogenetic

-

0.00022–0.00029 mut/site/10000

0.022–0.029

Brown [18]

Complete mtDNA

Phylogenetic

-

0.005–0.01 mut/site/Myr

0.005–0.01

Vigilant et al. 1991

HVR I and II

Phylogenetic

6

17.3%/Myr

0.0865

Tamura and Nei 1993

HVR I and II

Phylogenetic

4–6 Myr

1.5×10-7-2.5×10-8/site/year

0.1500–0.0250

Pesole et al. 1992

HVR I and II

Phylogenetic

7.5 Myr

18 ± 10/100 site/Myr

0.1800 ± 0.1

Ho et al. [41]

D-loop

Population (calibration 80 kyr)

-

0.197 (0.115–0.293) mut/site/Myr

0.197 (0.115–0.293)

Santos et al. [37](1)

D-loop

Pedigree

-

3.5219×10-5/site/generation

1.4088

Santos et al. [37](2)

D-loop

Pedigree

-

1.9210×10-5/site/generation

0.7684

Santos et al. [37](4)

D-loop

Pedigree

-

1.2807×10-5/site/generation

0.5123

Santos et al. [37](6)

D-loop

Pedigree

-

4.1878×10-6/site/generation

0.1675

Heyer et al. [36]c

HVR I and II

Pedigree

-

11.7/site/million generations

0.4680

Sigurðardóttir et al [34]c

HVR I and II

Pedigree

-

0.32/site/Myr

0.2529

Parsons et al [32](1)

HVR I and II

Pedigree

-

2.5/site/Myr

1.7957

Howell et al [31]d (2)

D-loop

Pedigree

-

9.48×10-6 mut/site/generation

0.3791

Mishmar et al. [2]

Coding region

Phylogenetic

6.5

1.26 × 10-8 mut/site/year

0.0126

Ingman et al. [28]

Coding region

Phylogenetic

5

1.70 × 10-8 mut/site/year

0.017

Howell et al. [31](2)

Coding regionb

Pedigree

-

1.52 × 10-6 mut/site/generation

0.0609

Present study(1)

1102 bp Coding region

Pedigree

-

8.75 × 10-6 mut/site/generation

0.3501

Present study(2)

1102 bp Coding region

Pedigree

-

5.84 × 10-6 mut/site/generation

0.2334

Present study(3)

1102 bp Coding region

Pedigree

-

8.75 × 10-6 mut/site/generation

0.3501

Present study(4)

1102 bp Coding region

Pedigree

-

5.84 × 10-6 mut/site/generation

0.2334

Present study(5)

1102 bp Coding region

Pedigree

-

1.03 × 10-6 mut/site/generation

0.0411

Present study(6)

1102 bp Coding region

Pedigree

-

5.89 × 10-7 mut/site/generation

0.0236

Present study(7)

1102 bp Coding region

Pedigree

-

4.39 × 10-7 – 4.97 × 10-7 mut/site/generation

0.0176–0.0199

Present study(8)

1102 bp Coding region

Pedigree

-

0–5.84 × 10-8 mut/site/generation

0–0.0023


a. Assuming a generational time of 25 years;

b. Assumed 15447 pb but used fragments of coding region; 4 mutations in 170 transmissions.

c. All the mutations considered were in homoplasmy.

d. Value pooling all the family studies performed until 2003 (table 2 in Howell et al. [31])

(1) All the substitutions that were detected were considered for the mutation rate calculation;

(2) Only the substitutions for which there was evidence of a germinal origin were considered;

(3) Only the substitutions present in women were considered;

(4) Only the substitutions present in women for whom there was evidence of a germinal origin were considered;

(5) Only the substitutions present in women that would become fixed at the individual level considering neutrality were considered;

(6) Only the substitutions with a confirmed germinal origin present in women that would become fixed at the individual level considering neutrality were considered;

(7) Only the substitutions present in women that would become fixed at the individual level considering the effect of selection;

(8) Only the substitutions with a confirmed germinal origin present in women that would become fixed at the individual level considering the effect of selection;

Santos et al. BMC Evolutionary Biology 2008 8:167   doi:10.1186/1471-2148-8-167

Open Data