Mutation patterns of mtDNA: Empirical inferences for the coding region
© Santos et al; licensee BioMed Central Ltd. 2008
Received: 30 August 2007
Accepted: 02 June 2008
Published: 02 June 2008
Human mitochondrial DNA (mtDNA) has been extensively used in population and evolutionary genetics studies. Thus, a valid estimate of human mtDNA evolutionary rate is important in many research fields. The small number of estimations performed for the coding region of the molecule, showed important differences between phylogenetic and empirical approaches. We analyzed a portion of the coding region of mtDNA (tRNA Leu , ND1 and tRNA Ile genes), using individuals belonging to extended families from the Azores Islands (Portugal) with the main aim of providing empirical estimations of the mutation rate of the coding region of mtDNA under different assumptions, and hence to better understand the mtDNA evolutionary process.
Heteroplasmy was detected in 6.5% (3/46) of the families analyzed. In all of the families the presence of mtDNA heteroplasmy resulted from three new point mutations, and no cases of insertions or deletions were identified. Major differences were found in the proportion and type of heteroplasmy found in the genes studied when compared to those obtained in a previous report for the D-loop. Our empirical estimation of mtDNA coding region mutation rate, calculated taking into account the sex of individuals carrying new mutations, the probability of intra-individual fixation of mutations present in heteroplasmy and, to the possible extent, the effect of selection, is similar to that obtained using phylogenetic approaches.
Based on our results, the discrepancy previously reported between the human mtDNA coding region mutation rates observed along evolutionary timescales and estimations obtained using family pedigrees can be resolved when correcting for the previously cited factors.
There are several reasons why the mitochondrial genome (mtDNA) of humans as well as of other mammalians has been considered to be useful in population genetics, phylogeographic, and phylogenetic studies. Besides the usually invoked mtDNA characteristics (high copy number per cell, compact organization and maternal transmission), mtDNA has been widely used because it provides easy access to an orthologous set of genes with little or no recombination and rapid evolution . Moreover, from a theoretical perspective, it has been accepted for a long time that mtDNA haplotype frequencies are controlled primarily by migration and genetic drift and that most of the variation within a species is selectively neutral . However, more recent reports sustain the hypothesis that mtDNA frequency variation is due to natural selection [2–4].
Given the importance of mitochondrial function, it is not straightforward to assume a priori that mtDNA evolves as a strictly neutral marker. Changes in the mtDNA sequence can have substantial impacts on the fitness of the organelle/cell (within individuals) and on the fitness of the individual host organism. Deviations from a strictly neutral model of evolution have been found in a variety of organisms [5–9]. Ballard and Rand , in a revision, gave three main reasons why it is reasonable to predict that mtDNA variation may be under strong selection: i) Mitochondrion is the powerhouse of the cell and, in most organisms, a reduction in ATP production is expected to reduce fecundity. In humans, a reduction in the efficiency of ATP production is known to be highly deleterious or lethal in the extreme case; ii) Proteins from mtDNA interact with those imported from the nuclear genome to form four of the five complexes of the electron transport chain; and iii) The assumption of total absence of recombination in mtDNA means that each genome has a single genealogical history and all genes will share that history. Any evolutionary force acting at any one site will equally affect the history of the whole molecule. Thus, the fixation of an advantageous mutation by selection, for example, will cause the fixation of all other polymorphisms by a process known as "genetic hitchhiking" . Even the quickly evolving non-coding mtDNA region (D-loop) cannot be assumed to have neutral allele frequencies: It is linked to the rest of the genome (where selection has been documented) and conserved motifs within this region exhibit variation that affects mitochondrial transcription and replication in significant ways . Alternatively, polymorphism within a mitochondrial genome may be depressed through selection against linked deleterious mutations, a process known as "background selection" [12–14].
Besides the significance of mtDNA selection per se, the assessment of the impact of selection in mtDNA is crucial in the establishment of mtDNA evolutionary rate, as was previously demonstrated by Denver et al. . In a strict neutral model of evolution, the substitution rate depends only on the mutation rate per individual; however, if there was any, even if slight, effect of selection this would not be true. According to Ohta [15, 16] very slightly deleterious mutants are effectively selected against in populations large enough; however these same mutants should be governed by random drift in small populations behaving as selectively neutral. Thus, small populations may accumulate deleterious mitochondrial mutations at an increased rate .
Human mtDNA substitution rate has been estimated using mainly phylogenetic [18–29] and empirical methods [30–37]. Estimations for the D-loop, based on phylogenetic approaches, range from 0.0575 mutations/site/Myr  to 0.2860 mutations/site/Myr , whereas estimations using an empirical methodology range from 0 mutations/site/Myr [33, 35] to 2.5 mutations/site/Myr . On what concerns the coding region, the few estimations performed so far showed that the substitution rate of the coding region is ~10 times lower than that reported for the D-loop; furthermore, and as observed for the D-loop, important differences between phylogenetic and empirical estimations have been pinpointed . Mishmar et al.  applying a phylogenetic approach to complete sequences of the coding mtDNA region obtained a substitution rate of 0.0126 mutations/site/Myr, whereas Howell et al. , using an empirical estimation for the coding region of mtDNA, report a value of 0.075 mutations/site/Myr.
Since the first empirical D-loop estimation of mtDNA evolutionary rate by Howell et al.  an intense debate about the causes of the discrepancies between phylogenetic and empirical rates has taken place [9, 31, 34, 36–40]. Such discrepancy has been attributed to distinct causes, namely: to differences in the rate of mutation at different mtDNA positions; to the effect of selection and genetic drift; to the occurrence of somatic mutations; to the unintended sequencing of nuclear mitochondrial pseudogenes; and to the leakage of paternal mtDNA and recombination. Moreover Ho et al. [9, 41] described an acceleration of the rate of substitution at evolutionarily short timescales and among other factors, the authors attributed this acceleration to purifying selection acting on mtDNA [9, 41]. However, Emerson  reanalyzing the data of Ho et al.  suggested that it would seem that the time-scale upon which the pedigree rate converges to the evolutionary rate is very much shorter than the timescale that Ho et al.  have focused on, and it is debatable whether this convergence would follow an exponential distribution, or if such a pattern existed, whether it could not be equally explained by coalescent effects.
Recently, we reported on the mtDNA mutation rate of the D-loop , using an empirical approach. Our results supported the conclusion that the discrepancy between phylogenetic and pedigree derived rates cannot be attributed neither to the inclusion of somatic mutations in calculations, nor to the use of families with mtDNA disease, or even to paternal contribution of mtDNA. Moreover, the discrepancy cannot be justified by the fact that mutations observed in families occurred preferentially in hypervariable sites. Santos et al.  advanced two additional factors that must be taken into account: the gender of individuals carrying germinal mutations (mutations carried exclusively by men will never be passed to the next generation) and "the weight" of heteroplasmic germinal mutations (for mutations in mtDNA to reach polymorphism levels in the population – and eventually become fixed – it is first necessary that they pass from an heteroplasmic to an homoplasmic state, at the individual level, and this will be dictated by the initial levels of heteroplasmy).
To date there are only two studies that deal with the empirical mutation rate estimation of coding mtDNA region [31, 35]. Moreover, the discussion of the effect of selection in the fate of new arising mutations in coding and non-coding portions of mtDNA has not been fully addressed. In this work we present the results of the analysis of a portion of the coding region of mtDNA, using individuals belonging to extended families from the Azores Islands (Portugal). The main aims are: a) to provide empirical estimations of the mutation rate of the coding region of mtDNA under different assumptions, and b) to better understand the mtDNA evolutionary process, including the factors that control the levels and progress of mtDNA heteroplasmy until the intraindividual fixation of new arising mutations.
Heteroplasmy was detected in 6.5% of the families analyzed. In all of the families the presence of mtDNA heteroplasmy resulted from three new point mutations, and no cases of insertions or deletions were identified. Our empirical estimation of mtDNA coding region mutation rate, calculated taking into account several factors is similar to that obtained using phylogenetic approaches.
tRNA Leu , ND1 and tRNA Ile genes sequence analysis in Azorean pedigrees
From the 208 individuals first analyzed, six appear to present mtDNA heteroplasmy in the fragment of the coding region that was analyzed. The six individuals presenting heteroplasmy belong to three distinct families, which will be further described. Thus, 6.5% (3/46) of the families present mtDNA heteroplasmy produced by mutations in the region analyzed. In all of the cases, heteroplasmy was produced by a point mutation and no cases of insertions or deletions have been detected.
Description and segregation of heteroplasmy in tRNA Leu , ND1 and tRNA Ile genes
For each family analyzed, code (according to figure 1), sex and proportion of variants in individuals presenting heteroplasmy.
Proportion height peaks Forward Primer
Proportion height peaks Reverse Primer
Mean proportion height peaks
Proportion clone number (N)
84.6%A : 15.4%G
85.7%A : 14.3%G
85.15%A : 14.85%G
82.6%A : 17.4%G
77.8%A : 22.2%G
80.20%A : 19.80%G
81.8%A : 18.2%G (22)
95.6%A : 4.4%G
96.2%A : 3.8%G
95.90%A : 4.10%G
87.5%T : 12.5%C
82.4%T : 17.6%C
84.95%T : 15.05%C
87.7%A : 12.3%G
88.4%A : 11.6%G
88.05%A : 11.95%G
92.3%A : 7.7%G
96.0%A : 4.0%G
94.15%A : 5.85%G
98.0%A : 2.0%G (50)
64.7%A : 35.3%G
66.7%A : 33.3%G
65.70%A : 34.30%G
81.8%A : 18.2%G
84.2%A : 15.8%G
83.00%A : 17.00%G
82.8%A : 17.2%G
85.7%A : 14.3%G
84.25%A : 15.75%G
88.2%A : 11.8%G
89.3%A : 10.7%G
88.75%A : 11.25%G
Characterization of positions presenting heteroplasmy.
Type of mutation and Implication
Homoplasmic individuals of the family/Referencea/Chimpanzeeb
Number of hitsc
Population Database frequency
Substitution in the tRNA Leu associated with Myopaty and Cardiomiopaty
100% A 0% G
Synonymous substitution in ND1
99.73% T 0.27% C
Nonsynonymous substitution in ND1 that implies an Asparagine to Serine amino acid change.
100% A 0% G
Families showing point heteroplasmy can be subdivided into:
1) One family in which only one individual presented heteroplasmy produced by a point mutation:
- Family CG_II (Fig. 1): in the first step of the analysis we sequenced the tRNA Leu , ND1 and tRNA Ile region of five maternally related individuals (5 women) from which, one (II2) displayed low levels of heteroplasmy (84.95%T:15.05%C) as the result of a T->C mutation in position 3396 (Table 1). This mutation, although in a coding region, is a synonymous mutation since it does not imply an aminoacid change and the mitotype C(3396) was detected, although at low frequency, at the population level (Table 2). In this family the reported heteroplasmy may have resulted from a somatic mutation that occurred in the individual herself, or alternatively, it may have resulted from germline mutations that occurred in the oocyte from which the heteroplasmic individual developed. Thus, it is not clear if this mutation can be transmitted to the next generation
2) Two families in which various individuals displayed heteroplasmy produced by a point mutation:
- Family AV (Fig. 1): we first sequenced the 3230–4331 region in ten maternally related individuals (5 men and 5 women). From these, one man (IV3) and one woman (IV4) showed low levels of heteroplasmy (85.15%A:14.85%G and 80.20%A:19.80%G respectively) as a consequence of a point mutation in position 3260 of the tRNALeu(UUR) (Table 1). The subsequent analysis of their mother (III3) and grandmother (II1) showed the presence of very low levels of heteroplasmy in the mother (95.90%A:4.10%G) and the absence of heteroplasmy in the grandmother. Thus, it is likely that the transition from A to G in position 3260 occurred in individual III3 and was transmitted to individuals IV3 and IV4.
- Family JS (Fig. 1): The 3230–4331 region was first sequenced in four maternally related individuals (3 men and 1 woman). From these, one man (II5) showed medium levels of heteroplasmy (65.70%A:34.30%G), whereas another man (III1) and one woman (III2) showed low levels of heteroplasmy (88.05%A:11.95%G and 94.15%A:5.85%G respectively) (Table 1). The heteroplasmy resulted from a point mutation in position 3602 of the ND1 gene (Table 1). This mutation is a non-synonymous mutation that changes the aminoacid residue 99 of the ND1 sub-unit from asparagine to serine. The subsequent analysis of their maternal ancestors (I2, II2 and II3) showed the presence of low levels of heteroplasmy in all of them (G(3602) mitotype in a frequency inferior to 17%). Thus, it was not possible to identify directly the individual where the mutation arose and, by consequence, the ancestral state for this position in this family. If we take into account that this position appears to be invariant at the population level (100% A) (Table 2) and that the state in the reference sequences [28, 44] is an adenine, we can hypothesize that this mutation could represent an A to G change at position 3602. As the conservation index of this mutation is 100%, we may consider that it may have some functional consequence and that is not neutral. However, at this point we cannot predict if, this mutation will be deleterious or beneficial.
Overall Analysis of Mutations: mutation pattern and mutation rate in tRNA Leu , ND1 and tRNA Ile genes
We detected three transitions that gave rise to heteroplasmy in three distinct positions. One can be somatic or germinal and two can be considered germinal (Table 2). One mutation was detected in the tRNA Leu and the other two were found in the ND1 gene. All the mutations take place at sites that present a very low number of hits in the mtDNA phylogeny, a high conservation index, and that don't appear to be polymorphic in human populations.
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 ).
Human-chimpanzee divergence time (Myr)
Substitution rate as expressed by authors
Standardized substitution rate mutations/site/Myra
Horai et al. 
3.89 × 10-8 mut/site/year
Kivisild et al. 
4212 synonymous positions
3.5 × 10-8 transversions/site/year
Kivisild et al. 
2.1 × 10-9 transversions/site/year
Kivisild et al. 
4.1 × 10-10 transversions/site/year
Cann et al. 
Torroni et al. 
Vigilant et al. 1991
HVR I and II
Tamura and Nei 1993
HVR I and II
Pesole et al. 1992
HVR I and II
18 ± 10/100 site/Myr
0.1800 ± 0.1
Ho et al. 
Population (calibration 80 kyr)
0.197 (0.115–0.293) mut/site/Myr
Santos et al. (1)
Santos et al. (2)
Santos et al. (4)
Santos et al. (6)
Heyer et al. c
HVR I and II
Sigurðardóttir et al c
HVR I and II
Parsons et al (1)
HVR I and II
Howell et al d (2)
Mishmar et al. 
1.26 × 10-8 mut/site/year
Ingman et al. 
1.70 × 10-8 mut/site/year
Howell et al. (2)
1.52 × 10-6 mut/site/generation
Present study (1)
1102 bp Coding region
8.75 × 10-6 mut/site/generation
Present study (2)
1102 bp Coding region
5.84 × 10-6 mut/site/generation
Present study (3)
1102 bp Coding region
8.75 × 10-6 mut/site/generation
Present study (4)
1102 bp Coding region
5.84 × 10-6 mut/site/generation
Present study (5)
1102 bp Coding region
1.03 × 10-6 mut/site/generation
Present study (6)
1102 bp Coding region
5.89 × 10-7 mut/site/generation
Present study (7)
1102 bp Coding region
4.39 × 10-7 – 4.97 × 10-7 mut/site/generation
Present study (8)
1102 bp Coding region
0–5.84 × 10-8 mut/site/generation
Proportion and type of heteroplasmy: coding region vsD-loop
The analysis of individuals belonging to 46 families of Azorean ancestry (Fig. 1) reveals that in 6.5% of the families there is at least one individual that presents mtDNA heteroplasmy produced by mutation in the analyzed coding region. This value is significantly lower than that obtained by Santos et al.  for the D-loop (72.9% – 35 of 48 families) using almost the same set of families (Proportion test: Z = -6.556; p < 0.0001). This difference is still significant (Proportion test: Z = -2.009; p = 0.0222) if only point heteroplasmy is considered for the D-loop (20.8% – 10 of 48 families).
Frequency of insertions/deletions in poly-C tracts (minimum of seven cytosine residues that may be or not interrupted by another base) of human mtDNA from a database of 1457 sequences.
% in/del in database individuals
% heteroplasmic families in empirical studies
CCCCCCCTCCCCC or CCCCCCCTCCCCCC
D-loop (Hypervariable region II, conserved sequence block 2)
12S ribosomal RNA
12S ribosomal RNA
NADH Dehydrogenase subunit 1
NADH Dehydrogenase subunit 1
Cytochrome c oxidase subunit I
Cytochrome c oxidase subunit III
NADH dehydrogenase subunit 3
NADH dehydrogenase subunit 4
NADH dehydrogenase subunit 5
NADH dehydrogenase subunit 6
D-loop (Hypervariable region I)
Factors influencing mutation rate estimation in pedigrees
The mutation rate obtained for the coding region of mtDNA considering only germinal mutations was 0.2334 mutations/site/Myr, the highest value reported so far, and much higher than those obtained by phylogenetic methods (Table 3). Moreover, empirical estimations for the D-loop and for the coding region of mtDNA (see Table 3 and references therein), clearly show that the evolutionary rate was higher for the D-loop, as it was previously demonstrated by other works [31, 41].
The possible causes for the discrepancy between phylogenetic and empirical estimations of mutation rate will be discussed further ahead, implicating mainly the process by which heteroplasmy is resolved as well as the effect of sex proportion and selection at the different nested hierarchies of populations covered by the mtDNA molecule (the organelle, the cell, the tissue, the organism, and so on up through natural populations and species) .
For the coding region analyzed, confirmed germinal mutations occurred in very stable positions conserved among species. These results reinforce our previous observations for the D-loop  that the discrepancy observed in the mutation rate reported in family and phylogenetic studies can not be attributed to the inclusion of somatic mutations in calculations or to the use of families with mtDNA disease, neither to the occurrence of mutations preferentially in hypervariable sites. As it was previously realized by Santos et al. , there are other factors that may be considered in the estimation of mutation rate using empirical approaches; mainly, the sex of individuals where new mutations were found (this correction would be the equivalent of considering the effective population size for the coalescent estimation of the mutation rate, N, for the mtDNA ), as well as the probability of intra-individual fixation of the new arising mutations (for a detailed explanation see Santos et al. ).
The accuracy of the proposed corrections can be ascertain by two different results: 1) if we consider the data of Heyer et al.  (only homoplasmic mutations were found and the number of men and women analyzed were similar) and we correct for gender proportion the mutation rate would be 5.85×10-6mutations/site/generation, a value similar to that obtained by Santos et al.  for the D-loop, after correcting for the sex of transmitters and for the presence of heteroplasmy; 2) the value obtained for the D-loop , after correcting for sex and heteroplamy is similar to that reported by Ho et al.  using population data (Table 3).
It is important to note that our study addresses a different question to that analyzed by Ho et al. [9, 41]. While they are analyzing the discrepancies in the "rate of change" when it is estimated using short or long-term calibration points, our concern is precisely the process inside the rate of change, i.e., the factors responsible for the differences between the mutation and substitution rates. Therefore, in the comparisons of Ho et al. [9, 41] the short-term points are represented by populations, where the mutations observed are already fixed at least at the individual level (they do not report any effect derived from heteroplasmic mutations). Moreover, our results support the idea proposed by Emerson  that it would seem likely that the time-scale upon which the pedigree rate converges to the evolutionary rate is very much shorter than the timescale which Ho et al.  have focused on. Furthermore, we have to consider the higher uncertainty surrounds the estimation of short-term mutation rates than in the estimation of long-term rates . This uncertainty results from the fact that smaller errors in calibration points may have larger consequences in short-term mutation rates and "because as the calibrations move closer to the present, there is a decreasing amount of information in the sequences" . Even when using ancient DNA sequences, as proposed by Ho et al. , we should consider that an haplotype observed at any given time could represent a time span of thousands of years, so radiocarbon dates will provide an additional source of error in determining the actual age of the haplotype.
Assuming that the correction for sex and heteroplasmy are important to empirically estimate the evolutionary rate of mtDNA, if we take into account these two factors, and we assume that mutations detected are neutral or nearly neutral (and by consequence that the probability that the new variant will eventually become fixed – homoplasmic – in the individual is approximately the proportion of the new variant) the number of new mutations that can be fixed at the individual level decreased to 0.202 (if only confirmed germinal mutations are included) – 0.3525 (if all the mutation are included) and by consequence the mutation rate would be reduced to 0.0236 mutations/site/Myr – 0.0411 mutations/site/Myr (Table 3). However, our data clearly evidences that some of the mutations detected cannot be considered neutral and by consequence its probability of intra-individual fixation may be smaller than the frequency in heteroplasmic individuals. As referred by Santos et al.  a suitable strategy to solve this problem would be to empirically estimate the proportion of intra-individual fixation by observing the number of heteroplasmic transmissions that become fixed for the new variant. In these circumstances, all the factors affecting the segregation of heteroplasmy, including selection, would be averaged and therefore implicitly considered. Furthermore, assuming that selection pressure will be similar at the intra-individual level and the population level, the rate of mutations that reach intra-individual fixation will be similar to the rate of population (and species) fixation. This means that only neutral and mildly deleterious mutations will be fixed at an intra-individual level but not deleterious mutations, as is observed in the majority of mitochondrial diseases in which the mutant type never reaches intra-individual fixation. Selection, however, could still modify the population fixation rate in cases in which a change in environment modifies the selective pressure . Unfortunately, at this time, we cannot empirically estimate the probability of intra-individual fixation and we will try to access this question by indirect approaches.
The new mutation arising in family AV in position 3260 has been associated with the development of maternally inherited myopathy and cardiomyopathy [51, 52]; the wild-type A(3260) is normally bound to the U(3272) as part of a 4 bp palindrome that forms the anticodon stem of the tRNALeu(UUR) cloverleaf, the G(3260) mutation creates a non-standard base pair with the corresponding U(3272). The A-U pair is highly conserved through mammalian species  and it is probable that the G(3260) affects the stability of the tRNA anticodon stem . The biochemical analysis of oxygen consumption in transformant cybrids suggested that for the G(3260) mutation the threshold for detectable impairment of mitochondrial respiration is higher than 60% mutant mtDNA . Moreover, all symptomatic patients described by Zeviani et al.  had a percentage of mutated mitotypes in muscle of at least 87%, whereas one unaffected individual had a percentage of mutant molecules of around 78%. These observations are consistent with our finding that the individuals used in this study are healthy individuals, since the percentages of mutant mtDNA detected in the three individuals of AV family are lower than 20%. The challenge is now to predict the fate of this new arising pathogenic mutation; the IV3 man cannot transmit the new mutation; however her sister can have descendents carrying the mutation. Assuming that selection will not act against the G variant, the fate of the mutation will be entirely governed by drift. According to the model proposed by Santos et al.  (that allowed us to predict the probability that a variant drift from ~20% of copies to more than 60% in one generation) it is unlikely that the disease will affect the children of IV4. Moreover, even if this mutation can reach fixation at the individual-level in a future generation, it would never reach fixation at the population level, unless an environmental change, or any factor relaxing the selective pressure, reduce its negative effect. Mitochondrial DNA evolution at the population level may be modulated for example by the climatic variables  or by the diet of individuals .
The non-synonymous A to G mutation at position 3602 was not described so far, both at the population level or associated to pathology. The conservation index of this position is 100% indicating that it has a functional relevance and that probably is not neutral. The problem here is to determine if this mutation has a negative or positive effect. At this time, it is difficult to determine this issue without any functional assay. Furthermore, we cannot predict if weather, or any other factor, will change in the future, changing in turn the effect of the mutation.
Taking together these evidences, the number of mutations that reach fixation at the individual level should range from 0 (if both germinal mutations detected are considered to be deleterious) to 0.02 (if it is assumed that the mutation in position 3602 is in fact neutral). This represents a mutation rate for the coding fragment analyzed ranging between 0 mutations/site/Myr and 0.0023 mutations/site/Myr and similar to that obtained using phylogenetic approaches (Table 3). If we include the mutation in position 3396, the mutation rate for the coding fragment analyzed ranges between 0.0176 mutations/site/Myr and 0.0199 mutations/site/Myr. These value are similar to that values reported by phylogenetic estimations (Table 3).
Given the importance of mitochondrial function, changes in the mtDNA sequence can have a substantial impact on the fitness of the organelle/cell/individual and may be eliminated at the different levels of organization of mtDNA. Our results are in agreement with this assumption. First of all, major differences were detected in the proportion and type of heteroplasmy found in the coding and non-coding regions of mtDNA. If we assume that mutations occur randomly in mtDNA genome, the present results support the idea that newly arising mutations in the coding region are eliminated probably at the organelle and cell levels, before they reach a detectable frequency in heteroplasmy. Moreover, some of the mutations found in heteroplasmy in the coding region would never reach fixation at the individual level, since they appear to be deleterious, and would be latter eliminated.
Our empirical estimation of mtDNA coding region mutation rate, calculated taking into consideration the sex of individuals carrying new mutations, the probability of intra-individual fixation of mutations present in heteroplasmy and the effect of selection, is similar to that obtained using phylogenetic approaches. Based on our results, the discrepancy previously reported between the human mtDNA coding region mutation rate observed along evolutionary timescales and estimations obtained using family pedigrees can be understood when correcting for the above cited factors.
Genealogies and Samples
The genealogical information and sample databank were previously described in Santos et al. . All the individuals included in the sample bank were informed by members of the research team about the aims and ethical guidelines of the project and signed an informed consent form before the sampling procedure, conducted by mouth scrap. For this work, we selected 406 individuals belonging to 46 independent mtDNA lineages and corresponding to 311 mtDNA transmissions (Fig. 1).
The analysis of the samples was done following a strategy similar to that used in Santos et al. , with 5 main steps:
1) DNA extraction, PCR amplification and sequencing of the region that encompasses the tRNA Leu , ND1 and tRNA Ile genes, of the individuals from the most recent generation (represented by filled black squares and circles in Figure 1); 2) Confirmation by a second PCR amplification and sequencing of the individuals that appeared to be heteroplasmic in step 1; 3) DNA extraction, PCR amplification and sequencing of the ancestors of individuals confirmed as heteroplasmic in step 2 (individuals represented by half tone squares and circles in Figure 1). Whenever heteroplasmy was not present in the mother, the paternal mtDNA was analyzed to exclude a possible paternal contribution; 4) To authenticate results an independent DNA extraction, PCR amplification and sequencing were subsequently performed for all individuals showing heteroplasmy; 5) Cloning and sequencing of multiple clones of individuals that presented heteroplasmy and that are relevant to the mutation rate calculation.
DNA extraction, PCR amplification and sequencing
DNA from the buccal cells was extracted using the JETQUICK Blood and Cell DNA Purification Kit (Genomed) according to the manufacturer's specifications. The mtDNA region from position 3120 to 5129 (according to the revised Cambridge Reference Sequence – CRS ), was amplified using new designed primers L-MT3120 (5'-CCTGTACGAAAGGACAAGAG-3') and H-MT5129 (5'-GTTGAGTAGTAGGAATGCGGT-3'). The new primers were verified, using the BLAST procedure, to prevent the amplification of nuclear mitochondrial pseudogenes. The PCR reaction program involved an initial 5 min. denaturation step at 94°C followed by 35 cycles of 94°C for 1 min., 57°C for 45 s and 72°C for 2 min., and a final extension step of 7 min. at 72°C. PCR products were purified using the JETQUICK PCR Purification Spin Kit (Genomed).
All samples were fully sequenced between positions 3230 and 4331 (tRNA Leu , ND1 and tRNA Ile genes) using four new designed primers, two in the direct direction [L-MT3120 (5'-CCTGTACGAAAGGACAAGAG-3') and L-MT3746 (5'-CCATCATTCTACTATCAACA-3')] and two in the reverse direction [H-MT3889 (5'-GGTTGGTCTCTGCTAGTGTG-3') and H-MT4432 (5'-GGCCCGATAGCTTATTTAG-3')]. Sequence reactions were carried out using the sequencing kit BigDye® Terminator v.3 (Applied Biosystems) according to the manufacturer's specifications and ran in an ABI Prism 3100 sequencer.
To quantify the proportion of heteroplasmy in samples that appeared to be relevant to mutation rate calculation, a PCR using primers L-MT3120 and H-MT3889 was performed. The PCR products were subsequently cloned into the pCR®4-TOPO® vector with the TOPO TA Cloning® Kit for Sequencing (Invitrogen) and multiple clones for each sample were sequenced using the same primers used for PCR.
Detection of heteroplasmy and Sequence alignment
Sequences were analyzed using the Sequencing Analysis 5.2.0 software (Applied Biosystems), considering a value of 2% in the option of Mixed Base Identification. Moreover, al the sequences were visually verified and compare with other from the same run to detect the presence of heteroplasmy. Only sequences with a good intensity and with background almost imperceptible were used.
Subsequently sequences were aligned in relation to the revised CRS , using BioEdit . All polymorphic positions were confirmed in sequencing electropherograms. Sequences without ambiguities were obtained between positions 3230–4331.
Levels of heteroplasmy
Levels of heteroplasmy were determined as described in Santos et al.  using the height of the peaks in the electropherograms and/or the cloning of PCR products.
Population Database and Reference Sequences
To calculate the frequency of each variant for a particular nucleotide position, we created a population database of 1457 mtDNA coding region sequences [2, 28, 54–59]. To infer the ancestral state in a given nucleotide position we used two sequences: a) the reference sequence proposed by Ingman et al.  – GeneBank accession number NC_001807 – that originates from an African sequence (GeneBank accession number AF347015); and b) the Pan troglodytes mtDNA sequence – GeneBank accession number X93335 .
Mutation Rate Estimation
The mutation rate was derived from the number of detected mutations per number of "meioses" or transmission events, which is the number of cumulative generations tracing back to the maternal ancestor. When the mutation rate is expressed as mutations per base pair per million years (Myr), the generational time was assumed to be 25 years . The mutation rate (considering substitutions only) was estimated according to different assumptions: 1) all the substitutions that were detected were considered for the mutation rate calculation, 2) only the substitutions for which a germinal origin was evidenced were considered (applied by the majority of authors, such as ), 3) only the substitutions present in women for whom there was evidence of a germinal origin were considered (this takes into account that the mutations present in men have the same evolutionary weight of somatic mutations, since they cannot be transmitted to the next generation), and 4) only the substitutions with a germinal origin present in women that would become fixed at the individual level were considered. To perform these estimations we tried to distinguish if a mutation is neutral or not. A mutation was considered deleterious if it had been previously described as correlated with any form of disease. On the other hand, non-neutral mutations may have functional consequences that may be assessed by analyzing the conservation indices. Neutral mutations would have a low conservation index, whereas non-neutral (deleterious or adaptive) mutations would have a high conservation index . Conservation Index was estimated as in Ruiz-Pesini et al. , using the same set of species. For neutral mutations the probability of intra-individual fixation of the new variant was considered to be equal to its frequency in the heteroplasmic individual. For non-neutral deleterious mutations the probability of intra-individual fixation was considered to vary between zero and the frequency in the heteroplasmic individual. The 95% confidence intervals for proportions were computed using the program OpenStat2 v1.42 .
This work was supported by the Project BIOPOLIS (05/MAC/2.3/C14), funded by Interreg IIIB. C. Santos and R. Montiel are postdoctoral fellows of the Fundação para a Ciência e a Tecnologia (CS: SFRH/BPD/20944/2004; RM: SFRH/BPD/32473/2006).
- Ballard JWO, Rand DM: The population biology of mitochondrial DNA and its phylogenetic implications. Annual Review of Ecology Evolution and Systematics. 2005, 36: 621-642. 10.1146/annurev.ecolsys.36.091704.175513.View Article
- Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, Brandon M, Easley K, Chen E, Brown MD, Sukernik RI, Olckers A, Wallace DC: Natural selection shaped regional mtDNA variation in humans. Proceedings of the National Academy of Sciences of the United States of America. 2003, 100 (1): 171-176. 10.1073/pnas.0136972100.PubMed CentralView ArticlePubMed
- Wallace DC, Ruiz-Pesini E, Mishmar D: mtDNA variation, climatic adaptation, degenerative diseases, and longevity. Cold Spring Harb Symp Quant Biol. 2003, 68: 479-486. 10.1101/sqb.2003.68.471.View ArticlePubMed
- Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC: Effects of purifying and adaptive selection on regional variation in human mtDNA. Science. 2004, 303 (5655): 223-226. 10.1126/science.1088434.View ArticlePubMed
- Nachman MW: Deleterious mutations in animal mitochondrial DNA. Genetica. 1998, 102–103 (1–6): 61-69. 10.1023/A:1017030708374.View ArticlePubMed
- Rand DM, Kann LM: Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica. 1998, 102–103 (1–6): 393-407. 10.1023/A:1017006118852.View ArticlePubMed
- Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK: High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science. 2000, 289 (5488): 2342-2344. 10.1126/science.289.5488.2342.View ArticlePubMed
- Rand DM: The units of selection on mitochondrial DNA. Annu Rev Ecol Syst. 2001, 32: 415-448. 10.1146/annurev.ecolsys.32.081501.114109.View Article
- Ho SYW, Phillips MJ, Cooper A, Drummond AJ: Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular biology and evolution. 2005, 22 (7): 1561-1568. 10.1093/molbev/msi145.View ArticlePubMed
- Smith JM, Haigh J: The hitch-hiking effect of a favourable gene. Genet Res. 1974, 23: 23-35.View ArticlePubMed
- Coskun PE, Beal MF, Wallace DC: Alzheimer's brains harbor somatic mtDNA control-region mutations that suppress mitochondrial transcription and replication. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101 (29): 10726-10731. 10.1073/pnas.0403649101.PubMed CentralView ArticlePubMed
- Charlesworth B: The Effect of Background Selection against Deleterious Mutations on Weakly Selected, Linked Variants. Genetical Research. 1994, 63 (3): 213-227.View ArticlePubMed
- Charlesworth B, Morgan MT, Charlesworth D: The Effect of Deleterious Mutations on Neutral Molecular Variation. Genetics. 1993, 134 (4): 1289-1303.PubMed CentralPubMed
- Charlesworth D, Charlesworth B, Morgan MT: The pattern of neutral molecular variation under the background selection model. Genetics. 1995, 141 (4): 1619-1632.PubMed CentralPubMed
- Ohta T: Population Size and Rate of Evolution. Journal of Molecular Evolution. 1972, 1 (4): 305-&. 10.1007/BF01653959.View Article
- Ohta T: Slightly Deleterious Mutant Substitutions in Evolution. Nature. 1973, 246 (5428): 96-98. 10.1038/246096a0.View ArticlePubMed
- Bergstrom CT, Pritchard J: Germline bottlenecks and the evolutionary maintenance of mitochondrial genomes. Genetics. 1998, 149 (4): 2135-2146.PubMed CentralPubMed
- Brown WM: Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proceedings of the National Academy of Sciences of the United States of America. 1980, 77 (6): 3605-3609. 10.1073/pnas.77.6.3605.PubMed CentralView ArticlePubMed
- Cann RL, Stoneking M, Wilson AC: Mitochondrial DNA and human evolution. Nature. 1987, 325 (6099): 31-36. 10.1038/325031a0.View ArticlePubMed
- Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC: African populations and the evolution of human mitochondrial DNA. Science. 1991, 253 (5027): 1503-1507. 10.1126/science.1840702.View ArticlePubMed
- Hasegawa M, Horai S: Time of the deepest root for polymorphism in human mitochondrial DNA. Journal of Molecular Evolution. 1991, 32 (1): 37-42. 10.1007/BF02099927.View ArticlePubMed
- Pesole G, Sbisá E, Preparata G, Saccone C: The evolution of the mitochondrial D-loop region and the origin of modern man. Mol Biol Evol. 1992, 9 (4): 587-598.PubMed
- Stoneking M, Bhatia K, Wilson AC: Rate of sequence divergence estimated from restriction maps of mitochondrial DNAs from Papua New Guinea. Cold Spring Harb Symp Quant Biol. 1986, 51 (Pt 1): 433-439.View ArticlePubMed
- Stoneking M, Sherry ST, Redd AJ, Vigilant L: New Approaches to Dating Suggest a Recent Age for the Human Mtdna Ancestor. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences. 1992, 337 (1280): 167-175. 10.1098/rstb.1992.0094.View Article
- Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993, 10 (3): 512-526.PubMed
- Torroni A, Chen YS, Semino O, Santachiara-Beneceretti AS, Scott CR, Lott MT, Winter M, Wallace DC: mtDNA and Y-chromosome polymorphisms in four Native American populations from southern Mexico. American journal of human genetics. 1994, 54 (2): 303-318.PubMed CentralPubMed
- Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N: Recent African Origin of Modern Humans Revealed by Complete Sequences of Hominoid Mitochondrial Dnas. Proceedings of the National Academy of Sciences of the United States of America. 1995, 92 (2): 532-536. 10.1073/pnas.92.2.532.PubMed CentralView ArticlePubMed
- Ingman M, Kaessmann H, Paabo S, Gyllensten U: Mitochondrial genome variation and the origin of modern humans. Nature. 2000, 408 (6813): 708-713. 10.1038/35047064.View ArticlePubMed
- Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ: The role of selection in the evolution of human mitochondrial genomes. Genetics. 2006, 172 (1): 373-387. 10.1534/genetics.105.043901.PubMed CentralView ArticlePubMed
- Howell N, Kubacka I, Mackey DA: How rapidly does the human mitochondrial genome evolve?. American journal of human genetics. 1996, 59 (3): 501-509.PubMed CentralPubMed
- Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C: The pedigree rate of sequence divergence in the human mitochondrial genome: There is a difference between phylogenetic and pedigree rates. American journal of human genetics. 2003, 72 (3): 659-670. 10.1086/368264.PubMed CentralView ArticlePubMed
- Parsons TJ, Muniec DS, Sullivan K, Woodyatt N, AllistonGreiner R, Wilson MR, Berry DL, Holland KA, Weedn VW, Gill P, Holland MM: A high observed substitution rate in the human mitochondrial DNA control region. Nature genetics. 1997, 15 (4): 363-368. 10.1038/ng0497-363.View ArticlePubMed
- Soodyall H, Jenkins T, Mukherjee A, du Toit E, Roberts DF, Stoneking M: The founding mitochondrial DNA lineages of Tristan da Cunha Islanders. American journal of physical anthropology. 1997, 104 (2): 157-166. 10.1002/(SICI)1096-8644(199710)104:2<157::AID-AJPA2>3.0.CO;2-W.View ArticlePubMed
- Sigurðardóttir S, Helgason A, Gulcher JR, Stefansson K, Donnelly P: The mutation rate in the human mtDNA control region. American journal of human genetics. 2000, 66 (5): 1599-1609. 10.1086/302902.View Article
- Cavelier L, Jazin E, Jalonen P, Gyllensten U: MtDNA substitution rate and segregation of heteroplasmy in coding and noncoding regions. Human Genetics. 2000, 107 (1): 45-50. 10.1007/s004390050009.View ArticlePubMed
- Heyer E, Zietkiewicz E, Rochowski A, Yotova V, Puymirat J, Labuda D: Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. American journal of human genetics. 2001, 69 (5): 1113-1126. 10.1086/324024.PubMed CentralView ArticlePubMed
- Santos C, Montiel R, Sierra B, Bettencourt C, Fernandez E, Alvarez L, Lima M, Abade A, Aluja MP: Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Mol Biol Evol. 2005, 22 (6): 1490-1505. 10.1093/molbev/msi141.View ArticlePubMed
- Paabo S: Mutational hot spots in the mitochondrial microcosm. American journal of human genetics. 1996, 59 (3): 493-496.PubMed CentralPubMed
- Macaulay VA, Richards MB, Forster P, Bendall KE, Watson E, Sykes B, Bandelt HJ: mtDNA mutation rates – No need to panic. American journal of human genetics. 1997, 61 (4): 983-986. 10.1016/S0002-9297(07)64211-6.PubMed CentralView ArticlePubMed
- Hagelberg E: Recombination or mutation rate heterogeneity? Implications for Mitochondrial Eve. Trends in Genetics. 2003, 19 (2): 84-90. 10.1016/S0168-9525(02)00048-3.View ArticlePubMed
- Ho SY, Shapiro B, Phillips MJ, Cooper A, Drummond AJ: Evidence for time dependency of molecular rate estimates. Syst Biol. 2007, 56 (3): 515-522. 10.1080/10635150701435401.View ArticlePubMed
- Emerson BC: Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates. Syst Biol. 2007, 56 (2): 337-345. 10.1080/10635150701258795.View ArticlePubMed
- Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N: Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature genetics. 1999, 23 (2): 147-147. 10.1038/13779.View ArticlePubMed
- Arnason U, Gullberg A, Janke A, Xu X: Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. Journal of Molecular Evolution. 1996, 43 (6): 650-661. 10.1007/BF02202113.View ArticlePubMed
- Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC: An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic acids research. 2007, 35: D823-D828. 10.1093/nar/gkl927.PubMed CentralView ArticlePubMed
- Hauswirth WW, Clayton DA: Length heterogeneity of a conserved displacement-loop sequence in human mitochondrial DNA. Nucleic acids research. 1985, 13 (22): 8093-8104. 10.1093/nar/13.22.8093.PubMed CentralView ArticlePubMed
- Lee HY, Chung U, Yoo JE, Park MJ, Shin KJ: Quantitative and qualitative profiling of mitochondrial DNA length heteroplasmy. Electrophoresis. 2004, 25 (1): 28-34. 10.1002/elps.200305681.View ArticlePubMed
- Hauswirth WW, Walle Van de MJ, Laipis PJ, Olivo PD: Heterogeneous mitochondrial DNA D-loop sequences in bovine tissue. Cell. 1984, 37 (3): 1001-1007. 10.1016/0092-8674(84)90434-3.View ArticlePubMed
- Ruiz-Pesini E, Wallace DC: Evidence for adaptive selection acting on the tRNA and rRNA genes of human mitochondrial DNA. Human Mutation. 2006, 27 (11): 1072-1081. 10.1002/humu.20378.View ArticlePubMed
- Lundstrom R, Tavare S, Ward RH: Estimating substitution rates from molecular data using the coalescent. Proceedings of the National Academy of Sciences of the United States of America. 1992, 89 (13): 5961-5965. 10.1073/pnas.89.13.5961.PubMed CentralView ArticlePubMed
- Zeviani M, Gellera C, Antozzi C, Rimoldi M, Morandi L, Villani F, Tiranti V, DiDonato S: Maternally inherited myopathy and cardiomyopathy: association with mutation in mitochondrial DNA tRNA(Leu)(UUR). Lancet. 1991, 338 (8760): 143-147. 10.1016/0140-6736(91)90136-D.View ArticlePubMed
- Mariotti C, Tiranti V, Carrara F, Dallapiccola B, DiDonato S, Zeviani M: Defective respiratory capacity and mitochondrial protein synthesis in transformant cybrids harboring the tRNA(Leu(UUR)) mutation associated with maternally inherited myopathy and cardiomyopathy. J Clin Invest. 1994, 93 (3): 1102-1107. 10.1172/JCI117061.PubMed CentralView ArticlePubMed
- Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 1999, 41: 95-98.
- Attardi G: The elucidation of the human mitochondrial genome: a historical perspective. Bioessays. 1986, 5 (1): 34-39. 10.1002/bies.950050111.View ArticlePubMed
- Obayashi T, Hattori K, Sugiyama S, Tanaka M, Tanaka T, Itoyama S, Deguchi H, Kawamura K, Koga Y, Toshima H, Takeda N, Nagano M, Ito T, Ozawa T: Point mutations in mitochondrial DNA in patients with hypertrophic cardiomyopathy. Am Heart J. 1992, 124 (5): 1263-1269. 10.1016/0002-8703(92)90410-W.View ArticlePubMed
- Ingman M, Gyllensten U: Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Research. 2003, 13 (7): 1600-1606. 10.1101/gr.686603.PubMed CentralView ArticlePubMed
- Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, Fuku N, Guo LJ, Hirose R, Fujita Y, Kurata M, Shinoda K, Umetsu K, Yamada Y, Oshida Y, Sato Y, Hattori N, Mizuno Y, Arai Y, Hirose N, Ohta S, Ogawa O, Tanaka Y, Kawamori R, Shamoto-Nagai M, Maruyama W, Shimokata H, Suzuki R, Shimodaira H: Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 2004, 14 (10A): 1832-1850. 10.1101/gr.2286304.PubMed CentralView ArticlePubMed
- Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, Li ZY, Lin M: Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. Plos Biology. 2005, 3 (8): 1362-1372. 10.1371/journal.pbio.0030247.View Article
- Pellekaan van Holst SM, Ingman M, Roberts-Thomson J, Harding RM: Mitochondrial genomics identifies major haplogroups in Aboriginal Australians. American journal of physical anthropology. 2006, 131 (2): 282-294. 10.1002/ajpa.20426.View Article
- Miller WG: OpenStat2 (OS2) Version 1.4.4. 2003, West DeMoines, Iowa
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