Biocenter and Department of Neurology, University of Oulu, Oulu, Finland
Correspondence: E-mail: kari.majamaa{at}oulu.fi.
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Abstract |
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Key Words: human mitochondrial DNA rates of evolution selective constraints structural/functional domains phylogenetics
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Introduction |
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The oxidative phosphorylation system is located in the inner mitochondrial membrane, and it consists of five protein complexes (I, II, III, IV, and V) in which mitochondrial- and nuclear-encoded subunits are in close proximity and subject to mutual interactions (Schmidt et al. 2001). Oxidative phosphorylation has a central role in cellular energy metabolism, because it is the final common pathway in the production of adenosine triphosphate (ATP) from glucose, and it is likely that the functionality of the various subunits is maintained by purifying selection. The genes in mtDNA are subject to different selective constraints (Pesole et al. 1999; Tourasse and Li 2000) and are therefore expected to evolve at different rates, but the rank order of these rates should be the same in all lineages of a phylogeny (Rand 2001). Analyses of Drosophila mtDNA have indicated, however, that specific regions of mtDNA have experienced different histories of selection in different lineages (Ballard 2000a, 2000b). Lineage-specific interactions have been suggested to explain this finding (Blier, Dufresne, and Burton 2001). Such interactions between gene products, either mitochondrial-nuclear or mitochondrial-mitochondrial, might expose a region of the mtDNA genome to unusual selection, which should result in a local decrease in polymorphism or a shift in the allele frequency spectrum that is not present in other lineages. Alternatively, environmental factors such as climate could also impose different selective forces in different lineages, and lineage-specific differences have recently been identified in the nonsynonymous/synonymous rate ratio between human mtDNA lineages from the tropical, temperate, and arctic zones (Mishmar et al. 2003).
We report here on a systematic search for patterns suggesting lineage-specific selective influences in 837 human mtDNA sequences (Ingman et al. 2000; Finnilä, Lehtonen, and Majamaa 2001; Maca-Meyer et al. 2001; Herrnstadt et al. 2002). We aligned the sequences and calculated molecular polymorphism indices and neutrality tests for classes of functional sites and genes and compared the results between continent-specific mtDNA lineages. Furthermore, nonsynonymous/synonymous rate ratios for protein-coding genes were calculated, and a sliding window analysis of allele frequency distribution and a maximum-likelihood sliding window method were used to identify differences in the patterns of polymorphism between haplogroups. The results of the individual analyses suggest that there are haplogroup-specific differences in the intensity of selection against particular regions of the mitochondrial genome.
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Materials and Methods |
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The sequences were aligned by assuming that indel events changing the length of a repeat sequence had occurred at the 3' end of the repeat sequence, and functional regions, genes, codon positions and nondegenerate, twofold degenerate and fourfold degenerate sites (Li 1997, p. 87) were identified according to the MITOMAP reference sequence, a modified version of the 2001 Revised Cambridge Reference Sequence (Andrews et al. 1999) and mtDNA function locations (available at http://www.mitomap.org). The full alignment of the 837 sequences was 16,620 bp in length. Sites with alignment gaps representing indels were excluded from the analyses, making the length of the alignment 16,526 bp (coding region 15,420, D-loop 1,106 bp). The sequence data were stored in a relational SQL database and partitioned into sequence data sets which were defined by haplogroups and classes of sites. For each sequence, the nucleotides belonging to a given class of sites were concatenated and extracted from the database by methods provided by the SQL query language and the programming language Perl.
The 192 Finnish sequences have been deposited in the GenBank database (accession numbers AY339402AY339593).
Diversity Indices and Neutrality Tests
The sequence data sets defined by haplogroups and classes of sites were analyzed in terms of nucleotide polymorphism indices and phylogenetic tests of neutrality. According to the coalescent theory, the population mutation parameter for mtDNA is = 2Nµ, where N is the effective population size and µ is the neutral mutation rate per generation (Fu 1997). The methods used for estimating
in a set of sequences include k or
, the average number of pairwise nucleotide differences (Tajima 1983), Watterson's estimate (
s), based on the number of polymorphic sites in the sample (Watterson 1975), and
s, which is based on the number of singleton mutations (
s) in the sample (Fu and Li 1993). Under neutrality and certain demographic assumptions (Nielsen 2001) these three estimates should yield similar values (Simonsen, Churchill, and Aquadro 1995). However,
s and
s are affected by the presence of low-frequency alleles in the sample, whereas these have little impact on
, leading to differences between the estimates when selection is present (Fu and Li 1993). These differences form the basis of phylogenetic tests of neutrality, including Tajima's D, which is based on the difference between
and
s and its variance (Tajima 1989), Fu and Li's F*, which is based on the difference between
and
s and its variance (Fu and Li 1993), and Fu's Fs, which is based on the probability of the observed number of haplotypes or more being observed under neutrality (Fu 1997). An excess of low-frequency alleles as compared with that expected under neutrality results in negative values for these tests, whereas a relative lack of low-frequency alleles results in a shift toward positive values.
Nucleotide diversity indices and neutrality tests, including ,
s,
s, D, F*, and Fs, were calculated for each sequence data set. The three
estimators were standardized by the length of the sequence analyzed (Li 1997, pp. 237242). The standard error of nucleotide diversity (
;
/site) was computed to include the variance over the stochastic process (Nei 1987, pp. 254258), and both this and the standard error of
s/site were computed assuming neutrality and population equilibrium (Li 1997, pp. 237242). DnaSP 3.53 (Rozas and Rozas 1999), Arlequin 2.000 (available at http://anthro.unige.ch/arlequin), and dnastats 0.92 (available at http://cc.oulu.fi/
jukkamoi/mtres/) were used for the analyses with convergent results, except that DnaSP and Arlequin sometimes provided conflicting results for Fu's Fs test and ran into problems with the largest sequence data sets. In such instances the results obtained with dnastats were preferred, as the source code is available for review. The statistical significance levels for D and F* were obtained using the DnaSP default mode, which does not involve coalescent simulations.
Nonsynonymous/Synonymous Rate Ratios in Protein-Coding Genes
The ratio of the number of nonsynonymous mutations per nonsynonymous sites (dN) to the number of synonymous mutations per synonymous sites (dS) indicates the level of selection against nonsynonymous mutations relative to synonymous ones. In the presence of positive selection dN should be higher than dS (Nielsen 2001). dN/(dN + dS) distributions in pairwise comparisons between sequences were calculated (Nei and Gojobori 1986) for the 13 protein-coding genes in the sequence sets defined by the continent-specific haplogroup clusters (African, Asian, European, HV, JT, KU, and IWX) using DnaSP, and these distributions were plotted and the significances of the differences between lineages in the location of the distribution were assessed using the Kruskal-Wallis rank-sum test as implemented in R 1.4.1 (Ihaka and Gentleman 1996).
Sliding Window Analysis of Allele Frequency Distribution
Neutrality tests are summaries of the allele frequency spectrum (Przeworski, Hudson, and Di Rienzo 2000), and as such they may be used to identify genome regions that show patterns of nucleotide substitution that are not consistent with the average pattern for the genome (Nielsen 2001; Rand 2001). Coding region sequence data sets were analyzed by a sliding window method as implemented in DnaSP and dnastats, and using the three estimators and D, F*, and Fs. By definition, the sequences in each data set shared their genetic history, because the sets were defined by haplogroups. Therefore, we assumed that lineage-specific local anomalies in the allele frequency spectrum would indicate selective forces specific to the corresponding lineage.
In the sliding window method, the relevant statistics are computed for a region (window) of nucleotide positions and plotted at the median position of that window. A low number of polymorphisms within the window results in high stochastic fluctuations or discontinuity for the diversity indices and neutrality tests, imposing a practical lower limit on the window size. Patterns narrower than the window become smoothed, and therefore the selection of the window size is a compromise between stochastic patterns and the desired resolution. In the present analysis a window size of 1,000 bp was used and the window was moved in 40-bp steps. This decision was based on preliminary analyses which suggested that markedly narrower window sizes would have caused discontinuity in the sets with the smallest numbers of sequences.
The hypothesis of correlation between sliding window estimates and nucleotide position was assessed by linear regression as implemented in R. The significance of each correlation was estimated from nonoverlapping 1,000-bp segments, because the points in each sliding window curve are autocorrelated because of the partial overlap of the windows.
As expectations and variances of summary statistics for allele frequency distribution may depend on the demographic model, small variations in these statistics should not be interpreted as evidence for selection (Nielsen 2001). Therefore, one of the most extreme lineage-specific local deviations in allele frequency distribution was analyzed in more detail to assess the possible causes of the observed deviation. A median network (Bandelt et al. 1995) was constructed manually for the respective gene, and segregating sites within and outside the observed pattern were identified. Amino acid translations of the sequences were obtained using the Bio::PrimarySeqI interface of Bioperl (Stajich et al. 2002) and nonsynonymous mutations were subsequently identified. Nonsynonymous and synonymous mutations were counted as differences relative to the reference sequence. Fisher's two-tailed exact test was used to assess the hypothesis that the frequencies of segregating sites and nonsynonymous and synonymous mutations within and outside the observed anomalous region were distributed evenly between haplogroups.
Maximum-Likelihood Sliding Window Analysis
The analysis of allele frequency distribution does not assess the significance of the patterns identified and, furthermore, the best resolution of the analysis is limited by the window size selected. Therefore, the coding region sequence data sets were also analyzed by a maximum-likelihood sliding window method which identifies regions which do not fit with a single phylogenetic topology and nucleotide substitution process along the entire sequence. This method has good spatial resolution and it also assesses the significance of findings, but it only detects fast-evolving regions; i.e., invariable regions subject to purifying selection may not be detected. Regions subject to an increased rate of evolution and recombination should be detectable, however. The method uses a maximum-likelihood phylogeny to calculate the likelihoods for each site in the sequence data. A measure (Q) of the average likelihood of the window with respect to the rest of the sequence is subsequently calculated for windows of varying sizes and positions. The maximum values of Q are associated with regions showing low likelihood, given the global maximum-likelihood model. Significance is tested assuming a normally distributed null distribution of maximized Q, which allows calculation of the Z-values corresponding to a given significance level using a Monte Carlo simulation and Bonferroni inequality (Grassly and Holmes 1997).
Sequence data sets consisting of tRNA and rRNA genes and nondegenerate, twofold degenerate and fourfold degenerate sites of protein-coding genes were analyzed separately, as they are presumably subject to different selective constraints and their transition/transversion rates may differ. Genes encoded by the L-strand (MTND6 and eight tRNA genes) were excluded in order to avoid pooling template and non-template DNA. Maximum-likelihood trees were reconstructed for each sequence data set using TREE-PUZZLE 5.0 (Strimmer and von Haeseler 1996), enforcing the HKY substitution model (Hasegawa, Kishino, and Yano 1985) with a uniform rate over all the sites. An African sequence (GenBank AF347015.1) was used as the root for each tree. The transition/transversion parameter (ti/tv) was estimated from the data. Multifurcations were resolved by adding zero-length branches where necessary to convert the trees into bifurcating ones, as required by the subsequent analysis. The sequence data, maximum-likelihood tree, and ti/tv parameter were used as inputs to PLATO 2.11 (Grassly and Holmes 1997). The HKY substitution model and rate homogeneity were assumed, and the number of trials in the Monte Carlo simulations was set at 250. The minimum window size was set at 10. The mutations responsible for each significant pattern found in the analysis of each sequence set were identified, and homologies in the other sets were screened for by considering each pair of mutations within the region, as the presence of the same 2 mutations in
2 lineages might indicate that the region has been subject to ancient recombination.
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Results and Discussion |
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Nucleotide diversity () does not depend on the length of the sequence analyzed or the sample size (Nei 1987, pp. 267273), and therefore it can be used for direct comparison of the extents of polymorphism between classes of functional sites and lineages. In the total data set
was 0.087%1.085%, and the rank order of functional classes of sites was in accordance with previous studies, as
increased in the order of nondegenerate sites/codon position 12 < tRNA < rRNA < coding sequence (CDS) < twofold degenerate sites < codon position 3 < fourfold degenerate sites < D-loop. The different levels of
between classes of sites are commonly assumed to arise from differential selection against these. This was also supported by the finding that the highest ratio of transitions to transversions was 41.5 (as estimated without correction for multiple hits) in twofold degenerate sites, in which all transitions are synonymous and transversions are nonsynonymous (Li 1997, pp. 88, 177184), whereas the lowest ratio was 8.6 in fourfold degenerate sites, where all mutations are synonymous. Our results therefore support the assumption that selection has a significant role in the evolution of mtDNA as a whole. Moreover, comparison between our estimates and those reported for nuclear sequence variation (Przeworski, Hudson, and Di Rienzo 2000) indicated that
for mtDNA, excluding the D-loop, is generally not much higher than that found for many genes in nuclear DNA, despite the high mutation rate of mtDNA (Parsons et al. 1997), suggesting that selection limits the rate of fixation of mutations in the coding region of mtDNA.
Nucleotide diversity indices and neutrality tests were then analyzed in the major continent-specific haplogroup clusters to identify possible deviations from the general trends inferred from the total data set. A low haplotype diversity (0.424 ± 0.061) was identified in the Asian tRNA sequence data set, where the estimate for (0.043%) was also lower than that for nondegenerate sites and lower than that in the African (0.156%) and European (0.094%) sets (fig. 1A). Furthermore, Tajima's D was highly significantly negative (P < 0.001) in the Asian tRNA data set. This could imply that mutations within tRNA genes may have been more deleterious in Asian populations and that such mutations have not become fixed as easily as in other populations. Such an effect could result from environmental factors or mitochondrial-mitochondrial or mitochondrial-nuclear interactions (Blier, Dufresne, and Burton 2001) specific to the Asian mtDNA lineages.
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Nonsynonymous/Synonymous Rate Ratios in Protein-Coding Genes
The relative levels of selection against protein-coding genes in different haplogroup clusters were assessed by computing dN/(dN + dS) ratios (fig. 2). The locations of the dN/(dN + dS) distributions for certain genes differed markedly between lineages. The European JT and African lineages appeared to be better conserved than the remaining ones with respect to MTATP6 and MTATP8, whereas the Asian lineages had relatively high amino acid variation in these genes. In MTCYB and MTCO3, the European lineages, except JT, had a high dN/(dN + dS) ratio relative to the African and Asian lineages. MTCO1 was equally conserved in all the lineages, whereas MTCO2 and MTND6 were highly conserved in all lineages except the Asian ones. The JT cluster showed surprisingly high nonsynonymous variation in MTND2, JT and KU in MTND3, and HV in MTND5. Differences in the location of the distributions between lineages were highly significant because of the large numbers of sequences in the analyses.
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Sliding Window Analysis of Allele Frequency Distribution
Sliding window analysis of diversity indices and neutrality tests revealed an unexpected correlation between nucleotide position and the three population mutation parameters and neutrality tests. The correlation was positive and significant for ,
s, and
s and negative and significant for F* and Fs (fig. 3). Such a correlation could imply a different mutation rate or systematically different selection for genes at the 5' and 3' ends of the human mtDNA coding-region sequence. Different portions of mtDNA remain single-stranded and vulnerable to oxidative damage for different periods during the asymmetric replication of mtDNA, possibly leading to different mutation rates (Nedbal and Flynn 1998). This would result in a correlation that depends on the distance from the L-strand origin at np 57215798, but our results did not suggest such a correlation (fig. 3). Moreover, the maximum-likelihood sliding window analysis of fourfold degenerate sites (below) did not support the hypothesis that significant differences in the silent mutation rate would exist between different regions of the genome. Analyses in other species might indicate whether the observed correlation is a phenomenon specific to human mtDNA or a more universal one.
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The sliding window analysis also revealed narrow regions in which the polymorphism indices and allele frequency distribution (as indicated by neutrality tests) differed from the surrounding regions of the genome and from the other haplogroup clusters. This was most conspicuous for np 1247813611 (amino acids 48425) within the MTND5 gene in haplogroup cluster JT (fig. 4B), which was found to result from a lack of segregating sites and singleton mutations in this region, while the number of pairwise differences had not decreased. The median network of the 113 MTND5 sequences from haplogroup cluster JT (fig. 5) revealed a total of 36 segregating sites, 9 of which (25%) were within np 1247813611. In the remaining 724 non-JT sequences there were a total of 209 segregating sites, 112 (54%) of which were within this region (JT vs. non-JT, P = 0.0019, Fisher's exact test). In haplogroup J, 2/16 segregating sites (12.5%) were within np 1247813611 (J vs. non-JT, P = 0.0015), whereas in haplogroup T 5/17 (29%) were within this region (T vs. non-JT, P = 0.076). Significant differences were also observed for nonsynonymous mutations in JT and J (JT vs. non-JT, 1/16 vs. 25/66, P = 0.016; J vs. non-JT, 0/8 vs. 25/66, P = 0.045; T vs. non-JT, 1/8 vs. 25/66, P = 0.25) but not for synonymous mutations (JT vs. non-JT, 8/21 vs. 89/147, P = 0.061; J vs. non-JT, 3/10 vs. 89/147, P = 0.094; T vs. non-JT, 5/11 vs. 89/147, P = 0.35). Thus there were fewer segregating sites and nonsynonymous mutations than were to be expected within np 1247813611 in haplogroup J.
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Maximum-Likelihood Sliding Window Analysis
Several sequence data sets included at least one region which did not fit the phylogenetic topology and nucleotide substitution process estimated for the entire set (fig. 6). The largest number of regions with a significantly low likelihood was found in haplogroup cluster KU, where narrow regions within nondegenerate and twofold degenerate sites and rRNA and tRNA genes yielded significant Z values. The regions identified within nondegenerate and twofold degenerate sites were at different positions in the genome in different sequence sets, with the exception of the 3' end of MTND5 in the African (np 1364314148), JT (np 1392713940), and KU (np 1392814002) sets. Regions with significantly low likelihood in the African and KU sets also overlapped at the 5' end of MTCYB. The regions with low likelihood within rRNA genes were at different positions in different haplogroup clusters. From the tRNA genes, MTTT had a region with significantly low likelihood in the HV, KU and IWX sets, and the region also spanned the MTTH, MTTS2, and MTTL2 genes in the KU set. In contrast to nondegenerate and twofold degenerate sites, the variation at fourfold degenerate sites was explained well by a single phylogenetic topology and nucleotide substitutions process in each sequence set, with the exception of np 48504889 in the Asian set. The region in MTND5 with the unusual pattern of polymorphism was not identified in this analysis, most likely because regions evolving at lower rates than the rest of the sequence do not tend to have a lower likelihood, as transition probabilities for a base staying the same never become particularly low (Grassly and Holmes 1997). There were not many regions which had a significantly low likelihood in the analysis of protein-coding sequences, and the regions did not generally span entire genes, suggesting that adaptive protein evolution has involved only certain regions of genes, if it has occurred at all. Regions with a low likelihood could also result from recombination (Grassly and Holmes 1997), but we found no homologous pairs of alleles within the identified regions which could have been consistent with ancient recombination events between the lineages.
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Supplementary Material |
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Acknowledgements |
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Footnotes |
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