Lineage-Specific Evolutionary Rate in Mammalian mtDNA

Carmela Gissi*, Aurelio Reyes{dagger}, Graziano Pesole{ddagger} and Cecilia SacconeGo,*{dagger}

*Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Bari, Italy;
{dagger}Centro Studio Mitocondri e Metabolismo Energetico, Consiglio Nazionale delle Ricerche, Bari, Italy; and
{ddagger}Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Milano, Italy


    Abstract
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 
The existence of a lineage-specific nucleotide substitution rate in mammalian mtDNA has been investigated by analyzing the mtDNA of all available species, that is, 35 complete mitochondrial genomes from 14 mammalian orders. A detailed study of their evolutionary dynamics has been carried out on both ribosomal RNA and first and second codon positions (P12) of H-strand protein-coding genes by using two different types of relative-rate tests. Results are quite congruent between ribosomal and P12 sites. Significant rate variations have been observed among orders and among species of the same order. However, rate variation does not exceed 1.8-fold between the fastest (Proboscidea and Primates) and the slowest (Perissodactyla) evolving orders. Thus, the observed mitochondrial rate variations among taxa do not invalidate the suitability of mtDNA for drawing mammalian phylogeny. Dependence of evolutionary rate differences on variations in mutation and/or fixation rates was examined. Body size, generation time, and metabolic rate were tested, and no significant correlation was observed between them and the taxon-specific evolutionary rates, most likely because the latter might be influenced by multiple overlapping variable constraints.


    Introduction
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 
The mitochondrial genome (mtDNA) of vertebrates has become a common tool for resolving phylogenetic relationships at different evolutionary depths due to its peculiar properties, such as the presence of strictly orthologous genes, the lack of recombination, and an appropriate substitution rate. The mitochondrial genome has been used extensively for the elucidation of the mammalian phylogeny; it has been completely sequenced in a large number of species, and several sequencing projects are now in progress.

Molecular phylogenies derived from the analysis of complete mtDNA genomes have extensively remodeled the classical view of intra- and interordinal mammalian relationships previously based mainly on morphological data (D'Erchia et al. 1996Citation ; Janke, Xu, and Arnason 1997Citation ; Springer et al. 1997Citation ; Reyes, Pesole, and Saccone 1998Citation ; Stanhope et al. 1998Citation ). However, several inconsistencies have surfaced, not only between molecular and morphological phylogenies, but also between nuclear and mtDNA molecular data. If left unresolved, these differences would weaken the reliability of molecular evolutionary inferences. Hence, a detailed study of the evolutionary dynamics of the mitochondrial genome in the different mammalian species is needed to find possible explanations for the observed inconsistencies and conflicts. In particular, marked differences in lineage-specific evolutionary rates and/or nucleotide composition heterogeneity could significantly affect phylogenetic reconstruction; they could mislead inference methods (Pesole et al. 1995Citation ) or cause long-branch attraction effects (Philippe and Laurent 1998Citation ). Furthermore, a careful check of the molecular- clock hypothesis is needed if phylogenetic trees are to be used to estimate the divergence times between species.

Previous studies have suggested that significant rate heterogeneity exists between mammalian and other vertebrate mtDNAs. In particular, the nucleotide substitution rate calculated from fourfold-degenerate sites of shark mtDNA genes appears to be seven to eight times as slow as that of primates or ungulates (Martin, Naylor, and Palumbi 1992Citation ), and teleost fish mtDNA has been reported to evolve four- to fivefold slower than mammalian mtDNA at the level of nonsynonymous positions (Cantatore et al. 1994Citation ). Controversial results have been reported for turtle mtDNA: cytochrome b gene and restriction-site comparisons suggest a significant slowdown in the evolutionary rate of turtles compared with other vertebrates (Avise 1992Citation ; Bowen, Nelson, and Avise 1993Citation ), whereas 12S rRNA sequences do not support such a rate reduction (Seddon, Baverstock, and Georges 1998Citation ). Heterogeneity of amino acid substitution rates of mitochondria-encoded proteins has been reported, with mammals evolving at least six times as fast as fishes and rates increasing from fishes to amphibians, birds, and mammals (Adachi, Cao, and Hasegawa 1993Citation ).

Within mammals, information on mtDNA rate variation is mostly limited to a few genes or species. The most comprehensive study has been carried out on the 13 protein-coding genes, but only for six species belonging to five orders. Results have shown that the nonsynonymous mitochondrial rates are clocklike for the majority of mitochondrial genes (Janke et al. 1994Citation ) in the reduced mammalian sample available at that time. More recent studies on large-sequence data sets have reported that primates evolve faster than any other order (Honeycutt et al. 1995Citation ; Adkins, Honeycutt, and Disotell 1996Citation ; Arnason et al. 1996Citation ; Arnason, Gullberg, and Xu 1996Citation ; Arnason, Gullberg, and Janke 1998Citation ), with baboons and orangutans being the fastest among primates (Horai et al. 1992Citation ; Adachi and Hasegawa 1995Citation ; Xu and Arnason 1996Citation ; Arnason, Gullberg, and Janke 1998Citation ). Furthermore, Proboscidea cytochrome b and 12S rRNA genes evolve more rapidly than those from any other mammalian order (Irwin, Kocher, and Wilson 1991Citation ; Ma et al. 1993Citation ; Lavergne et al. 1996Citation ). Artiodactyla, then, evolve faster than fin whales (Honeycutt et al. 1995Citation ). Intraordinal comparisons indicate equal rates within rodents (Adkins, Honeycutt, and Disotell 1996Citation ) and variable rates within perissodactyls (Xu and Arnason 1997Citation ) and artiodactyls (Honeycutt et al. 1995Citation ). In a recent study, Pesole et al. (1999)Citation estimated the absolute rate of mammalian mtDNA evolution by comparing closely related pairs of species whose divergence times were known with sufficient accuracy. They observed some rate heterogeneity at the level of nonsynonymous sites; primates (humans, chimps) evolved about 1.8 times as faster as perissodactyls (horses, donkeys) and 1.5 times as faster as carnivores (gray and harbor seals).

We report here a comprehensive study on the existence of lineage-specific evolutionary rates in mammalian mtDNA by using all available complete mitochondrial genomes belonging to 35 species and 14 orders. Analyses were carried out on both ribosomal RNAs and first and second codon positions of protein-coding genes.

In order to avoid dependence on divergence time estimations, which are often controversial and unreliable (Springer 1995Citation ), we used the relative-rate method based on the comparison of two species (ingroups) with a third, reference, group (outgroup) which was more distantly related to the two ingroup taxa than they were to each other (Sarich and Wilson 1973Citation ). The only prerequisite for the test is the identification of one or more unambiguous outgroup species, which should be as close as possible to the ingroups in order to minimize errors in evolutionary distance estimations. The observed rate heterogeneity was correlated to body size, generation time, and metabolic rate. In addition, since the existence of a compositional bias may strongly affect estimates of nucleotide substitution rates (Pesole et al. 1995Citation ), we also investigated heterogeneity in mtDNA base composition for the different mammalian lineages.


    Materials and Methods
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 
Complete mtDNA sequences from 35 mammalian species were retrieved from the EMBL database (release 61). These sequences are representative of 14 mammalian orders, and their accession numbers are reported in table 1 . The complete Xenopus laevis mtDNA sequence (X02890) was included in this study for use as an outgroup in comparisons between noneutherian species.


View this table:
[in this window]
[in a new window]
 
Table 1 Complete Mammalian Mitochondrial Genomes Analyzed in the Present Study

 
Multiple alignments of the 12 H-stranded protein-coding genes and of 12S and 16S ribosomal RNA genes were carried out with the PILEUP program (GCG 1994Citation ), and, when necessary, manual adjustments were made with the LINEUP program (GCG 1994Citation ). The alignments of protein-coding genes were guided by the corresponding amino acid alignments. Protein-coding (CDS) and rRNA supergenes were then obtained by concatenating alignments of all 12 protein-coding genes and the 2 rRNA genes, respectively.

The analyses were carried out on gap-free alignments. For protein-coding sequences, only the first and second codon positions (P12 CDS) were taken into account. For ribosomal RNAs, ambiguously aligned sites (mostly adjacent to gaps and belonging to loop secondary-structure regions) were also excluded. The total numbers of analyzed sites were 7,401 for the P12 CDS and 2,136 for the ribosomal sequences.

Homogeneity of base composition for both protein-coding and ribosomal genes was defined by checking the stationarity condition, that is, the existence of similar base frequencies within statistical fluctuations at equivalent positions (Saccone et al. 1990Citation ). For each sequence pair, the normalized frequencies of the two sequences were compared by means of a {chi}2 test (statistical significance at P < 0.05). Furthermore, principal-component analysis (PCA) was carried out on the base composition of P12 CDS and rRNA supergenes using the ADE-4 software (Thioulouse et al. 1997Citation ).

In order to investigate the existence of a global clock over mammalian mitochondrial phylogeny, Takezaki's test of the molecular clock based on the least-squares method was used (Takezaki, Rzhetsky, and Nei 1995Citation ), assuming the substitution model of Tamura and Nei (1993)Citation . Such a test is designed to identify sequences that evolve significantly faster or slower than the average rate of all other sequences examined, starting from a tree topology determined without the assumption of rate constancy.

To detect rate differences between specific mammalian species, two different relative-rate approaches were applied: the relative-rate test of Muse and Gaut (Muse and Weir 1992Citation ; Muse and Gaut 1994Citation ) and that of Robinson (1998)Citation . Muse and Gaut's test is a three-species relative-rate test which is applied in a likelihood framework. Robinson's relative-rate test is a multiple-species test that allows comparison of the mean rates of two lineages, each consisting of many sequences, using several outgroup sequences simultaneously. Statistical significance of the two relative-rate tests was assessed by means of the {chi}2 test (P < 0.05).

The phylogenetic relationships used to identify the outgroup species for each species pair were set on a consensus tree of mammalian phylogeny inferred from both molecular and morphological data (de Jong 1998Citation ), available on request. Species with a controversial position in the mammalian phylogenetic trees were never used as outgroups and are indicated in table 1 . When for a given species pair the nearest outgroup could not be identified with confidence, as many outgroups as possible were used. Possible bias due to usage of unbalanced taxonomic samples in the relative-rate test was avoided. Robinson's test was carried out with a guide tree reporting the mammalian consensus phylogeny; for Muse and Gaut's test, as many closest outgroups as possible were used for each species pair, and the rate differences were considered statistically significant when at least 50% of the outgroups used supported the rate difference.

The relative rate ({Delta}R) between two species was quantified only for statistically significant rate differences. For the ingroup species pair AB, diverging from internal node 1, the relative rate {Delta}RAB was calculated as


with O being the outgroup species and d being the genetic distance calculated with the stationary Markov model (Saccone et al. 1990Citation ). The relative rate between species A and a set of species, i.e., B1, B2, ... , Bn, was calculated as the average of the relevant {Delta}RABi values.

Estimates of the metabolic rate, the body size, and the generation time for some of the 35 species analyzed (see table 2 ) were obtained from the literature (McNab 1988Citation ; Heusner 1991Citation ; Purvis and Harvey 1995Citation ; Bromham, Rambaut, and Harvey 1996Citation ) and are available on request. The metabolic rate is represented as weight-specific standard metabolic rate (SMR) and expressed in W/g. Body size is represented by the mean female adult body weight, expressed in grams. The generation time is represented by age at first reproduction, expressed in days. When different estimates were available, the mean value was used. When there was a lack of information on life history variable values for a given species, data obtained from a different species belonging to the same genus were taken into account.


View this table:
[in this window]
[in a new window]
 
Table 2 Correlation Coefficient and P Values for the Regressions of {Delta}R on P12 and Ribosomal Sites Against Life History Variables (body size, standard metabolic rate [SMRrsqb;, and generation time) for Species Comparisons with Statistically Significant Rate Differences

 
For each species pair showing significant rate differences in the relative-rate tests, the ratio values of the previously described life history variables and of the corresponding {Delta}R were calculated and logarithmically transformed to carry out correlation analyses.


    Results
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 
Before undertaking rate heterogeneity measurements, we evaluated the compositional bias in both protein-coding and ribosomal genes by checking the stationarity condition (see Materials and Methods and Saccone et al. [1990Citation ]). On the P12 protein-coding supergene, the stationarity condition was fulfilled for all pairwise comparisons, except for those involving the hedgehog. On ribosomal sequences, instead, all pairwise comparisons fulfilled the stationarity condition. Since the stationarity test measures similarity in base composition within statistical fluctuations, differences that are not statistically significant can be present even in the case of stationarity. In order to detect small compositional differences, we reduced the number of variables and maximized the corresponding variability by means of PCA carried out on the base composition of each species. In figure 1A and B, the two first PCA components are plotted for each of the 35 species considered. The PCA components were calculated on the base composition of P12 CDS and ribosomal supergenes, respectively. For the P12 CDS supergene, the first axis accounts for 51.65% variance and the second axis accounts for 37.68%, for a cumulative 89.31% total variance. For P12 CDS, the hedgehog (point 32 in fig. 1A ) appeared as an outlier due to its rather divergent base composition compared with that of other mammals. This is also demonstrated by the absence of the stationarity condition. Points corresponding to primate species (see points 1–7 in fig. 1A ) form a separate group identified mostly by the first component, in spite of the verified stationary condition with all other species. Within Primates, the baboon showed the most divergent base composition. On the ribosomal supergene, the first axis extracted by PCA accounted for 77.28% variance, and the second axis accounted for 16.67% (a cumulative 93.95% total variance). On ribosomal supergenes, Primates (see points 1–7 in fig. 1B ) again form a separate cluster due to their peculiar base composition, with the orangutan being the species deviating the most. Unlike the P12 CDS, the base composition of hedgehog rRNAs (see point 32 in fig. 1B ) does not differ significantly from that of the other species, which is also demonstrated by the fulfilment of the stationary condition. It is noteworthy that Primates form a distinct cluster with respect to other mammals in both PCA plots. This might be due to differences in their base compositions; they have a higher percentage of C and a lower percentage of T than the other mammalian sequences examined (data not shown). It has been remarked that such a compositional bias is also present, and much more markedly, in third codon positions (Reyes et al. 1998Citation ).



View larger version (15K):
[in this window]
[in a new window]
 
Fig. 1.—Plot of 35 mammalian species on the first two axes produced by a principal-component analysis of base composition in P12 protein-coding (A) and ribosomal (B) supergenes. See table 1 for designation of the species

 
Takezaki's molecular-clock test (Takezaki, Rzhetsky, and Nei 1995Citation ) rejected the hypothesis of rate constancy (P < 0.01) on both P12 CDS and rRNA genes; thus, one or more mammalian lineages have statistically significant rate differences compared with the average evolutionary rate of all species at both of the mitochondrial sites considered. To identify such lineages, the heterogeneity in nucleotide substitution rate between species was investigated by two different relative-rate tests (see Material and Methods). The results are shown schematically in figure 2 , where P12 CDS and ribosomal supergene comparisons are shown above and below the diagonal, respectively. Comparisons with statistically significant rate differences have been marked with an arrow pointing to the species with the higher evolutionary rate, and the arrow types are different for the results obtained with Muse-Gaut's and Robinson's tests. In most cases, the two tests give congruent results, with differences being found mostly in the rRNA comparisons involving rodents or primates species. The results allowed the definition of a relative order of evolutionary rate between mammalian taxa.



View larger version (86K):
[in this window]
[in a new window]
 
Fig. 2.—Schematic representation of the relative- rate test results for P12 of protein-coding (above the diagonal) and ribosomal supergenes (below the diagonal). Each cell represents a pairwise comparison. Arrows indicate rate differences and point to the taxon with the faster rate. Normal arrows indicate results obtained from both Muse and Gaut's and Robinsons's relative-rate tests. Open triangles indicate results obtained from Robinsons's test only, and closed triangles indicate results obtained from Muse and Gaut's test only. Thick borders mark intraorder comparisons.

 
In general, taxon-specific rate differences were detected in P12 CDS and ribosomal sites both at intra- and interorder levels. Statistically significant rate differences on P12 CDS sites were found within several orders. Baboons and orangutans showed significantly faster rates than other primates ({Delta}R = 1.30 ± 0.09 and 1.30 ± 0.08, respectively). Indian rhinoceroses evolved 1.22 ± 0.08 times as fast as other Perissodactyla. Within Artiodactyla, the rate of the hippopotamus was 1.22 ± 0.08 times as fast as those of the other ruminants we considered. In Rodentia, the squirrel was the slowest-evolving species ({Delta}R = 0.82 ± 0.10), while the dormouse evolved 1.17 ± 0.05 times as fast as the mouse. With ribosomal genes, no significant rate differences were observed in the same intraordinal comparisons except for the higher rate of orangutans ({Delta}R = 1.61 ± 0.22) among primates and the higher rate of Indian rhinoceroses ({Delta}R = 1.77 ± 0.29) compared with equiides.

For interordinal comparisons, the significant rate differences found in one or both of the relative-rate tests and the relevant relative rates ({Delta}R) are reported in figure 3 . The rate differences vary between 1.08 and 1.76 for the P12 CDS sites and between 1.10 and 1.71 for the ribosomal sites. On P12 CDS sites, Primates and Proboscidea are the fastest-evolving orders, evolving at 1.2–1.8 times the rate of other mammalian orders (figs. 2 and 3 ). The nucleotide substitution rate of the baboon, the fastest-evolving primate, was 1.16 ± 0.08 times that of elephant. The rate of the Insectivore hedgehog was comparable to that of Primates and significantly higher than those of all other mammalian orders (fig. 3 ). However, in the case of hedgehog, the observed high evolutionary rate may be due to its deviating base composition. After Primates, Proboscidea, and Insectivora, the order Rodentia (with the exception of the squirrel) had the next fastest rate, 1.1–1.4 times those of the remaining orders (fig. 3 ). Depending on the rodent species considered, however, some comparisons of Rodentia versus Cetacea and Chiroptera did not support rate differences. Perissodactyla were the slowest- evolving mammals, as their rate turned out to be significantly slower than those of all other orders except Tubulidentata, which show a comparable rate. Among the remaining orders, rate differences were mostly not significant (see figs. 2 and 3 ); only Chiroptera evolved faster than Artiodactyla and Tubulidentata, whereas Cetacea evolved faster than Artiodactyla (fig. 3 ). No clear conclusion could be drawn on the relative rates of Marsupialia and Monotremata compared with all other mammalian orders, probably because of the much weaker resolution of the relative-rate test when a distantly related outgroup (X. laevis) was used.



View larger version (52K):
[in this window]
[in a new window]
 
Fig. 3.—Mean relative rates and standard deviations for P12 protein-coding (P12 CDS) and ribosomal RNA (rRNA) supergenes for the interorder comparisons, with significant rate differences identified in the results of one or both of the relative-rate tests. Relative rate was calculated according to the formula reported in Materials and Methods, considering only interorder comparisons with significant rate differences reported in figure 1 .

 
For the ribosomal genes, the interorder comparisons described a trend of taxon-specific rate differences similar to that found for P12 CDS sites. However, a lower congruency between results obtained from the two different relative-rate tests was found, particularly for some comparisons involving hedgehogs, primates, and perissodactyls (fig. 2 ). For the CDS P12, Primates and Proboscidea were found to evolve at similar rates that were faster than those of most of the remaining orders (see figs. 2 and 3 ); the order Rodentia had the second-fastest rate, and the remaining interordinal comparisons did not show significant rate differences except for the faster evolutionary rate of Edentata compared with Tubulidentata, the faster rate of Cetacea compared with Chiroptera, and the slower rate of Perissodactyla compared with Artiodactyla and Chiroptera (fig. 3 ). Again, no clear conclusion could be drawn on the relative rates of Marsupialia and Monotremata, most likely owing to the use of a distantly related outgroup species. The insectivore hedgehog has an unclear evolutionary-rate pattern, as shown by the inconsistent results obtained with the two different tests (fig. 2 ). On the whole, the hedgehog appeared to evolve at a rate not significantly different from those of Primates, Proboscidea, and Rodentia but faster than those of Carnivora, Perissodactyla, and Artiodactyla (see fig. 3 ).

On the whole, the pattern of evolutionary rates was found to be quite similar between ribosomal and P12 sites. Most comparisons showed rate differences at both sites, mostly involving the fastest-evolving taxa, that is, Primates (such as the orangutan), Proboscidea, and Rodentia (such as the rat). Excluding the hedgehog because of its heterogeneous base composition, a highly significant correlation was found between {Delta}R values calculated on P12 CDS and those calculated on ribosomal sites (r = 0.66, P < 0.001 in fig. 4 ) for comparisons showing statistically significant rate differences at both sites. Thus, very similar patterns of rate variation were present at P12 protein-coding and ribosomal sites.



View larger version (17K):
[in this window]
[in a new window]
 
Fig. 4.—Plot of the mean relative rate calculated on P12 protein-coding sites against that calculated on ribosomal sites for the interorder comparisons with statistically significant rate differences reported in figure 2 . The regression line and the correlation coefficient are also reported

 
Possible correlations between evolutionary rate and several physiological and metabolic variables were investigated for both P12 CDS and ribosomal sites. For species pairs showing rate differences, the relative values of SMR, generation time, and body size were plotted against the corresponding relative rates ({Delta}R). Since data on life history variables were not available for all 35 analyzed species, only some of the 393 and 258 comparisons with rate differences on P12 CDS and on ribosomal sites, respectively, were considered (table 2 ). Only the generation time showed some significant correlation (P < 0.05), but only for evolutionary rate differences observed on P12 CDS and with a very low correlation coefficient.


    Discussion
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 
In the present study, evolutionary rate differences in mtDNA among mammalian taxa have been carefully investigated. Our data represent the largest mtDNA sequence data set used to examine this problem, for both the number of genes and the number of species considered. Our analyses were carried out on two classes of genes involved in different mitochondrial functions, i.e., ribosomal RNA genes and H-stranded protein-coding genes.

Checking for a homogeneous base composition is a prerequisite to carrying out reliable relative-rate tests, since a compositional bias may distort the evolutionary distance estimates (Saccone, Pesole, and Preparata 1989Citation ; Saccone et al. 1990Citation ; Pesole et al. 1995Citation ) and result in erroneous assessment of the relative rate of evolution (Mindell and Thacker 1996Citation ) and of phylogenetic reconstructions. Thus, the third codon positions of protein-coding genes were not considered in our analyses because of their strong compositional bias.

Similar patterns of evolutionary rate differences between species have been identified for both P12 CDS and ribosomal sites (fig. 2 ). Compared with protein genes, rRNA genes give a less clear indication of rate differences; indeed, for some comparisons, only one of the two relative-rate tests evidenced significant rate differences (fig. 2 , below the diagonal). This could be explained with the peculiar substitution pattern in rRNA genes, where compensatory changes occur in the stem regions and insertion/deletions are common in the loop regions. Particularly in the 12S rRNA molecule, the heterogeneity of the transition/transversion bias between stems and loops and the rapid saturation of transitions (Springer and Douzery 1996Citation ) reduce the resolution of this gene for interordinal relationships among Eutheria, particularly when only stem regions are considered (Douzery and Catzeflis 1995Citation ; Springer and Douzery 1996Citation ). The same pattern should hold for the 16S rRNA; thus, some interordinal distances calculated on a ribosomal supergene might be underestimated.

The observed evolutionary pattern is taxon-specific. Proboscidea and Primates are the fastest-evolving mammalian orders, followed by Rodentia; Perissodactyla are the slowest. Compared with other mammals, the hedgehog clearly shows a higher evolutionary rate at P12 but not at ribosomal sites. This could be due to its divergent base composition only at P12 sites (point 32 in fig. 1 ), whereas in the ribosomal genes it shows a homogenous base composition with respect to other mammals. The fulfilment of the stationary condition in all comparisons involving the fastest orders allows us to exclude the possibility that the observed heterogeneity in evolutionary rate is an artifact due to base composition divergence. Furthermore, the fast-evolving orders Proboscidea and Rodentia have a base composition within the average of all other slow-evolving species for both P12 and ribosomal sites (fig. 1 ). Only Primates, although stationary, show a peculiar base composition both on P12 and rRNA sites (points 1–7 in fig. 1A and B ), which is also evident in third codon positions in which higher values of T and lower values of C are observed with respect to other mammals.

It is noteworthy that similar taxon-specificity (fig. 2 ) and approximately the same values of rate differences (fig. 4 ) have been found in both ribosomal RNA and protein-coding genes, although rRNA genes evolve between two- and threefold faster than P12 sites of protein-coding genes (Pesole et al. 1999Citation ). Thus, the taxon-specific rate differences appear to be a general property of mtDNA as a result of evolutionary forces operating on the whole mitochondrial genome.

In general, evolutionary rate differences can stem from variations in mutation rates and/or variations in fixation rates, both of which are influenced by multiple factors (Kimura 1987Citation ; Mindell and Thacker 1996Citation ). To date, the effects of mutation rate constraints (such as replication rate, repair efficiency, and exposure to mutagens) have not been analyzed directly but, rather, using biological variables that are supposed to be correlated with them. Among such variables are body size, generation time, and SMR (Laird, McConaughy, and McCarthy 1969Citation ; Martin and Palumbi 1993Citation ; Rand 1994Citation ).

According to the proposed theories, taxa with large body size, long generation time, and low weight-specific metabolic rate should have a slower mutation rate. It is noteworthy that the fastest-evolving orders, such as Proboscidea, Primates, and Rodentia, show both high and low values of body size, generation time, and SMR. Moreover, the evolutionary rate differences we observed for ribosomal and P12 sites are not related to body size and SMR (table 2 ). Generation time appears to be correlated with the observed rate differences only on P12 sites, but the correlation coefficient is very low, thus explaining a low percentage (17%) of variance.

Metabolic rate effect has been proposed to be very pronounced in mtDNA because of its constant exposure to oxygen radicals (Laird, McConaughy, and McCarthy 1969Citation ; Martin and Palumbi 1993Citation ; Rand 1994Citation ). However, a positive correlation between SMR and mutation rate would be found only in the case of an insufficient repertoire of oxidative-damage DNA repair. Mitochondria of higher organisms seem to be well equipped with base excision and oxidative-damage repair systems (Bogenhagen 1999Citation ; Sawyer and Van Houten 1999Citation ), which show about the same efficiency as their nuclear counterparts (Sawyer and Van Houten 1999Citation ). Indeed, the existence of taxon-specific DNA repair efficiency has not been proved until now. Moreover, it has been reported that the observed base composition constraints of mammalian mtDNAs are not due to oxidative damage, but mainly to spontaneous deamination during replication (Reyes et al. 1998Citation ).

Further evidence against the metabolic rate hypothesis is that SMR measures the steady-state rate of heat production as oxygen consumption of the whole organism under a set of standard conditions (Rolfe and Brown 1997Citation ). Thus, even supposing an influence of SMR on the mutation rate, SMR might not be an appropriate measure of oxidative stress and mutation rate in the female germ line responsible for mitochondrial inheritance. The existence of a different evolutionary rate of germinal and somatic tissues has been documented only in the mouse, in which the mutation rate per cell division is at least three times lower in germ cells than in somatic cells (Drake et al. 1998Citation ).

The link between organismal generation time and mitochondrial evolutionary rate is not easily understandable, because little is known about mechanisms that coordinate mitochondrial and cellular replication. In addition, mtDNA turnover, which is independent of nuclear DNA replication and cell division (Bogenhagen and Clayton 1977Citation ) and is tissue-specific, has not been comprehensively studied. In this light, generation time appears a poor predictor of the chances of mitochondrial mutation events (Rand 1994Citation ).

Body size is strongly correlated with SMR and generation time, but the complicated dependence of body size on many physiological, ecological, and life history variables might obscure possible relationships with factors regulating mitochondrial evolutionary rate.

The observed lack of correlation between any of these three life history variables and evolutionary rate (table 2 ) is also not surprising on account of the temporal scale. Indeed, evolutionary rates are calculated along a specific evolutionary line and reflect the evolutionary history of each lineage. In contrast, life history variables are measured in the present time and little or no information is available on their changes over time across a lineage. A clear example of this variation can be obtained from paleontological data, which show significant changes in body size in the evolution of different lineages such as perissodactyls, primates (Carrol 1988Citation ), and rodents (Benton 1997Citation ).

As discussed above, even in the case of equal mutation rates, different evolutionary rates can be the consequence of variable constraints that affect fixation rates. Protein function, purifying selection, and population size might account for different fixation rates (Mindell and Thacker 1996Citation ). However, we have no sufficient data on these parameters for the species so far studied, although important differences in evolutionary rate have been observed within several mammalian orders (e.g., Primates, Rodentia; fig. 2 ).

Another factor that could influence the evolution of mtDNA as a whole by modifying its global selective constraints is the nuclear genome. A cross-talk between nucleus and mitochondrion is required for mitochondrial biogenesis and maintenance; thus, coevolutionary processes between the two genomes are highly probable. Rate covariance of nucleus/mitochondrion has already been suggested for the accelerated amino acid rate in mitochondrial COII and nuclear cytochrome c genes in anthropoid primates (Adkins and Honeycutt 1994Citation ). Such an interaction could not be restricted only to the genes for the respiratory chain and could be even stronger for mitochondrial processes that are completely dependent on nuclear genes, such as DNA replication. Furthermore, this coevolutionary process could operate in a taxon-specific manner, as it is known that the isochore structure of the nuclear genome shows taxon-specific features (Sabeur et al. 1993Citation ). Thus, the pattern of rate heterogeneity between taxa found at the mitochondrial level should also be investigated at the nuclear level.

In conclusion, we observed that the rate of evolution of mammalian mitochondrial genomes is rather variable, not only between different orders, but also within orders and even between closely related species. This could explain the rejection of a general clocklike evolutionary pattern by the Takezaki test (Takezaki, Rzhetsky, and Nei 1995Citation ). However, the observed mtDNA rate differences in mammals are low, showing a variability that never exceeds 1.8-fold. Such a limited extent of rate variation should not affect qualitative phylogenetic inferences (tree topology); however, accurate estimates of molecular dating can be obtained by using appropriate weighting based on the observed evolutionary rate. Similarly, accurate measures of rate differences in a broad taxonomic range, such as among vertebrates or Metazoa, are necessary to test the reliability of mtDNA in phylogenetic studies of other animal groups, and this will be possible as the number of available sequences increases. Our data might provide a substantial contribution to studies for molecular dating, because a correct assessment of divergence time from molecular sequences can only be obtained if differences in the rates of evolution between lineages are taken into account.


    Acknowledgements
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 
We would like to thank M. Lonigro for revision of the manuscript. This work was supported within the EU programme Training and Mobility of Researchers, project ERB-FMRX-CT98-0221, and by MURST, Italy. C. G. and A.R. contributed equally to this paper.


    Footnotes
 
Manolo Gouy, Reviewing Editor

1 Keywords: mitochondrial DNA mammalian phylogeny molecular evolution nucleotide substitution rate body size metabolic rate generation time Back

2 Address for correspondence and reprints: Cecilia Saccone, Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Via Orabona 4/A, 70125 Bari, Italy. E-mail: saccone{at}area.ba.cnr.it Back


    literature cited
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 literature cited
 

    Adachi, J., Y. Cao, and M. Hasegawa. 1993. Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. J. Mol. Evol. 36:270–281.[ISI][Medline]

    Adachi, J., and M. Hasegawa. 1995. Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites. J. Mol. Evol. 40:622–628.[ISI][Medline]

    Adkins, R. M., and R. L. Honeycutt. 1994. Evolution of primate cytochrome c oxidase subunit II gene. J. Mol. Evol. 38:215–231.[ISI][Medline]

    Adkins, R. M., R. L. Honeycutt, and T. R. Disotell. 1996. Evolution of eutherian cytochrome c oxidase subunit II: heterogeneous rates of protein evolution and altered interaction with cytochrome c. Mol. Biol. Evol. 13:1393–1404.[Abstract/Free Full Text]

    Arnason, U., A. Gullberg, and A. Janke. 1998. Molecular timing of primate divergence as estimated by two nonprimate calibration points. J. Mol. Evol. 47:718–661.[ISI][Medline]

    Arnason, U., A. Gullberg, A. Janke, and X. Xu. 1996. Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J. Mol. Evol. 46:650–661.

    Arnason, U., A. Gullberg, and X. Xu. 1996. A complete mitochondrial DNA molecule of the white-handed gibbon, Hylobates lar, and comparison among individual mitochondrial genes of all hominoid genera. Hereditas 124:185–189.

    Avise, J. C. 1992. Mitochondrial DNA evolution at a turtle pace: evidence for low genetic variability and reduced microevolutionary rate in the testudines. Mol. Biol. Evol. 9:457–473.[Abstract]

    Benton, M. J. 1997. Vertebrate paleontology. Chapman and Hall, London.

    Bogenhagen, D. F. 1999. Repair of mtDNA in vertebrates. Am. J. Hum. Genet. 64:1276–1281.[ISI][Medline]

    Bogenhagen, D., and D. A. Clayton. 1977. Mouse L cell mitochondrial DNA molecules are selected randomly for replication throughout the cell cycle. Cell 11:719–727.

    Bowen, B. W., W. S. Nelson, and J. C. Avise. 1993. A molecular phylogeny for marine turtles: trait mapping, rate assesment, and conservation relevance. Proc. Natl. Acad. Sci. USA 90:5574–5577.

    Bromham, L., A. Rambaut, and P. H. Harvey. 1996. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43:610–621.[ISI][Medline]

    Cantatore, P., M. Roberti, G. Pesole, A. Ludovico, F. Milella, M. N. Gadaleta, and C. Saccone. 1994. Evolutionary analysis of cytochrome b sequences in some perciformes: evidence for slower rate of evolution than in mammals. J. Mol. Evol. 39:589–597.[ISI][Medline]

    Carrol, R. L. 1988. Vertebrate paleontology and evolution. W. H. Freeman and Company, New York.

    D'Erchia, A. M., C. Gissi, G. Pesole, C. Saccone, and U. Arnason. 1996. The guinea-pig is not a rodent. Nature 381:597–599.

    de Jong, W. W. 1998. Molecules remodel the mammalian tree. Trends Ecol. Evol. 13:270–275.[ISI]

    Douzery, E., and F. M. Catzeflis. 1995. Molecular evolution of the mitochondrial 12S rRNA in Ungulata (Mammalia). J. Mol. Evol. 41:622–636.[ISI][Medline]

    Drake, J. W., B. Charlesworth, D. Charlesworth, and J. F. Crow. 1998. Rates of spontaneous mutation. Genetics 148:1667–1686.

    GCG. 1994. Program manual for the GCG package. Genetics Computer GroupGCG. 1994. Program manual for the GCG package. Genetics Computer Group, Madison, Wis.

    Heusner, A. A. 1991. Size and power in mammals. J. Exp. Biol. 160:25–54.[Abstract]

    Honeycutt, R. L., M. A. Nebdal, R. M. Adkins, and L. L. Janecek. 1995. Mammalian mitochondrial DNA evolution: a comparison of the cytochrome b and cytochrome c oxidase II genes. J. Mol. Evol. 40:260–272.[ISI][Medline]

    Horai, S., Y. Satta, K. Hayasaka, R. Kondo, T. Inoue, T. Ishida, S. Hayashi, and N. Takahata. 1992. Man's place in hominoidea revealed by mitochondrial DNA genealogy. J. Mol. Evol. 35:32–43.[ISI][Medline]

    Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:128–144.[ISI][Medline]

    Janke, A., G. Feldmmaier-Fuchs, W. K. Thomas, A. von Haeseler, and S. Paabo. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243–256.

    Janke, A., X. Xu, and U. Arnason. 1997. The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia and Eutheria. Proc. Natl. Acad. Sci. USA 94:1276–1281.

    Kimura, M. 1987. Molecular evolutionary clock and the neutral theory. J. Mol. Evol. 26:24–33.[ISI][Medline]

    Laird, C. D., B. L. McConaughy, and B. J. McCarthy. 1969. Rate of fixation of nucleotide substitutions in evolution. Nature 224:149–154.

    Lavergne, A., E. Douzery, T. Stichler, F. M. Catzeflis, and M. S. Springer. 1996. Interordinal mammalian relationships: evidence for Paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences. Mol. Phylogenet. Evol. 61996:245–258.

    Ma, D. P., A. Zharkikh, D. Graur, J. L. Vandeberg, and W. H. Li. 1993. Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes. J. Mol. Evol. 36:327–334.[ISI][Medline]

    McNab, B. K. 1988. Complications inherent in scaling the basal rate of metabolism in mammals. Q. Rev. Biol. 63:25–54.[ISI][Medline]

    Martin, A. P., G. J. P. Naylor, and S. R. Palumbi. 1992. Rate in mitochondrial DNA evolution is slow in sharks compared to mammals. Nature 357:153–155.

    Martin, A. P., and S. R. Palumbi. 1993. Body size, metabolic rate, generation time, and molecular clock. Proc. Natl. Acad. Sci. USA 90:4087–4091.

    Mindell, D. P., and C. E. Thacker. 1996. Rates of molecular evolution: phylogenetic issues and applications. Annu. Rev. Syst. 27:279–303.[ISI]

    Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715–724.[Abstract/Free Full Text]

    Muse, S. V., and B. S. Weir. 1992. Testing for equality of evolutionary rates. Genetics 132:269–276.

    Pesole, G., G. Dellisanti, G. Preparata, and C. Saccone. 1995. The importance of base composition in the correct assessment of genetic distance. J. Mol. Evol. 41:1124–1127.[ISI]

    Pesole, G., C. Gissi, A. De Chirico, and C. Saccone. 1999. Nucleotide substitution rate of mammalian mitochondrial genomes. J. Mol. Evol. 48:427–434.[ISI][Medline]

    Philippe, H., and J. Laurent. 1998. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8:616–623.[ISI][Medline]

    Purvis, A., and P. H. Harvey. 1995. Mammalian life-history evolution: a comparative test of Charnov's model. J. Zool. Lond. 237:259–283.

    Rand, D. M. 1994. Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9:125–131.[ISI]

    Reyes, A., C. Gissi, G. Pesole, and C. Saccone. 1998. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol. 15:957–966.[Abstract]

    Reyes, A., G. Pesole, and C. Saccone. 1998. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly. Mol. Biol. Evol. 15:499–505.[Abstract]

    Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol. Evol. 15:1091–1098.[Abstract]

    Rolfe, D. S. F., and G. C. Brown. 1997. Cellular energy utilization and molecular origin of standard metabolic rate in mammals. Physiol. Rev. 77:731–758.[Abstract/Free Full Text]

    Sabeur, G., G. Macaya, F. Kadi, and G. Bernardi. 1993. The isochore patterns of mammalian genomes and their phylogenetic implications. J. Mol. Evol. 37:93–108.[ISI][Medline]

    Saccone, C., C. Lanave, G. Pesole, and G. Preparata. 1990. Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 183:570–583.[ISI][Medline]

    Saccone, C., G. Pesole, and G. Preparata. 1989. DNA microenvironments and the molecular clock. J. Mol. Evol. 29:407–411.[ISI][Medline]

    Sarich, V. M., and A. C. Wilson. 1973. Generation time and genomic evolution in primates. Science 179:1144–1147.

    Sawyer, D. E., and B. Van Houten. 1999. Repair of DNA damage in mitochondria. Mutat. Res. 434:161–167.[ISI][Medline]

    Seddon, J. M., P. R. Baverstock, and A. Georges. 1998. The rate of mitochondrial 12S rRNA gene evolution is similar in freshwater turtles and marsupials. J. Mol. Evol. 46:460–464.[ISI][Medline]

    Springer, M. S. 1995. Molecular clocks and the incompleteness of the fossil record. J. Mol. Evol. 41:531–538.[ISI]

    Springer, M. S., G. C. Cleven, O. Madsen, W. De Jong, V. G. Waddell, H. M. Amrine, and M. J. Stanhope. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388:61–64.

    Springer, M. S., and E. Douzery. 1996. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J. Mol. Evol. 43:357–373.[ISI][Medline]

    Stanhope, M. J., V. G. Waddell, O. Madsen, W. De Jong, S. B. Hedges, G. C. Cleven, D. Kao, and M. S. Springer. 1998. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Natl. Acad. Sci. USA 95:9967–9972.

    Takezaki, N., A. Rzhetsky, and N. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823–833.[Abstract]

    Tamura, K., and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512–526.[Abstract]

    Thioulouse, J., D. Chessel, S. Dolédec, and J.-M. Olivier. 1997. ADE-4: a multivariate analysis and graphical display software. Stat. Comput. 7:75–83.[ISI]

    Xu, X., and U. Arnason. 1996. A complete sequence of the mitochondrial genome of the western lowland gorilla. Mol. Biol. Evol. 13:691–698.[Abstract]

    ———. 1997. The complete mitochondrial DNA sequence of the white rhinocheros, Ceratotherium simum, and comparison with the mtDNA sequence of the indian rhinoceros, Rhinoceros unicornis. Mol. Phylogenet. Evol. 7:189–194.

Accepted for publication March 3, 2000.