Ecole Normale Superieure de Lyon, Lyon, France;
Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, England
It is generally believed that the mitochondrial genome is inherited from a single parent in animals and higher plants and that the inheritance of mitochondrial DNA (mtDNA) is therefore clonal (Birky 1995
). However, the clonality of human mtDNA has recently been questioned (Awadalla, Eyre-Walker, and Maynard Smith 1999
; Eyre-Walker, Smith, and Maynard Smith 1999a
; Hagelberg et al. 1999
) and keenly debated (Eyre-Walker, Smith, and Maynard Smith 1999b
; Macaulay, Richards, and Sykes 1999
; Awadalla, Eyre-Walker, and Maynard Smith 2000
; Eyre-Walker 2000
; Jorde and Bamshad 2000
; Kivisilid and Villems 2000
; Kumar et al. 2000
; Parsons and Irwin 2000
).
The evidence of recombination in human mtDNA comes from two sources. First, many phylogenetic trees constructed using mtDNA contain a large amount of homoplasy (e.g., Vigilant et al. 1991
; Ingman et al. 2000
), which has generally been attributed to the presence of hypervariable sites in the mtDNA (Hasegawa et al. 1993
; Wakeley 1993
). However, Eyre-Walker, Smith, and Maynard Smith (1999a, 1999b)
have suggested that the homoplasies could be due to recombination. Second, Awadalla, Eyre-Walker, and Maynard Smith (1999)
found that linkage disequilibrium (LD) declined as a function of the distance between sites in several human data sets and one chimpanzee mtDNA data set, a pattern which is highly consistent with recombination. However, their analysis was criticized on several grounds. In particular, Jorde and Bamshad (2000)
and Kumar et al. (2000)
argued that the measure of LD used by Awadalla, Eyre-Walker, and Maynard Smith (1999)
, r2, the squared correlation of allele frequencies (Hill and Robertson 1968
), was inappropriate since it is dependent on allele frequencies; they argued that the absolute value of D', the absolute value of D over its maximum value (Lewontin 1964
), was a more appropriate statistic, and they noted that |D'| was not correlated to the distance between sites for any of the data sets considered by Awadalla, Eyre-Walker, and Maynard Smith (1999)
. Awadalla, Eyre-Walker, and Maynard Smith (2000)
subsequently gave a number of reasons why they believed that r2 might be a better measure of LD for detecting recombination, but ultimately this is an argument which can only be resolved by investigation. Here, we present the results of some population genetic simulations we used to investigate our ability to detect recombination from the correlation between r2 or |D'| and distance.
We simulated a population of N haploid circular genomes of length L under a model of mutation, random genetic drift, and recombination. In each generation, U mutations and R recombination events were distributed across the population, where U and R were random numbers drawn from Poisson distributions with means of NLu and Nr, respectively, where u is the nucleotide mutation rate and r is the recombination rate per chromosome. For each recombination event, two genomes were chosen at random, along with a starting point. From the randomly chosen starting point, z nucleotides were transferred between the genomes in a gene conversion-type process. Most simulations were performed using reciprocal recombination, but we also investigated nonreciprocal recombination by transferring the information from one chromosome to the other but not reciprocating the process (this yielded very similar results; not shown). To form the next generation, we randomly sampled N genomes with replacement.
Initial simulations showed that the model parameterized in Nu and Nr as expected. We therefore performed all subsequent simulations with a population size of 500 genomes, assuming a chromosome length of 16,500 bases, the approximate length of the human mtDNA. The simulation was allowed to run for 10N generations to equilibrate, after which 100 samples of 49 genomes were sampled at intervals of 2N. These samples could be considered largely independent, since a haploid population is expected to coalesce, on average, every 2N generations; this was checked by calculating the autocorrelation between successive samples. For each sample, we calculated the correlation between r2 (and |D'|) and the distance between sites. Significance was assessed using a one-tailed Mantel test with 500 randomized data sets (see Awadalla, Eyre-Walker, and Maynard Smith [1999
] for details).
To begin our investigations, we followed Awadalla, Eyre-Walker, and Maynard Smith (1999)
and restricted our analysis to sites at which both alleles were present at a frequency of >10%, and we set the mutation rate so that
50 sites were polymorphic at that level. We arbitrarily chose to exchange 5,000 nt in each recombination event and varied the recombination rate across a broad range of values. The results are presented in table 1 . As expected, the probability of detecting recombination increased as the rate of recombination increased, and there was no evidence of excessive type I error when there was no recombination. Over all rates of recombination, r2 and |D'| performed at levels that were very similar to each other. We then investigated a broad range of other parameter combinations by varying (1) the recombination tract length from 500 to 8,000 bp, (2) the frequency above which alleles were included in the analysis from 0 to 0.2, and (3) the mutation rate such that either 50 or 10 polymorphisms were, on average, included in the analysis. While changing many of these parameters changed the probability of detecting recombination, it did not alter the relative performances of r2 and |D'|, which were very similar in all cases.
|
A similar pattern is observed in the human and chimpanzee data sets analyzed by Awadalla, Eyre-Walker, and Maynard Smith (1999)
and others; removing the PWCs with four genotypes from the analysis makes little difference in the value of the correlation between r2 and distance or the significance of the result (table 2
). Thus, the r2 test appears to make little use of the four-genotype cases, and this may be the reason |D'| and r2 give different results in the hominid mtDNA data setsthey use different information. But this leaves us with two questions: (1) if recombination is occurring, then why does |D'| not detect it in the hominid data sets, and (2) how does r2 detect recombination when it ignores the most obvious evidence of recombination, the presence of all four genotypes?
|
Resolving the different results obtained with r2 and |D'| in hominid mitochondria will require further work, but it seems likely that they are associated with the different information that the two statistics employ.
Acknowledgements
We thank John Maynard Smith, Philip Awadalla, Eddie Holmes, and three anonymous referees for helpful discussion and comments. A.E.-W. was funded by the Royal Society.
Footnotes
Edward Holmes, Reviewing Editor
2 Address for correspondence and reprints: Adam Eyre-Walker, Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom. a.c.eyre-walker{at}sussex.ac.uk
.
References
Awadalla P., A. Eyre-Walker, J. Maynard Smith, 1999 Linkage disequilibrium and recombination in hominid mitochondrial DNA Science 286:2524-2525
. 2000 Questioning evidence for recombination in human mitochondrial DNA Science 288:1931a
Ballinger S. W., T. G. Schurr, A. Torroni, Y. Y. Gan, J. A. Hodge, K. Hassan, K.-H. Chen, D. C. Wallace, 1992 Southeast Asian mitochondrial DNA analysis reveals genetic continuity of ancient Mongoloid migrations Genetics 130:139-152
Birky C. W. J., 1995 Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution Proc. Natl. Acad. Sci. USA 92:11331-11338[Abstract]
Chen Y. S., A. Torroni, L. Excoffier, A. S. Santachiara-Benerecetti, D. C. Wallace, 1995 Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups Am. J. Hum. Genet 57:133-149[ISI][Medline]
Eyre-Walker A., 2000 Do mitochondria recombine in humans? Philos. Trans. R. Soc. Lond. B Biol. Sci 355:1573-1580[ISI][Medline]
Eyre-Walker A., N. H. Smith, J. Maynard Smith, 1999a. How clonal are human mitochondria? Proc. R. Soc. Lond. B Biol. Sci 266:477-483[ISI][Medline]
. 1999b. Reply to Macaulay et al.: mtDNA recombinationreasons to panic Proc. R. Soc. Lond. B Biol. Sci 266:2041-2042[ISI]
Hagelberg E., N. Goldman, P. Lio, S. Whelan, W. Schiefenhovel, J. B. Clegg, D. K. Bowden, 1999 Evidence for mitochondrial recombination in a human population of island Melanesia Proc. R. Soc. Lond. B Biol. Sci 266:485-492[ISI][Medline]
Hasegawa M., A. Di Rienzo, T. D. Kocher, A. C. Wilson, 1993 Toward a more accurate time scale for the human mitochondrial DNA tree J. Mol. Evol 37:347-354[ISI][Medline]
Hill W. G., A. Robertson, 1968 Linkage disequilibrium in finite populations Theor. Appl. Genet 38:226-231
Hofmann S., M. Jaksch, R. Bezold, S. Mertens, S. Aholt, A. Paprotta, K. D. Gerbitz, 1997 Population genetics and disease susceptibility: characterization of central European haplogroups by mtDNA gene mutations, correlations with D loop variants and association with disease Hum. Mol. Genet 6:1835-1846
Ingman M., H. Kaessman, S. Paabo, U. Gyllensten, 2000 Mitochondrial genome variation and the origin of modern humans Nature 408:708-713[ISI][Medline]
Jorde L. B., M. Bamshad, 2000 Questioning evidence for recombination in human mitochondrial DNA Science 288:1931a
Kivisilid T., R. Villems, 2000 Questioning evidence for recombination in human mitochondrial DNA Science 288:1931a
Kumar S., P. Hedrick, T. Dowling, M. Stoneking, 2000 Questioning evidence for recombination in human mitochondrial DNA Science 288:1931a
Lewontin R. C., 1964 The interaction of selection and linkage. I. Genetic considerations; heterotic models Genetics 49:49-67
Macaulay V., M. Richards, E. Hickey, E. Vega, F. Cruciani, V. Guida, R. Scozzari, B. Bonne-Tamir, B. Sykes, A. Torroni, 1999 The emerging tree of west Eurasian mtDNAs: a synthesis of control region and RFLPs Am. J. Hum. Genet 64:232-249[ISI][Medline]
Macaulay V., M. Richards, B. Sykes, 1999 mtDNA recombinationno need to panic Proc. R. Soc. Lond. B Biol. Sci 266:2037-2040[ISI][Medline]
Parsons T. J., J. A. Irwin, 2000 Questioning evidence for recombination in human mitochondrial DNA Science 288:1931a
Stoneking M., 2000 Hypervariable sites in the mtDNA control region are mutational hotspots Am. J. Hum. Genet 67:1029-1032[ISI][Medline]
Torroni A., K. Huoponen, P. Francalacci, M. Petrozzi, L. Morelli, R. Scozzari, D. Obinu, M. L. Savontaus, D. C. Wallace, 1996 Classification of European mtDNAs from an analysis of three European populations Genetics 144:1835-1850
Torroni A., M. T. Lott, M. F. Cabell, Y. Chen, L. Lavergne, D. C. Wallace, 1992a. mtDNA and the origin of Caucasians: identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-Loop region Am. J. Hum. Genet 55:760-776
Torroni A., J. A. Miller, L. G. Moore, S. Zamudio, J. Zhuang, T. Droma, D. C. Wallace, 1994 Mitochondrial DNA analysis in Tibet: implications for the origin of the Tibetan population and its adaptation to high altitude Am. J. Phys. Anthropol 93:189-199[ISI][Medline]
Torroni A., T. G. Schurr, C.-C. Yang, et al. (11 co-authors) 1992b. Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations Genetics 130:153-162
Torroni A., R. I. Sukernik, T. G. Schurr, Y. B. Starikorskaya, M. F. Cabell, M. H. Crawford, A. G. Comuzzie, D. C. Wallace, 1993 mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans Am. J. Hum. Genet 53:591-608[ISI][Medline]
Vigilant L., M. Stoneking, H. Harpending, K. Hawkes, A. C. Wilson, 1991 African populations and the evolution of human mitochondrial DNA Science 253:1503-1507[ISI][Medline]
Wakeley J., 1993 Substitution rate heterogeneity variation among sites in hypervariable region 1 of human mitochondrial DNA J. Mol. Evol 37:613-623[ISI][Medline]
Wise C. A., M. Sraml, S. Easteal, 1998 Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees Genetics 148:409-421