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Organisms: the Clonal Theory of Parasitic Protozoa M 228 Parasitology Today, vol. 7, no. 9, 199 / Towards a Population Genetics of Micro- organisms: The Clonal Theory of Parasitic Protozoa M. Tibayrenc and F.J. Ayala Over the past 15 years, molecular investigations, gathering additional evidence based on larger including the study of isozymes and DNA markers, samples and more genetic markers. Whether or not have provided much information on the genetic vari- parasitic protozoa reproduce clonally is of consider- ation, population structure, breeding system and other able medical importance (see below). Moreover, population characteristics of parasitic protozoa. For given recent claims that sexuality and even pan- some parasitic protozoa, but not for others, the evidence mixia are common modes of reproduction for para- indicates that their reproduction is prevailingly clonal. sitic protozoa 3, the matter deserves attention. In this article, Michel Tibayrenc and Francisco Ayala propose that the issue of whether the predominant mode Sexual reproduction of reproduction of a given micro-organism is clonal or The case of Plasmodium falciparum deserves sexual can only be settled by population genetics infor- special attention. The hypothesis of uniparental mation, and they summarize evidence favoring a clonal propagation would seem particularly iconoclastic in population structure for a number of parasitic protozoa. this case, since an obligatory sexual phase is thought to be required in the life cycle of the parasite. Our The main feature determining the population analysis of a very limited data set (showing, in one structure of an organism is the mating system of the case, strong linkage disequilibrium [see Box 1] in a species. What matters, of course, is the prevailing multilocus allozyme survey of 17 individuals and, in mode of reproduction in natural populations. Thus, two other studies, the presence in widely separated successful interbreeding experiments in the labora- localities of identical genotypes as evidenced by tory show that the potential for sexual reproduction two-dimensional gel electrophoresis or RFLPs) exists but that it does not occur in nature. Even the suggests that gene flow might be biologically re- occasional observation of sexual reproduction in stricted, at least in some cases ~'2. There is, of nature cannot settle the issue of how prevalent course, the possibility that these results are aberrant sexual reproduction is in natural populations. We as a consequence of small sample sizes or of acci- submit that the mode of reproduction in parasitic dental laboratory mixups, the more so since some protozoa and other microbial organisms can be studies favor a sexual population structure for P. ascertained only by population genetic consider- falciparum (Refs 4, 5 and D. Walliker, this issue). ations of the distribution of genotypes (especially But the matter cannot be settled just by pointing multilocus genotypes) in populations. out that the life cycle of P. falciparum includes a We have previously used population genetic sexual phase. There are many organisms, including methods to determine the population structure of a higher metazoa, in which meiosis (and, in some number of parasitic protozoan species I and have cases, fertilization) occurs but without fusion of more recently extended these methods to other gametes or genetic recombination. In automictic protozoan species and some yeasts and other fungi2. parthenogenesis, meiosis and recombination take There is evidence of clonal propagation for many place but fusion occurs between two haploid nuclei species, although the strength of the evidence varies from the same individual. In apomictic partheno- (in part at least) because the strength of the tests genesis, meiosis in the eggs typically involves only depends on the number of genetic markers and the one maturation division, which is equational and size of the population samples (see Table 1). The yields eventually zygotes that are genetic clones of evidence for a clonal population structure is the parental genotype. Self-fertilization, as it occurs often overwhelming (eg. many Trypanosoma and in many annual plants, promotes homozygosis; self- Leishmania); in others it remains a working hypoth- fertilization in homozygous individuals yields esis that can readily be corroborated or falsified by genetic clones of the parent. Other mechanisms, such as gynogenesis, also yield progenies that are genetic clones of one parent even though meiosis Michel Tibayrenc is at the Laboratory of Genetics for Parasites and and fertilization occur. It may very well be the case Vectors, ORSTOM, BP 5045, 34032 Montpellier Cedex, France and (and, a priori, it seems most likely) that genetic Francisco J. Ayala is at the Department of Ecology and Evolutionary recombination typically, or at least often, occurs in Biology, University of California, Irvine, CA 92717, USA. P. falciparum. But the matter deserves to be settled ~) 1991, ELsevierScience Publishers Ltd, (LIK) 0169--4707/9I/$02.00 Parasitology Today, vol. 7, no. 9, 1991 229 Table I. Organisms surveyed and rank based on the strength of reject a null hypothesis does not establish its truth, evidence for clonal reproduction particularly when the statistical power of the test is Organism Rank a Criteria supporting low owing to small sample sizes. More extensive clonality b samples are required before the prevailing mode of Fungi reproduction of C. albicans is settled. Candida albicans i none The two relevant consequences of sexual repro- Candida tropicalis/ paratropicalis ii d l,d2,e,f duction are the segregation of alleles at a locus and Cryptococcus neoformans their recombination between loci. Evidence that B + C serotypes ii e,f these two processes are rare or absent amounts to Cryptococcus neoformans evidence that sexual reproduction is rare or absent A + D serotypes ii f in nature. Table 2 lists the sources of evidence that Cryptococcus neoformans all serotypes ii d I,d2,e,f should be sought to ascertain whether segregation Saccharomyces cerevisiae ii f and recombination are absent, as we have proposed elsewhere1. These are the criteria that we used in Protozoa Entamoeba histolytica iii d I,d2,e,f proposing a clonal population structure for T. Giardia sp. iii d I,d2,e,f,g cruzi6-9. The criteria expand the two classical Leishmania braziliensis statistics used in population genetics to ascertain guyanensis iv d I,d2,e,f random mating and free genetic recombination: Leishmania infantum iv d I ,d2,e,f Hardy-Weinberg equilibrium frequencies and Leishmania tropica iv a,d I ,d2,e,f Leishmania major iv d I,d2,e,f linkage disequilibrium (see Box 1). They should not Leishmania Old World be considered as redundant. The various criteria as a whole iv d I ,d2,e,f should all be tested whenever possible, although Leishmania sp. i ii g some of them may be either preferable or the only Naegleria australiensis ii a,d ones possible in certain circumstances. For Naegleria fowled ii a Naegleria gruberi i i a example, when particular alleles cannot be dis- Plasmodium falciparum ii d I ,d2,e,f,d cerned, or the organism is haploid, or the ploidy is Toxoplasma gondii ii d I,d2,f unknown, only the recombinant tests are appli- Trichomonas foetus ii d cable. Trichomonas vaginalis i i d Trypanosoma brucei s.I. The null hypothesis underlying the tests listed in West Africa iv d I ,d2,e,f Table 2 is panmixia. No real organism is perfectly East Africa iv d I ,d2,e,f panmictic, which raises the issue of how to dis- East Africa (wild) ii e,f tinguish absence of sexual reproduction from the Liberia iv d I,d2,e,f effects of population subdivision, ie. deviations Busoga, Uganda iv d I ,d2,e,f from random mating among populations with dif- Lambwe Valley, Kenya iv d I,d2,e,f Lambwe Valley ferent allelic frequencies. The concern is particu- (nonhuman stocks) iv d I ,d2,e,f larly vexing when samples obtained over wide geo- Ivory Coast iv d I,e,f graphic ranges are examined. However, the matter Ivory Coast (nonhuman can be discerned because the deviations from the stocks) iv d I,f expected random-mating pattern are different for Trypanosoma congolense iii a,d I ,d2,e,f Trypanosoma cruzi iv a,b,c,d,f,g geographic subdivisions and for clonal repro- Trypanosoma vivax iv d I ,d2,e,f duction 2. First, deviations from Hardy-Weinberg a Rank i indicates that the available data do not show clonality; ii, clonality is due to population subdivision entail a deficiency of only a working hypothesis because the supporting evidence comes from heterozygotes (Wahlund effect), whereas clonal small sample numbers; iii, there is evidence for clonality but the limited reproduction is often associated with an excess of number of markers prevents equating the strains with actual clones; iv, clonal population structure is well ascertained. heterozygotes (fixed heterozygosity, in the extreme b Criteria a, b, and d are qualitative; all others are based on statistical tests case). Moreover, when segregation or recombi- significant at the 0.05 level, or at the 0.01 level in the case of criterion f (see nation tests yield some genotypes in excess of the Ref. 2). These criteria are identified in Table 2. expected frequencies, particular genotypes will occur in excess only in particular localities in the case of geographic subdivision, whereas they may and can simply be resolved by obtaining population be ubiquitous in the case of clonal propagation. genetic information., as called for by the criteria listed in Table 2. Such studies are well worth Geographic subdivisions undertaking whatever the outcome, given that so In principle, it is always possible to overcome the little is known about this parasite's population consequences of geographic subdivision on geno- structure. typic frequencies by limiting any study to samples Another puzzling case is Candida albicans, a yeast that are extremely confined in space and time; in for which no sexual stage is known.
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