Update TRENDS in Genetics Vol.19 No.2 February 2003 57

|Research Focus How many lethal alleles?

Daniel L. Halligan and Peter D. Keightley

Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK

Knowledge of the frequency of lethal mutant alleles in a Drosophila, lethal alleles are thought to contribute as population is important for our understanding of popu- much to inbreeding depression as minor effect deleterious lation genetics and evolution, and yet there have been alleles [4,5]. few attempts to measure their number in wild popu- The majority of published estimates of the number of lations. A new study has revealed unexpectedly low lethal alleles per individual in wild populations come numbers of segregating lethal alleles in two species of from various Drosophila species. The general method for fish. More experiments are needed, however, to know detecting lethal genes in Drosophila was suggested by whether this result is general. Muller [6], and involves the use of BALANCER CHROMO- SOMES to test for lethal alleles in a specific chromosome There have been very few attempts to estimate the mean (Fig. 1). It is then possible to estimate the number of lethal number of lethal alleles per individual in wild populations alleles per individual (R), by accounting for the proportion (R, see Glossary), and until recently there was only one of the genome in the chromosome tested. Much of the data reliable estimate available from any vertebrate species. In have been summarized and converted to estimates of R by a recent article, McCune et al. [1] provided new estimates Lewontin [7] (see also [8]). In 18 such experiments [7], all from populations of two different species of fish, bluefin but one estimate of R fell in the range 0.5 to 3. killifish (Lucania goodei) and zebrafish (Danio rerio). The Reliable estimates from other taxa are needed to make estimates were both unexpectedly low, if it is assumed that general conclusions about R, and to know whether R is R should scale to genome size or gene number across taxa. correlated to or affected by genome size, the number and Below we discuss previous results and the potential impact length of coding regions, EFFECTIVE POPULATION SIZE or of these latest findings. other demographic factors. Unfortunately, other than for Mutations with positive effects on fitness are necessary Drosophila, there are very few estimates of R, and not all for adaptive evolution, but the vast majority of spontane- are reliable. In humans, there are no good quantitative ous mutations have negative effects on fitness in all data, although it has been suggested that there are at taxa studied [2]. New mutant alleles arise spontaneously, most 1.4 LETHAL EQUIVALENTS per individual [9], which and although they are purged from a population by natural is suggestive of a low R. However, it is very difficult to selection, a MUTATION–SELECTION BALANCE (see Glossary) quantify the effects of recessive deleterious alleles that is expected to exist, in which the frequency of deleterious manifest themselves before birth in humans, and their alleles fluctuates around an equilibrium. These dele- effects could be substantial. Many species of fish and terious mutations could explain many observed phenom- amphibians fertilize their eggs externally, which provides ena in evolutionary biology. For instance, INBREEDING an excellent opportunity for estimating mortality after DEPRESSION is widely believed to be caused by recessive inbreeding: Any maternal effects should be small, owing to deleterious mutations becoming homozygous in the off- the fact that eggs do not develop inside the mother (if there spring of related individuals. Knowledge of the frequency and nature of deleterious alleles could help in predicting levels of inbreeding depression, which could have an Glossary impact in conservation genetics. Furthermore, the infor- Balancer chromosome: A chromosome that suppresses recombination by mation has relevance for human genetics in the context of having multiple large inversions, and is identifiable by phenotype when heterozygous or homozygous. They are often chosen to be lethal when genetic counselling in cases of consanguineous marriages. homozygous although this is not necessary.

Despite the potential importance of deleterious muta- Effective population size (Ne): A number reflecting the size of an idealized tions, there are still very few estimates of the number of population (i.e. large, random mating, even sex ratio, non-overlapping generations) that is affected by drift and selection to the same extent as the deleterious alleles segregating in individuals from wild population under consideration. populations. One problem in obtaining such estimates is Gynogenesis: A form of female parthenogenesis in which the embryo only that the majority of deleterious mutations have very small contains maternal chromosomes, owing to the sperm failing to fuse with the egg’s nucleus. or effectively undetectable effects on fitness [3]. It is much Inbreeding depression: The reduction in fitness due to increasing more straightforward to estimate the frequency of reces- homozygosity. Lethal equivalent: A group of mutant genes that would cause on average one sive mutations with very large homozygous effects. In genetic death. particular, it should be possible to estimate the number Mutation–selection balance: the equilibrium formed between spontaneous of recessive lethal alleles per individual in wild popu- mutation introducing new deleterious mutations, and natural selection removing them. lations objectively and unambiguously. Furthermore, in R: The mean number of recessive lethal alleles carried by an individual in a population. Corresponding author: Peter D. Keightley ([email protected]). http://tigs.trends.com 58 Update TRENDS in Genetics Vol.19 No.2 February 2003

Recessive Recessive KEY lethal marker lethal allele Balancer chromosome containing a recessive lethal marker (M1) and multiple M1 WT1 M2 WT2 inversions to suppress recombination Marker chromosome containing a recessive lethal marker (M2) Wild-type chromosome containing a recessive lethal allele (WT1) M1 WT1 Wild-type chromosome free from M2 M1 recessive lethal alleles (WT2) Recessive lethal marker gene Single male Many males WT1 WT1 Single female M1 M1 Many females

M1 WT1 WT1 M1 M1 WT1 All die All die if there is a recessive lethal present in the chromosome tested TRENDS in Genetics

Fig. 1. Balancer chromosome crossing scheme for the detection of recessive lethal alleles on a particular chromosome of interest in Drosophila (adapted from [7]). This scheme allows the detection of recessive lethal alleles in one chromosome from a wild-type individual by crossing the individual to a balanced marker stock population. A single wild-type male (carrying two homologous wild-type chromosomes) is crossed to many balanced marker stock females. The balanced marker stock have two different dominant marker genes (M1 and M2) on homologous chromosomes. One of these chromosomes (M1) also contains recombination suppressing inversions that keep the wild-type chromosome intact. A single male is selected from the F1 offspring on the basis of having the M1 heterozygous phenotype, thereby choosing one wild-type chromosome to study, and backcrossed to the marker stock. The backcrossed offspring are intercrossed, producing many offspring, which are scored. If a recessive lethal is present on the wild-type chromosome tested, as in this case, then only heterozygous individuals will be produced from the final cross, providing a simple and objective scheme to test for the presence of a recessive lethal on a random wild chromosome. are large maternal effects, then only an upper limit for R than crosses between unrelated parents if the related can be estimated [10]). Amphibians and fish also produce parents share recessive deleterious alleles. Wild-caught large numbers of offspring, allowing expectations of men- parents were mated and their offspring (F1 sibships) were delian ratios to be tested, and offspring that fail to develop used in brother–sister matings (Fig. 2). Recessive lethal can be counted directly. An experiment of this type was alleles would reveal themselves in most cases as severe carried out in wild-caught Xenopus laevis [11]. The experi- morphological mutants in expected mendelian ratios in 25% mental design used GYNOGENESIS and inbreeding, to of brother-sister crosses (Fig. 2). For each species, McCune detect the effects of rare recessive lethal alleles in their et al. estimated R using a maximum-likelihood method. The homozygous state. Fourteen mutants were recovered from estimated numbers of recessive lethal alleles in both the eight females giving an estimate of R of 1.875, which is species (R ¼ 1.87 for L. goodei and R ¼ 1.43 for D. rerio)are similar to the estimates from Drosophila discussed above. entirely consistent with the Xenopus estimate and fall in the There have been a number of reports of estimates of R middle of the range of the Drosophila estimates. in species other than Drosophila, but their validity has This similarity of R estimates across Drosophila and been questioned [1]. An estimate of R ¼ 1.6 from the vertebrate taxa is perhaps surprising, given that the Mexican salamander (Ambystoma mexicanum) [12,13] Drosophila genome is substantially smaller and is thought was reported in [11], although it was not possible to to have fewer genes than the vertebrate genome. Further- recover this estimate from the original papers [1]. A large more, numbers of deleterious mutations that arise in the estimate of R was also reported in the pacific oyster protein-coding genes appear to be positively correlated Cassostrea gigas [14], although it has been suggested that with the generation time of a species, and Drosophila have departures from mendelian ratios could be caused by a substantially shorter generation time than the fishes factors other than recessive lethal alleles in this species in question [17]. All else being equal, therefore, higher [1]. Another estimate of R ¼ 3–6 has been reported from numbers of segregating lethal alleles are expected in Loblolly pine (Pinus taeda) [15], although this estimate vertebrate populations. There are several possible factors was based on data from only one individual. that could reduce the numbers of segregating lethal alleles Until the latest experiment, therefore, the study in in vertebrates. Greater selection against heterozygotes in Xenopus provided the only reliable estimate from a verte- vertebrates would reduce the frequency of segregating brate species. Recently, however, McCune et al. studied recessive lethal alleles. Selection against heterozygotes bluefin killifish and zebrafish [1] with an experimental potentially accounts for the majority of selection against design suggested by Timofe´eff-Ressovski [16] to estimate lethal alleles, because they are not completely recessive, on R, based on the idea that offspring from crosses between average, in Drosophila [8]. Furthermore, with incomplete related parents are expected to have fewer viable offspring recessivity, effective population size of populations and http://tigs.trends.com Update TRENDS in Genetics Vol.19 No.2 February 2003 59 bottlenecks in the past could have a major role in deter- the level of inbreeding depression before and after purging mining the frequency of lethal alleles [18]. However, there would allow the inference of the proportional contribution of are no data to suggest that this selection is stronger in lethal alleles to the overall inbreeding load [21]. vertebrates [1]. Alternatively, a lower fraction of essential In summary, with only a handful of reliable estimates of loci in vertebrates could explain the observation, but pro- R outside of Drosophila, it is still unclear whether we portions of essential loci in Drosophila and humans are should expect to observe similar frequencies of lethal not, apparently, dissimilar (,20% in both) [1]. More plau- alleles in other outbreeding species. We will therefore need sible explanations are higher levels of inbreeding in the more data in order to draw general conclusions about the vertebrate populations or population subdivision; both frequency of recessive lethal alleles across different taxa. these factors can have the effect of increasing the rate of With further information of the kind outlined above, it purging of recessive deleterious mutations [19,20].Itis might then be possible to make more general inferences also possible that population size and structure could have about the contribution of lethal alleles to inbreeding changed recently, and that historically inbreeding was depression and how this varies across taxa. more prevalent, purging mutations and reducing the number present today. Unfortunately data about the Acknowledgements population structure at present, or in the past, are very We would like to thank Brian Charlesworth for useful comments. limited, making these hypotheses difficult to test. An approximate constancy for R across taxa would have implications for our understanding of inbreeding References depression. In Drosophila, recessive lethal alleles cause 1 McCune, A.R. et al. (2002) A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish. Science 296, about a half of the inbreeding load [5]. If vertebrates 2398–2401 typically carry a similar number of lethal alleles then we 2 Keightley, P.D. and Lynch, M. Towards a realistic model of mutations could expect these to cause a similar level of inbreeding affecting fitness. Evolution (in press) depression as in Drosophila. However, the contribution 3 Keightley, P.D. and Eyre-Walker, A. 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(2001) High genetic load in the pacific oyster Crassostrea gigas. Genetics 159, 255–265 15 Remington, D.L. and O’Malley, D.M. (2000) Whole-genome character- ization of embryonic stage inbreeding depression in a selfed loblolly pine family. Genetics 155, 337–348 16 Timofe´eff-Ressovsky, H.A. and Timofe´eff-Ressovsky, N.W. (1927) Genetische analyse einer freilebenden Drosophila melanogaster – population. Wilhelm Roux’ Arch. Entwicklungsmech. Org. 109, 70–109 17 Keightley, P.D. and Eyre-Walker, A. (2000) Deleterious mutations and 1/4 1/2 1/4 the evolution of sex. Science 290, 331–333 All die 18 Hedrick, P.W. (2002) Lethals in finite populations. Evolution 56, 654–657 TRENDS in Genetics 19 Wang, J.L. et al. (1999) Dynamics of inbreeding depression due to deleterious mutations in small populations: mutation parameters and inbreeding rate. Genet. Res. 74, 165–178 Fig. 2. Crossing scheme used to infer the number of recessive lethal alleles present 20 Whitlock, M.C. (2002) Selection, load and inbreeding depression in a in two unrelated wild-caught parents. Sibships are produced by mating the two large metapopulation. Genetics 160, 1191–1202 wild-caught parents, and brother–sister crosses are carried out within these 21 Willis, J.H. (1999) The role of genes of large effect on inbreeding sibships. If there is a recessive lethal allele (red) present in either parent, then 25% of these brother–sister crosses (both the brother and the sister have to be depression in Mimulus guttatus. Evolution 53, 1678–1691 heterozygous) will be able to reveal it. In such a cross, 25% of the offspring are expected to show the effects of the recessive lethal allele by failing to survive to 0168-9525/03/$ - see front matter q 2002 Elsevier Science Ltd. All rights reserved. reproductive age. PII: S0168-9525(02)00045-8 http://tigs.trends.com