John F. Y. Brookfield

A simple new method for estimating null allele frequency from heterozygote deficiency

At minisatellite and microsatellite loci of humans and other species heterozygote deficiencies relative to Hardy-Weinberg expectations are sometimes observed. While such deficiencies are consistent with a WahIund effect arising from population subdivision, or inbreeding due to consanguineous mating, they may also be explained by the presence of null alleles, such that many of the apparent homozygotes are, in reality, heterozygotes between a visible and a null allele (Chakraborty et al. 2994; Pemberton et al. 1995). Such genotypes will appear to be homozygotes since they show a single band on the autoradiogram. For microsatellites, such null alleles can arise when mutations prevent primers from binding (Callen et al. 1993). Nulls in minisatellites will arise when a restriction fragment runs off the end of a gel. In allozymes, also, null alleles, lacking the enzyme activity that allows loci to be scored, may exist (Foltz 1986). Notwithstanding the capacity of such null alleles to greatly affect apparent heterozygosity, the expected frequency of n d homozygotes may be quite low, and such individuals may be lacking in the sample. Furthermore, even if such individuals are seen, the conclusion may be drawn that the DNA sample is degraded, or another technical problem has arisen, and the observation may be ignored. Chakraborty et al. (1992) discuss a method of estimating the frequency of null alleles (r in their terminology) from the apparent deficiency of heterozygotes that they induce. They deal with a situation in which all individuals in the sample show either one or two bands at a minisatellite (or microsatellite) locus. Null homozygotes are not represented in the sample.

The ecology of the genome — mobile DNA elements and their hosts

The genomes of multicellular eukaryotes provide information that determines the phenotype. However, not all sequences in the genome are required for this purpose. Other sequences are often selfish in their actions and interact in complex ways. Here, an analogy is developed between the components of the genome, including mobile DNA elements, and an ecological community. Unlike ecological communities, however, the slow rates at which genomes change allow us to reconstruct patterns of interaction that stretch back tens or hundreds of millions of years.

Cloning and characterization of an ftsZ homologue from a bacterial symbiont of Drosophila melanogaster.

A 1194 by open reading frame that codes for a 398 amino acid peptide was cloned from a λgt11 library of Drosophila melanogaster genomic DNA. The predicted peptide sequence is very similar to three previously characterized protein sequences that are encoded by the ftsZ genes in Escherichia coli, Bacillus subtilis and Rhizobium meliloti. The FtsZ protein has a major role in the initiation of cell division in prokaryotic cells. Using a tetracycline treatment that eradicates bacterial parasites from insects, the ftsZ homologue has been found to be derived from a bacterium that lives within the strain. However, polymerase chain reaction (PCR) amplification of the gene from treated embryos suggests that it is not derived from a gut bacterium. Nevertheless, by amplifying and characterizing part of the 16S rRNA from this bacterium we have been able to demonstrate that it is a member of the genus Wolbachia, a parasitic organism that infects, and disturbs the sexual cycle of various strains of Drosophila simulans. We suggest that this ftsZ homologue is implicated in the cell division of Wolbachia, an organism that fails to grow outside the host organism. Sequence and alignment analysis of this ftsZ homologue show the presence of a potential GTP-binding motif indicating that it may function as a GTPase. The consequences of this function particularly with respect to its role in cell division are discussed.

Population genetics models of transposable elements

The control of transposable element copy number is of considerable theoretical and empirical interest. Under simple models, copy numbers may increase without limit. Mechanisms that can prevent such an increase include those in which the effect of selection increases with copy number, those in which the rate of transposition decreases with copy number, and those where unlimited increase in copy number is prevented by the consequences of functional heterogeneity in the transposable element family. Finite population sizes may attenuate the power of natural selection to act on transposable element copy number in a number of ways that may be of particular importance in laboratory populations. First, a small host population size will create occasional periods in which the variance between individuals in copy number is diminished, and with it the power of natural selection, even when the expected variance is Poisson. Second, small population sizes will produce high-frequency transposable element sites, systematically reducing the variance in copy number. The consequences will be particularly profound when the selective damage of transposable elements follows from their heterozygosity, as when ectopic exchange limits copy number.

Behavioral insensitivity to DEET in Aedes aegypti is a genetically determined trait residing in changes in sensillum function.

N,N-Diethyl-m-toluamide (DEET) is one of the most effective and commonly used mosquito repellents. However, during laboratory trials a small proportion of mosquitoes are still attracted by human odors despite the presence of DEET. In this study behavioral assays identified Aedes aegypti females that were insensitive to DEET, and the selection of either sensitive or insensitive groups of females with males of unknown sensitivity over several generations resulted in two populations with different proportions of insensitive females. Crossing experiments showed the “insensitivity” trait to be dominant. Electroantennography showed a reduced response to DEET in the selected insensitive line compared with the selected sensitive line, and single sensillum recordings identified DEET-sensitive sensilla that were nonresponders in the insensitive line. This study suggests that behavioral insensitivity to DEET in A. aegypti is a genetically determined dominant trait and resides in changes in sensillum function.

Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population of Drosophila melanogaster

The insertion site polymorphism of the copia, mdg1, mdg3, gypsy, and P transposable elements was analysed by in situ hybridization to the polytene chromosomes in genomes of males from a natural population of Drosophila melanogaster. Parameters of various theoretical models of the population biology of transposable elements were estimated from our data, and different hypotheses explaining TE copy number containment were tested. The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. On the contrary, mdg3 and P copy numbers fit a neutral model with a balance between regulated transposition and excisions. There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. For all chromosome arms but 3L, however, the TE site density increases from the proximal to the distal parts of the chromosomes (the centromeric regions were excluded in this analysis) with sometimes a sharp decrease in density at the extreme tip, following in part the exchange coefficient. The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element.

Evidence for a Wolbachia symbiont in Drosophila melanogaster

The bacterial cell division gene, ftsZ, was used as a specific probe to show the presence of a symbiotic bacterium in two wild type strains of Drosophila melanogaster. Under stringent hybridization conditions we have shown that the bacterium is transferred to the progeny of these strains from infected mothers and can be eradicated by treatment with the antibiotic tetracycline. We have characterized this bacterium, by amplifying and sequencing its 16S rRNA gene, as being a member of the genus Wolbachia, an organism that is known to parasitize a range of insects including Drosophila simulans. In a series of reciprocal crosses no evidence was found that the symbiont causes cytoplasmic incompatibility (CI) which is known to occur in infected strains of D. simulans. The implications of these findings are discussed.

Aedes aegypti mosquitoes exhibit decreased repellency by DEET following previous exposure.

DEET (N,N-Diethyl-m-toluamide) is one of the most widely used mosquito repellents. Although DEET has been shown to be extremely effective, recent studies have revealed that certain individual insects are unaffected by its presence. A genetic basis for this has been shown in Aedes aegypti mosquitoes and the fruit fly Drosophila melanogaster, but, for the triatomine bug, Rhodnius prolixus, a decrease in response to DEET occurred shortly after previous exposure, indicating that non-genetic factors may also be involved in DEET “insensitivity”. In this study, we examined host-seeking behaviour and electrophysiological responses of A. aegypti after pre-exposure to DEET. We found that three hours after pre-exposure the mosquitoes showed behavioural insensitivity, and electroantennography revealed this correlated with the olfactory receptor neurons responding less to DEET. The change in behaviour as a result of pre-exposure to DEET has implications for the use of repellents and the ability of mosquitoes to overcome them.

Selection on Alu sequences

The draft of the human genome project reveals an unexpected distribution of Alu interspersed repetitive sequences [1xInitial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium. Nature. 2001; 409: 860–921Crossref | PubMed | Scopus (12778)See all References[1]. This has been interpreted as evidence that Alu sequences ‘may benefit their human hosts’ [1xInitial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium. Nature. 2001; 409: 860–921Crossref | PubMed | Scopus (12778)See all References[1] and that they ‘have a positive function’ [2xOur genome unveiled. Baltimore, D. Nature. 2001; 409: 814–816Crossref | PubMed | Scopus (204)See all References[2]. The implication is that the majority of Alu sequences increase the Darwinian fitness of their bearers. Here I suggest that this conclusion is inconsistent with our knowledge of human population genetics.There is a relationship between the time since an Alu sequence was inserted into the genome and the GC content of its surrounding DNA. Alu sequences inferred to have inserted within the last five million years are slightly more abundant in low-GC, gene-poor regions, whereas older Alus, in classes inserted from 5 to 100 million years ago, are increasingly found in high-GC gene-rich regions. Contrary to the conclusions drawn in the report [1xInitial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium. Nature. 2001; 409: 860–921Crossref | PubMed | Scopus (12778)See all References[1] and the associated News and Views article [2xOur genome unveiled. Baltimore, D. Nature. 2001; 409: 814–816Crossref | PubMed | Scopus (204)See all References[2], this observation does not indicate that Alu sequences are advantageous to their human hosts. While one could imagine that Alu sequences active 50million years ago were targeting GC-rich regions while todays Alus target AT-rich regions, a more parsimonious interpretation is to assume that the sequences insertion preferences have been constant, and that the change in the sequences relative abundance reflects a process in which, following insertion, it increases its relative abundance in GC-rich DNA with time. The most likely such process, and one considered and dismissed by the authors [1xInitial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium. Nature. 2001; 409: 860–921Crossref | PubMed | Scopus (12778)See all References[1], is that deletions removing Alu sequences from GC-rich DNA are likely to be harmful and prevented from spreading in the population by natural selection. This implies no functional importance for an Alu sequence itself, but merely that, as the deletions of Alus are very unlikely to be precise, a deletion event removing an Alu is also likely to remove valuable sequences around it, and the chromosome bearing the deletion will be lost by selection.The explanation favoured by the authors for Alu enrichment in gene-rich regions is that of positive selection in favour of Alus in GC-rich DNA. This theory, however, cannot explain the observations. The data show that Alu sequences up to five million years old are not enriched in GC-rich regions. But in human population genetics, estimated times to common ancestry of typical genomic regions show that Alu sequences which are five million years old have already been fixed (found in all individuals) in the population. This observation is also what would be expected from neutrality and genetic drift, given the human effective population size. (Alu sequences which are truly advantageous will spread to fixation much more quickly.) Earlier human ancestors would also be expected to have had similar fixation times for Alu insertions. Yet it is only during the spread to fixation of Alu sequences that positive natural selection has any opportunity to act. Thus, an increasing abundance of Alu sequences in GC-rich DNA as they age beyond five million years cannot be the result of natural selection for positive functions of Alu insertions.

Evolution and evolvability: celebrating Darwin 200.

The concept of ‘evolvability’ is increasingly coming to dominate considerations of evolutionary change. There are, however, a number of different interpretations that have been put on the idea of evolvability, differing in the time scales over which the concept is applied. For some, evolvability characterizes the potential for future adaptive mutation and evolution. Others use evolvability to capture the nature of genetic variation as it exists in populations, particularly in terms of the genetic covariances between traits. In the latter use of the term, the applicability of the idea of evolvability as a measure of populations capacity to respond to natural selection rests on one, but not the only, view of the way in which we should envisage the process of natural selection. Perhaps the most potentially confusing aspects of the concept of evolvability are seen in the relationship between evolvability and robustness.