Chung-I Wu

The genic view of the process of speciation

The unit of adaptation is usually thought to be a gene or set of interacting genes, rather than the whole genome, and this may be true of species differentiation. Defining species on the basis of reproductive isolation (RI), on the other hand, is a concept best applied to the entire genome. The biological species concept (BSC; Mayr, 1963 ) stresses the isolation aspect of speciation on the basis of two fundamental genetic assumptions – the number of loci underlying species differentiation is large and the whole genome behaves as a cohesive, or coadapted genetic unit. Under these tenets, the exchange of any part of the genomes between diverging groups is thought to destroy their integrity. Hence, the maintenance of each species’ genome cohesiveness by isolating mechanisms has become the central concept of species. In contrast, the Darwinian view of speciation is about differential adaptation to different natural or sexual environments. RI is viewed as an important by product of differential adaptation and complete RI across the whole genome need not be considered as the most central criterion of speciation. The emphasis on natural and sexual selection thus makes the Darwinian view compatible with the modern genic concept of evolution. Genetic and molecular analyses of speciation in the last decade have yielded surprisingly strong support for the neo‐Darwinian view of extensive genetic differentiation and epistasis during speciation. However, the extent falls short of what BSC requires in order to achieve whole‐genome ‘cohesiveness’. Empirical observations suggest that the gene is the unit of species differentiation. Significantly, the genetic architecture underlying RI, the patterns of species hybridization and the molecular signature of speciation genes all appear to support the view that RI is one of the manifestations of differential adaptation, as Darwin (1859 , Chap. 8) suggested. The nature of this adaptation may be as much the result of sexual selection as natural selection. In the light of studies since its early days, BSC may now need a major revision by shifting the emphasis from isolation at the level of whole genome to differential adaptation at the genic level. With this revision, BSC would in fact be close to Darwin’s original concept of speciation.

Rapid evolution of male reproductive genes in the descent of man

A diverse body of morphological and genetic evidence has suggested that traits pertaining to male reproduction may have evolved much more rapidly than other types of character. Recently, DNA sequence comparisons have also shown a very high level of divergence in male reproductive proteins between closely related Drosophila species, among marine invertebrates and between mouse and rat. Here we show that rapid evolution of male reproductive genes is observable in primates and is quite notable in the lineages to human and chimpanzee. Nevertheless, rapid evolution by itself is not necessarily an indication of positive darwinian selection; relaxation of negative selection is often equally compatible with the DNA sequence data. By taking three statistical approaches, we show that positive darwinian selection is often the driving force behind this rapid evolution. These results open up opportunities to test the hypothesis that sexual selection plays some role in the molecular evolution of higher primates.

Genes and speciation

It is only in the past five years that studies of speciation have truly entered the molecular era. Recent molecular analyses of a handful of genes that are involved in maintaining reproductive isolation between species (speciation genes) have provided some striking insights. In particular, it seems that despite being strongly influenced by positive selection, speciation genes are often non-essential, having functions that are only loosely coupled to reproductive isolation. Molecular studies might also resolve the long-running debate on the relative importance of allopatric and parapatric modes of speciation.

Evolution of Postmating Reproductive Isolation: The Composite Nature of Haldane's Rule and Its Genetic Bases

The patterns of postmating reproductive isolation in general follow Haldanes rule that the heterogametic sex is much more likely to become inviable or sterile than the homogametic sex. There are two approaches to explaining the rule. The first approach assumes that genic divergence affects both sexes equally but their difference in chromosome constitution leads to the sex:dependent manifestation; for example, the heterogametic hybrids have a greater degree of X-autosome imbalance. The second approach assumes that genes affecting the heterogametic sex have evolved more rapidly and the genotypic difference between sexes is unimportant. Neither approach in its search for a unitary genetic basis of Haldanes rule has been successful. The major point of this article is that Haldanes rule is most likely a composite rule--the first approach is appropriate for hybrid inviability but is not sufficient for hybrid sterility, which requires the second approach in addition. Three lines of evidence are presented: (1) genes causing hybrid inviability generally do not behave in a sex-dependent manner and, thus, X-autosome imbalance is crucial; (2) interspecific crosses yielding sterility outnumber those yielding inviability by more than 10-fold in Drosophila and mammals; and (3) in Drosophila, genes causing hybrid male sterility greatly outnumber genes causing male inviability. Several models pertaining to the faster evolution of hybrid sterility in the heterogametic sex (than in the homogametic sex) are discussed. Finally, genes affecting the viability and fertility of interspecific hybrids seem to belong in a class distinct from those represented in mutagenic studies or those detected as intraspecific variations. The implications of this qualitative and quantitative break at the species level need to be heeded.

Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications.

SummaryWe have obtained a revised estimate of the pattern of point mutation by considering more pseudogene sequences. Compared with our previous estimate, it agrees better with expectations based on the double-strand structure of DNA. The revised pattern, like the previous one, indicates that mutation occurs nonrandomly among the four nucleotides. In particular, the proportion of transitional mutations (59%) is almost twice as high as the value (33%) expected under random mutation. The same high proportion of transitions is observed in synonymous substitutions in genes. The proportion of transitional changes observed among electrophoretic variants of human hemoglobin is about the same as that predicted by the revised pattern of mutation. We also show that nonrandom mutation increases, by about 15%, the proportion of synonymous mutations due to single-nucleotide changes in the codon table, and increases, from 10% to 50%, the rate of synonymous mutation in the seven genes studied. However, nonrandom mutation reduces (by about 10%) the proportion of polar changes among nonsynonymous mutations in a gene. As far as single-nucleotide changes (in the codon table) are concerned, nonrandom mutation only slightly favors relatively conservative amino acid interchanges, and has virtually no effect on the proportions of radical changes and nonsense mutations.

Testing the neutral theory of molecular evolution with genomic data from Drosophila

Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence. A comparison of the A/S ratio of polymorphism in Drosophila melanogaster with that of divergence from Drosophila simulans shows that the A/S ratio of divergence is twice as high—a difference that is often attributed to positive selection. But an increase in selective constraint owing to an increase in effective population size could also explain this observation, and, if so, all genes should be affected similarly. Here we show that the difference between polymorphism and divergence is limited to only a fraction of the genes, which are also evolving more rapidly, and this implies that positive selection is responsible. A higher A/S ratio of divergence than of polymorphism is also observed in other species, which suggests a rate of adaptive evolution that is far higher than permitted by the neutral theory of molecular evolution.

Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants

By comparing the low-, intermediate-, and high-frequency parts of the frequency spectrum, we gain information on the evolutionary forces that influence the pattern of polymorphism in population samples. We emphasize the high-frequency variants on which positive selection and negative (background) selection exhibit different effects. We propose a new estimator of θ (the product of effective population size and neutral mutation rate), θL, which is sensitive to the changes in high-frequency variants. The new θL allows us to revise Fay and Wus H-test by normalization. To complement the existing statistics (the H-test and Tajimas D-test), we propose a new test, E, which relies on the difference between θL and Wattersons θW. We show that this test is most powerful in detecting the recovery phase after the loss of genetic diversity, which includes the postselective sweep phase. The sensitivities of these tests to (or robustness against) background selection and demographic changes are also considered. Overall, D and H in combination can be most effective in detecting positive selection while being insensitive to other perturbations. We thus propose a joint test, referred to as the DH test. Simulations indicate that DH is indeed sensitive primarily to directional selection and no other driving forces.

The birth and death of microRNA genes in Drosophila

MicroRNAs (miRNAs) are small, endogenously expressed RNAs that regulate mRNAs post-transcriptionally. The class of miRNA genes, like other gene classes, should experience birth, death and persistence of its members. We carried out deep sequencing of miRNAs from three species of Drosophila, and obtained 107,000 sequences that map to no fewer than 300 loci that were not previously known. We observe a large class of miRNA genes that are evolutionarily young, with a rate of birth of 12 new genes per million years (Myr). Most of these new miRNAs originated from non-miRNA sequences. Among the new genes, we estimate that 96% disappeared quickly in the course of evolution; only 4% of new miRNA genes were retained by natural selection. Furthermore, only 60% of these retained genes became integrated into the transcriptome in the long run (60 Myr). This small fraction (2.5%) of surviving miRNAs may later on become moderately or highly expressed. Our results suggest that there is a high birth rate of new miRNA genes, accompanied by a comparably high death rate. The estimated net gain of long-lived miRNA genes, which is not strongly affected by either the depth or the breadth (number of tissues) of sequencing, is 0.3 genes per Myr in Drosophila.

Haldane's rule and its legacy: Why are there so many sterile males?

A general pattern of animal hybridization, known as Haldanes rule, is that the XY (ZW) sex is more severely affected in its viability or fertility than the XX (ZZ) sex. Recent evidence suggests that three different forces have shaped this pattern: (1) the X chromosome and autosomes are in greater disharmony in the XY sex; (2) evolution of hybrid male sterility is greatly accelerated, at least in species with XY males; and (3) maternal-zygotic incompatibility preferentially affects the viability of the XX sex. In species with XY males, the rapid evolution toward hybrid male sterility may be responsible for the bulk of observations pertaining to Haldanes rule. One interesting and testable hypothesis is that sexual selection drives this rapid evolution.

Adaptive genic evolution in the Drosophila genomes

Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. In this study, we sequenced 419 genes from 24 lines of Drosophila melanogaster and its close relatives. Together with data from Drosophila simulans, these data reveal the following. (i) Approximately 10% of the loci in regions of normal recombination are much less polymorphic at silent sites than expected, hinting at the action of selective sweeps. (ii) The level of polymorphism is negatively correlated with the rate of nonsynonymous divergence across loci. Thus, even under strict neutrality, the ratio of amino acid to silent nucleotide changes (A:S) between Drosophila species is expected to be 25–40% higher than the A:S ratio for polymorphism when data are pooled across the genome. (iii) The observed A/S ratio between species among the 419 loci is 28.9% higher than the (adjusted) neutral expectation. We estimate that nearly 30% of the amino acid substitutions between D. melanogaster and its close relatives were adaptive. (iv) This signature of adaptive evolution is observable only in regions of normal recombination. Hence, the low level of polymorphism observed in regions of reduced recombination may not be driven primarily by positive selection. Finally, we discuss the theories and data pertaining to the interpretation of adaptive evolution in genomic studies.