Testing for evidence of inefficient selection in bdelloid rotifers: do sample size and habitat differences matter?

Preliminary evidence on inefficient selection has indicated that asexual (=parthenogenetic) animals suffer from a greater accumulation of deleterious mutations compared with their closest sexual sister taxa. However, previous work on bdelloid rotifers did not completely rule out the confounding effects of sample size and habitat differences. Here, we present further evidence of inefficient selection against deleterious mutations in the bdelloid rotifers in comparison with their closest clade, the monogononts, by taking account of larger samples. However, the analysis of samples from both clades co-occurring in the same location seems to contradict the hypothesis. Both groups show evidence of the accumulation of deleterious mutations in mitochondrial DNA, but further population sampling and inclusion of additional genes is needed to resolve this issue.     

Evolutionary Dynamics of ‘the’ Bdelloid and Monogonont Rotifer Life-history Patterns

Substantial differences in both life-table characteristics and reproductive patterns distinguish bdelloid from monogonont rotifers. Bdelloids reproduce only asexually, whereas most monogononts are cyclical parthenogens. We explore some of the adaptive consequences of these life-history differences using a computer model to simulate the evolutionary acquisition of new beneficial mutations. A one-locus mutation-selection regime based on the life-history characteristics of bdelloids indicates that asexuals can maintain higher levels of both allelic and genotypic diversity over a longer time period than obligate sexuals. These results are produced by differences in the magnitude of random genetic drift (RGD) associated with the different types of reproduction. Cyclical parthenogens have significantly higher evolutionary rates than sexual forms in a single-locus model, but incorporate beneficial mutations more slowly than sexuals in a two-locus simulation. Our results are therefore strongly influenced by the number of loci being evaluated as well as the pattern of reproduction. The asexual life history was found to maintain higher levels of allelic diversity than any pattern including sexual reproduction. This intriguing finding is amplified as the number of loci undergoing selection is increased. We end by considering the adaptive consequences of the remarkably divergent life histories found in typical bdelloid and monogonont rotifers.     

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra‐ and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation.     

Contrasting patterns of synonymous and nonsynonymous sequence evolution in asexual and sexual freshwater snail lineages

In asexual lineages, both synonymous and nonsynonymous sequence polymorphism may be reduced due to severe founder effects when asexual lineages originate. However, mildly deleterious (nonsynonymous) mutations may accumulate after asexual lineages are formed, because the efficiency of purifying selection is reduced even in the nonrecombining mitochondrial genome. Here we examine patterns of synonymous and nonsynonymous mitochondrial sequence polymorphism in asexual and sexual lineages of the freshwater snail Campeloma. Using clade-specific estimates, we found that synonymous sequence polymorphism was significantly reduced by 75% in asexuals relative to sexuals, whereas nonsynonymous sequence polymorphism did not differ significantly between sexuals and asexuals. Two asexual clades had high negative values for Tajima's D statistic. Coalescent simulations confirmed that various bottleneck scenarios can account for this result. We also used branch-specific estimates of the ratio of amino acid to silent substitutions, K(a)/K(s). Our study revealed that K(a)/K(s) ratios are six times higher in terminal branches of independent asexual lineages compared to sexuals. Coalescent-based reconstruction of gene networks for all sexual and asexual clades indicated that nonsynonymous mutations occurred at a higher frequency in recently derived asexual haplotypes. These findings suggest that patterns of synonymous and nonsynonymous nucleotide polymorphism in asexual snail lineages may be shaped by both severe founder effect and relaxed purifying selection.     

On the reality and recognisability of asexual organisms: morphological analysis of the masticatory apparatus of bdelloid rotifers

Species concepts and definitions have been a long-standing debate in evolutionary biology since before Darwin, and almost all proposed solutions are based upon grouping and clustering, with species conceived as somehow biological distinct entities, originated and maintained mainly by reproductive isolation. Lacking reproductive exchange, asexual organisms such as bdelloid rotifers, the best-supported clade of so-called 'ancient asexuals', pose an interesting challenge to debates over the reality of species. However, few data are available on bdelloid rotifers. The only evidence has been that bdelloid species have been more consistently recognised than in their sister sexual group, the monogonont rotifers, across successive taxonomic treatments, but this is confounded by the much lesser degree of taxonomic interest in bdelloids. We applied geometric morphometrics analyses on shape and size of hard masticatory pieces, named trophi, of 1420 bdelloids, belonging to 48 populations of eight traditional species, to test the hypothesis of recognisability of bdelloids. Our morphological analysis confirms that traditional bdelloid species are separated distinct entities, possessing trophi morphologies divided by gaps between taxa, similar to patterns of morphological features in sexually reproducing organisms. In common with most microscopic understudied organisms, bdelloid rotifers harbour much previously undescribed diversity: we found significant differences in trophi morphology within traditional species, revealing the existence of cryptic taxa, similar to those also found in facultatively sexual monogonont rotifers. We confirm that recognisability in bdelloids is not qualitatively different from other small understudied animals such as monogononts, and that sexual versus asexual reproduction does not lead to differences in morphological diversity patterns, as previously suggested based on interpretation of taxonomic revisions.     

Deleterious mutation accumulation in asexual Timema stick insects

Sexual reproduction is extremely widespread in spite of its presumed costs relative to asexual reproduction, indicating that it must provide significant advantages. One postulated benefit of sex and recombination is that they facilitate the purging of mildly deleterious mutations, which would accumulate in asexual lineages and contribute to their short evolutionary life span. To test this prediction, we estimated the accumulation rate of coding (nonsynonymous) mutations, which are expected to be deleterious, in parts of one mitochondrial (COI) and two nuclear (Actin and Hsp70) genes in six independently derived asexual lineages and related sexual species of Timema stick insects. We found signatures of increased coding mutation accumulation in all six asexual Timema and for each of the three analyzed genes, with 3.6- to 13.4-fold higher rates in the asexuals as compared with the sexuals. In addition, because coding mutations in the asexuals often resulted in considerable hydrophobicity changes at the concerned amino acid positions, coding mutations in the asexuals are likely associated with more strongly deleterious effects than in the sexuals. Our results demonstrate that deleterious mutation accumulation can differentially affect sexual and asexual lineages and support the idea that deleterious mutation accumulation plays an important role in limiting the long-term persistence of all-female lineages.     

Nonadaptive evolution of mitochondrial genome size

Genomes vary greatly in size and complexity, and identifying the evolutionary forces that have generated this variation remains a major goal in biology. A controversial proposal is that most changes in genome size are initially deleterious and therefore are linked to episodes of decrease in effective population sizes. Support for this hypothesis comes from large-scale comparative analyses, but vanishes when phylogenetic nonindependence is taken into account. Another approach to test this hypothesis involves analyzing sequence evolution among clades where duplications have recently fixed. Here we show that episodes of fixation of duplications in mitochondrial genomes of the gecko Heteronotia binoei (two independent clades) and of mantellid frogs (five distinct branches) coincide with reductions in the ability of selection to purge slightly deleterious mutations. Our results support the idea that genome complexity can arise through nonadaptive processes in tetrapods.     

Different Diversification Rates Between Sexual and Asexual Organisms

Patterns of diversity reflect the balance between speciation and extinction over time. Here we estimate net diversification rates for samples of sexual and asexual rotifers using phylogenetic reconstructions from sequence data of one mtDNA locus, cytochrome oxidase c subunit I. All four clades of bdelloid rotifers, obligate asexuals, had higher number of species per clade and significantly higher accumulation of diversification events towards the root of the trees than the four clades of their sexual relatives, the monogonont rotifers. Such differences were robust to confounding effects of number of analysed sequences, haplotype diversity, overall genetic divergence, age of the clades or geographic coverage. Our results support the idea that differences in diversification rates could thus be ascribed to different mechanisms of speciation, with ecological speciation as the most plausible mechanism for asexual organisms.     

High proportions of deleterious polymorphisms in constrained human genes

Previous studies on human mitochondrial genomes showed that the ratio of intra-specific diversities at nonsynonymous-to-synonymous positions was two to ten times higher than the ratio of interspecific divergences at these positions, suggesting an excess of slightly deleterious nonsynonymous polymorphisms. However, such an overabundance of nonsynonymous single nucleotide polymorphisms (SNPs) was not found in human nuclear genomes. Here, genome-wide estimates using >14,000 human-chimp nuclear genes and 1 million SNPs from four human genomes showed a significant proportion of deleterious nonsynonymous SNPs (～ 15%). Importantly, this study reveals a negative correlation between the magnitude of selection pressure and the proportion of deleterious SNPs on human genes. The proportion of deleterious amino acid replacement polymorphisms is 3.5 times higher in genes under high purifying selection compared with that in less constrained genes (28% vs. 8%). These results are explained by differences in the extent of contribution of mildly deleterious mutations to diversity and substitution.     

Genome structure and the benefit of sex

We examine the behavior of sexual and asexual populations in modular multipeaked fitness landscapes and show that sexuals can systematically reach different, higher fitness adaptive peaks than asexuals. Whereas asexuals must move against selection to escape local optima, sexuals reach higher fitness peaks reliably because they create specific genetic variants that "skip over" fitness valleys, moving from peak to peak in the fitness landscape. This occurs because recombination can supply combinations of mutations in functional composites or "modules," that may include individually deleterious mutations. Thus when a beneficial module is substituted for another less-fit module by sexual recombination it provides a genetic variant that would require either several specific simultaneous mutations in an asexual population or a sequence of individual mutations some of which would be selected against. This effect requires modular genomes, such that subsets of strongly epistatic mutations are tightly physically linked. We argue that such a structure is provided simply by virtue of the fact that genomes contain many genes each containing many strongly epistatic nucleotides. We briefly discuss the connections with "building blocks" in the evolutionary computation literature. We conclude that there are conditions in which sexuals can systematically evolve high-fitness genotypes that are essentially unevolvable for asexuals.     

Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models

Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods, the distribution can be estimated from DNA sequence data by phylogenetic-based models. Previous models have generally found unimodal distributions where the probability mass is concentrated between mildly deleterious and nearly neutral mutations. Here we use a sitewise mutation-selection phylogenetic model to estimate the distribution of selection coefficients among novel and fixed mutations (substitutions) in a data set of 244 mammalian mitochondrial genomes and a set of 401 PB2 proteins from influenza. We find a bimodal distribution of selection coefficients for novel mutations in both the mitochondrial data set and for the influenza protein evolving in its natural reservoir, birds. Most of the mutations are strongly deleterious with the rest of the probability mass concentrated around mildly deleterious to neutral mutations. The distribution of the coefficients among substitutions is unimodal and symmetrical around nearly neutral substitutions for both data sets at adaptive equilibrium. About 0.5% of the nonsynonymous mutations and 14% of the nonsynonymous substitutions in the mitochondrial proteins are advantageous, with 0.5% and 24% observed for the influenza protein. Following a host shift of influenza from birds to humans, however, we find among novel mutations in PB2 a trimodal distribution with a small mode of advantageous mutations.     

Genetic Diversity,Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex,Daphnia pulicaria,and Daphnia obtusa

Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.     

MUTATIONAL MELTDOWNS IN SEXUAL POPULATIONS

Although it is widely acknowledged that the gradual accumulation of mildly deleterious mutations is an important source of extinction for asexual populations, it is generally assumed that this process is of little relevance to sexual species. Here we present results, based on computer simulations and supported by analytical approximations, that indicate that mutation accumulation in small, random-mating monoecious populations can lead to mean extinction times less than a few hundred to a few thousand generations. Unlike the situation in obligate asexuals in which the mean time to extinction (t?_e) increases more slowly than linearly with the population carrying capacity (K), t?_e increases approximately exponentially with K in outcrossing sexual populations. The mean time to extinction for obligately selfing populations is shown to be equivalent to that for asexual populations of the same size, but with half the mutation rate and twice the mutational effect; this suggests that obligate selfing, like obligate asexuality, is inviable as a long-term reproductive strategy. Under all mating systems, the mean time to extinction increases relatively slowly with the logarithm of fecundity, and mutations with intermediate effects (similar to those observed empirically) cause the greatest risk of extinction. Because our analyses ignore sources of demographic and environmental stochasticity, which have synergistic effects that exacerbate the accumulation of deleterious mutations, our results should yield liberal upper bounds to the mean time to extinction caused by mutational degradation. Thus, deleterious mutation accumulation cannot be ruled out generally as a significant source of extinction vulnerability in small sexual populations or as a selective force influencing mating-system evolution.     

Genetic load in sexual and asexual diploids: segregation, dominance and genetic drift

In diploid organisms, sexual reproduction rearranges allelic combinations between loci (recombination) as well as within loci (segregation). Several studies have analyzed the effect of segregation on the genetic load due to recurrent deleterious mutations, but considered infinite populations, thus neglecting the effects of genetic drift. Here, we use single-locus models to explore the combined effects of segregation, selection, and drift. We find that, for partly recessive deleterious alleles, segregation affects both the deterministic component of the change in allele frequencies and the stochastic component due to drift. As a result, we find that the mutation load may be far greater in asexuals than in sexuals in finite and/or subdivided populations. In finite populations, this effect arises primarily because, in the absence of segregation, heterozygotes may reach high frequencies due to drift, while homozygotes are still efficiently selected against; this is not possible with segregation, as matings between heterozygotes constantly produce new homozygotes. If deleterious alleles are partly, but not fully recessive, this causes an excess load in asexuals at intermediate population sizes. In subdivided populations without extinction, drift mostly occurs locally, which reduces the efficiency of selection in both sexuals and asexuals, but does not lead to global fixation. Yet, local drift is stronger in asexuals than in sexuals, leading to a higher mutation load in asexuals. In metapopulations with turnover, global drift becomes again important, leading to similar results as in finite, unstructured populations. Overall, the mutation load that arises through the absence of segregation in asexuals may greatly exceed previous predictions that ignored genetic drift.     

The on‐again,off‐again relationship between mitochondrial genomes and species boundaries

The study of reproductive isolation and species barriers frequently focuses on mitochondrial genomes and has produced two alternative and almost diametrically opposed narratives. On one hand, mtDNA may be at the forefront of speciation events, with co‐evolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted. We argue that these seemingly contradictory patterns can result from a single underlying cause. Specifically, the accumulation of deleterious mutations in mtDNA creates a problem with two alternative evolutionary solutions. In some cases, compensatory or epistatic changes in the nuclear genome may ameliorate the effects of mitochondrial mutations, thereby establishing coadapted mitonuclear genotypes within populations and forming the basis of reproductive incompatibilities between populations. Alternatively, populations with high mitochondrial mutation loads may be rescued by replacement with a more fit, foreign mitochondrial haplotype. Coupled with many nonadaptive mechanisms of introgression that can preferentially affect cytoplasmic genomes, this form of adaptive introgression may contribute to the widespread discordance between mitochondrial and nuclear genealogies. Here, we review recent advances related to mitochondrial introgression and mitonuclear incompatibilities, including the potential for cointrogression of mtDNA and interacting nuclear genes. We also address an emerging controversy over the classic assumption that selection on mitochondrial genomes is inefficient and discuss the mechanisms that lead lineages down alternative evolutionary paths in response to mitochondrial mutation accumulation.     

A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata

Molecular and morphological data regarding the relationships among the three classes of Rotifera (Bdelloidea, Seisonidea, and Monogononta) and the phylum Acanthocephala are inconclusive. In particular, Bdelloidea lacks molecular-based phylogenetic appraisal. I obtained coding sequences from the mitochondrial genomes of twelve bdelloids and two monogononts to explore the molecular phylogeny of Bdelloidea and provide insight into the relationships among lineages of Syndermata (Rotifera + Acanthocephala). With additional sequences taken from previously published mitochondrial genomes, the total dataset included nine species of bdelloids, three species of monogononts, and two species of acanthocephalans. A supermatrix of these 10-12 mitochondrial proteins consistently recovered a bdelloid phylogeny that questions the validity of a generally accepted classification scheme despite different methods of inference and various parameter adjustments. Specifically, results showed that neither the family Philodinidae nor the order Philodinida are monophyletic as currently defined. The application of a similar analytical strategy to assess syndermate relationships recovered either a tree with Bdelloidea and Monogononta as sister taxa (Eurotatoria) or Bdelloidea and Acanthocephala as sister taxa (Lemniscea). Both outgroup choice and method of inference affected the topological outcome emphasizing the need for sequences from more closely related outgroups and more sophisticated methods of analysis that can account for the complexity of the data.     

EVOLUTIONARY FEEDBACKS BETWEEN REPRODUCTIVE MODE AND MUTATION RATE EXACERBATE THE PARADOX OF SEX

Evolutionary theory suggests that low mutation rates should favor the persistence of asexuals. Additionally, given the observation that most nonneutral mutations are deleterious, asexuality may strengthen selection for reduced mutation rates. This reciprocal relationship raises the possibility of a positive feedback loop between sex and mutation rate. We explored the consequences of this evolutionary feedback with an individual‐based model in which a sexual population is continually challenged by the introduction of asexual clones. We found that asexuals were more likely to spread in a population when mutation rates were able to evolve relative to a model in which mutation rates were held constant. In fact, under evolving mutation rates, asexuals were able to spread to fixation even when sexuals faced no cost of sex whatsoever. The added success of asexuals was the result of their ability to evolve lower mutation rates and thereby slow the process of mutation accumulation that otherwise limited their spread. Given the existence of ample mutation rate variation in natural populations, our findings show that the evolutionary feedback between sex and mutation rate may intensify the “paradox of sex,” supporting the argument that deleterious mutation accumulation alone is likely insufficient to overcome the reproductive advantage of asexual competitors in the short term.