Maintenance of clonal diversity in Dipsa bifurcata (Fallén, 1810) (Diptera: Lonchopteridae). I. Fluctuating seasonal selection moulds long-term coexistence

Aneuploidy during development in facultative parthenogenetic Drosophila

From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval brains of facultatively parthenogenetic Drosophila. We identified a background of aneuploidy in D. mercatorum strains and found increased levels of aneuploidy in the larval brain tissue of animals arising parthenogenetically versus those arising from sexual reproduction. There is also intra-individual variation in germline-derived aneuploidy within the same strain. To determine if this is a general feature of facultative parthenogenesis in drosophilids, we compared sexually reproduced and parthenogenetic offspring from an engineered facultative parthenogenetic strain of D. melanogaster. In addition to germline-derived aneuploidy, this revealed somatic aneuploidy that increased by up to fourfold in parthenogens compared to sexually reproduced offspring. Therefore, the genetic combination identified in D. mercatorum that causes facultative parthenogenesis in D. melanogaster results in aneuploidy, which indicates that the loss of mitotic control resulting in parthenogenesis causes subsequent genome variation within the parthenogenetic offspring. Our findings challenge the assumption that parthenogenetic offspring are near genetic replicas of their mothers.

Parthenogenesis in dipterans: a genetic perspective

Parthenogenesis has been documented in almost every phylum of animals, and yet this phenomenon is largely understudied. It has particular importance in dipterans since some parthenogenetic species are also disease vectors and agricultural pests. Here, we present a catalogue of parthenogenetic dipterans, although it is likely that many more remain to be identified, and we discuss how their developmental biology and interactions with diverse environments may be linked to different types of parthenogenetic reproduction. We discuss how the advances in genetics and genomics have identified chromosomal loci associated with parthenogenesis. In particular, a polygenic cause of facultative parthenogenesis has been uncovered in Drosophila mercatorum, allowing the corresponding genetic variants to be tested for their ability to promote parthenogenesis in another species, Drosophila melanogaster. This study probably identifies just one of many routes that could be followed in the evolution of parthenogenesis. We attempt to account for why the phenomenon has evolved so many times in the dipteran order and why facultative parthenogenesis appears particularly prevalent. We also discuss the significance of coarse genomic changes, including non-disjunction, aneuploidy, and polyploidy and how, together with changes to specific genes, these might relate to both facultative and obligate parthenogenesis in dipterans and other parthenogenetic animals.

Development of G: a test in an amphibious fish

Heritable variation in, and genetic correlations among, traits determine the response of multivariate phenotypes to natural selection. However, as traits develop over ontogeny, patterns of genetic (co)variation and integration captured by the G matrix may also change. Despite this, few studies have investigated how genetic parameters underpinning multivariate phenotypes change as animals pass through major life history stages. Here, using a self-fertilizing hermaphroditic fish species, mangrove rivulus (Kryptolebias marmoratus), we test the hypothesis that G changes from hatching through reproductive maturation. We also test Cheverud's conjecture by asking whether phenotypic patterns provide an acceptable surrogate for patterns of genetic (co)variation within and across ontogenetic stages. For a set of morphological traits linked to locomotor (jumping) performance, we find that the overall level of genetic integration (as measured by the mean-squared correlation across all traits) does not change significantly over ontogeny. However, we also find evidence that some trait-specific genetic variances and pairwise genetic correlations do change. Ontogenetic changes in G indicate the presence of genetic variance for developmental processes themselves, while also suggesting that any genetic constraints on morphological evolution may be age-dependent. Phenotypic correlations closely resembled genetic correlations at each stage in ontogeny. Thus, our results are consistent with the premise that-at least under common environment conditions-phenotypic correlations can be a good substitute for genetic correlations in studies of multivariate developmental evolution.

Longitudinal clines in the frequency distribution of 'super-clones' in an aphid crop pest

Parthenogenesis is the main mode of reproduction of aphids. Their populations are therefore composed of clones whose frequency distribution varies in space and time. Previous population genetic studies on aphids have highlighted the existence of highly abundant clones ('super-clones'), distributed over large geographic areas and persisting over time. Whether the abundance of 'super-clones' results from their ecological success or from stochastic forces, such as drift and migration, is an open question. Here, we looked for the existence of clines in clonal frequency along a climatic gradient in the cereal aphid Rhopalosiphum padi (Linnaeus, 1758) and examined the possible influence of geographical distance and environmental variables in the buildup and maintenance of such clonal clines. We investigated the spatial distribution of the commonest genotypes of R. padi by sampling populations along an east-west transect in maize fields in the northern half of France in both spring and late summer. Individual aphids were genotyped at several polymorphic loci, allowing the assessment of frequency distributions of multilocus genotypes (MLGs) across the cropping season. We found several MLGs showing longitudinal clines in their frequency distribution in both spring and summer. In particular, two dominant asexual genotypes of R. padi showed inverted geographical clines, which could suggest divergent adaptations to environmental conditions. We concluded that while the distribution of some 'super-clones' of R. padi seems most likely driven by the action of migration and genetic drift, selection could be also involved in the establishment of longitudinal clines of others.

Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila

In many species, genomic data have revealed pervasive adaptive evolution indicated by the fixation of beneficial alleles. However, when selection pressures are highly variable along a species' range or through time adaptive alleles may persist at intermediate frequencies for long periods. So called “balanced polymorphisms” have long been understood to be an important component of standing genetic variation, yet direct evidence of the strength of balancing selection and the stability and prevalence of balanced polymorphisms has remained elusive. We hypothesized that environmental fluctuations among seasons in a North American orchard would impose temporally variable selection on Drosophila melanogaster that would drive repeatable adaptive oscillations at balanced polymorphisms. We identified hundreds of polymorphisms whose frequency oscillates among seasons and argue that these loci are subject to strong, temporally variable selection. We show that these polymorphisms respond to acute and persistent changes in climate and are associated in predictable ways with seasonally variable phenotypes. In addition, our results suggest that adaptively oscillating polymorphisms are likely millions of years old, with some possibly predating the divergence between D. melanogaster and D. simulans. Taken together, our results are consistent with a model of balancing selection wherein rapid temporal fluctuations in climate over generational time promotes adaptive genetic diversity at loci underlying polygenic variation in fitness related phenotypes.

Herein, we investigate the genomic basis of rapid adaptive evolution in response to seasonal fluctuations in the environment. We identify hundreds of polymorphisms (seasonal SNPs) that undergo dramatic shifts in allele frequency – on average between 40 and 60% – and oscillate between seasons repeatedly over multiple years, likely inducing high levels of genome-wide genetic differentiation. We provide evidence that seasonal SNPs are functional, being both sensitive to an acute frost event and associated with two stress tolerance traits. Finally, we show that some seasonal SNPs are possibly ancient balanced polymorphisms. Taken together, our results suggest that environmental heterogeneity can promote the long-term persistence of functional polymorphisms within populations that fuels fast directional adaptive response at any one time.

Evidence for Inefficient Selection Against Deleterious Mutations in Cytochrome Oxidase I of Asexual Bdelloid Rotifers

Evolutionary theory predicts that natural selection should be less efficient in asexually than in sexually reproducing organisms. Obligate asexuals are expected to adapt slowly to changing environments and to accumulate mildly deleterious mutations to their genomes, potentially explaining their typically short evolutionary lifespans. One group of animals that appear to challenge these ideas is the bdelloid rotifers, a large and ancient clade of obligate asexuals. Previous work has found no evidence for inefficient selection against deleterious mutations in protein-coding genes of bdelloids. However, these studies relied mostly on between-species comparisons and were therefore unable to detect mildly deleterious mutations that persist within populations but are removed by selection over longer time periods. Here, we test for inefficient purifying selection acting on the cytochrome oxidase I (cox1) mitochondrial gene in 3 clades of bdelloids. Patterns of variation are compared to those of two facultatively sexual clades: a monogonont rotifer (Brachionus) and a branchiopod crustacean (Daphnia). As predicted due to the strict linkage between mitochondrial and nuclear genomes, bdelloids exhibit higher frequencies of putatively deleterious amino acid polymorphism within populations than the two facultatively sexual clades. While the monophyly and age of bdelloids makes it hard to rule out other explanations for the observed differences, several possible confounding factors, such as differences in effective population size or patterns of codon usage, are shown not to explain the observed differences. We therefore conclude that bdelloid mitochondrial DNA variation does display the signature of inefficient selection expected of obligate asexuals.

Temporal dynamics of genotypic diversity reveal strong clonal selection in the aphid Myzus persicae

Parthenogenetic organisms often harbour substantial genotypic diversity. This diversity may be the result of recurrent formations of new clones, or it may be maintained by environmental heterogeneity acting on ecological differences among clones. In aphids, both processes may be important because obligate and cyclical parthenogens can form mixed populations. Using microsatellites, I analysed the temporal dynamics of clonal diversity in such a population of the aphid Myzus persicae over a 1-year period. The frequency distribution of clonal genotypes was very skewed, with many rare and few common clones. The relative frequencies of common clones underwent strong and rapid changes indicative of intense clonal selection. Differences in their host associations suggest that these shifts may partly be caused by changes in the abundance of annual host plants. Other selective factors of potential importance are also discussed. New, sexually produced genotypes made a minor contribution to clonal diversity, consistent with the observed heterozygote excess characteristic of predominantly asexual populations in M. persicae.