Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome.

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.

Natal Dispersal, Mating Patterns, and Inbreeding in the Ant Formica exsecta.

Sex-biased dispersal and multiple mating may prevent or alleviate inbreeding and its outcome, inbreeding depression, but studies demonstrating this in the wild are scarce. Perennial ant colonies offer a unique system to investigate the relationships between natal dispersal behavior and inbreeding. Due to the sedentary life of ant colonies and lifetime sperm storage by queens, measures of dispersal distance and mating strategy are easier to obtain than in most taxa. We used a suite of molecular markers to infer the natal colonies of queens and males in a wild population of the ant Formica exsecta. Dispersal was male biased, with median male dispersal distances (∼140 m) twice those of queens (∼60 m). The results also showed that the population was inbred and that inbreeding avoidance behaviors--sex-biased dispersal, queen dispersal distance, and multiple mating--were all ineffective in reducing homozygosity among colony workers. Queen homozygosity did not affect dispersal behavior, but more homozygous queens had lower colony-founding success and were more incestuously mated themselves, with potentially accumulating effects on colony fitness. We also provide independent evidence that dispersal is sex biased and show that our estimate corresponds well with dispersal estimates derived from population-genetic estimates.

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila.

Spontaneous mutations are the source of genetic variation required for evolutionary change, and are therefore important for many aspects of evolutionary biology. For example, the divergence between taxa at neutrally evolving sites in the genome is proportional to the per nucleotide mutation rate, u (ref. 1), and this can be used to date speciation events by assuming a molecular clock. The overall rate of occurrence of deleterious mutations in the genome each generation (U) appears in theories of nucleotide divergence and polymorphism, the evolution of sex and recombination, and the evolutionary consequences of inbreeding. However, estimates of U based on changes in allozymes or DNA sequences and fitness traits are discordant. Here we directly estimate u in Drosophila melanogaster by scanning 20 million bases of DNA from three sets of mutation accumulation lines by using denaturing high-performance liquid chromatography. From 37 mutation events that we detected, we obtained a mean estimate for u of 8.4 x 10(-9) per generation. Moreover, we detected significant heterogeneity in u among the three mutation-accumulation-line genotypes. By multiplying u by an estimate of the fraction of mutations that are deleterious in natural populations of Drosophila, we estimate that U is 1.2 per diploid genome. This high rate suggests that selection against deleterious mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction.

Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster.

Mitochondrial DNA (mtDNA) variants are widely used in evolutionary genetics as markers for population history and to estimate divergence times among taxa. Inferences of species history are generally based on phylogenetic comparisons, which assume that molecular evolution is clock-like. Between-species comparisons have also been used to estimate the mutation rate, using sites that are thought to evolve neutrally. We directly estimated the mtDNA mutation rate by scanning the mitochondrial genome of Drosophila melanogaster lines that had undergone approximately 200 generations of spontaneous mutation accumulation (MA). We detected a total of 28 point mutations and eight insertion-deletion (indel) mutations, yielding an estimate for the single-nucleotide mutation rate of 6.2 x 10(-8) per site per fly generation. Most mutations were heteroplasmic within a line, and their frequency distribution suggests that the effective number of mitochondrial genomes transmitted per female per generation is about 30. We observed repeated occurrences of some indel mutations, suggesting that indel mutational hotspots are common. Among the point mutations, there is a large excess of G-->A mutations on the major strand (the sense strand for the majority of mitochondrial genes). These mutations tend to occur at nonsynonymous sites of protein-coding genes, and they are expected to be deleterious, so do not become fixed between species. The overall mtDNA mutation rate per base pair per fly generation in Drosophila is estimated to be about 10x higher than the nuclear mutation rate, but the mitochondrial major strand G-->A mutation rate is about 70x higher than the nuclear rate. Silent sites are substantially more strongly biased towards A and T than nonsynonymous sites, consistent with the extreme mutation bias towards A+T. Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of the mitochondrial genome of Drosophila.

Inbreeding and reproductive investment in the ant Formica exsecta.

In social animals, inbreeding depression may manifest by compromising care or resources individuals receive from inbred group members. We studied the effects of worker inbreeding on colony productivity and investment in the ant Formica exsecta. The production of biomass decreased with increasing inbreeding, as did biomass produced per worker. Inbred colonies produced fewer gynes (unmated reproductive females), whereas the numbers of males remained unchanged. As a result, sex ratios showed increased male bias, and the fraction of workers increased among the diploid brood. Males raised in inbred colonies were smaller, whereas the weight of gynes remained unchanged. The results probably reflect a trade-off between number and quality of offspring, which is expected if the reproductive success of gynes is more dependent on their weight or condition than it is for males. As males are haploid (with the exception of abnormal diploid males produced in very low frequencies in this population), and therefore cannot be inbred themselves, the effect on their size must be mediated through the workers of the colony. We suggest the effects are caused by the inbred workers being less proficient in feeding the growing larvae. This represents a new kind of social inbreeding depression that may affect sex ratios as well as caste fate in social insects.