The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.

Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.

We estimated mutational variance-covariance matrices, M, for wing shape and size in two genotypes of Drosophila melanogaster after 192 generations of mutation accumulation. We characterized 21 potentially independent aspects of wing shape and size using geometric morphometrics, and analyzed the data using a likelihood-based factor-analytic approach. We implement a previously unused analysis that describes those directions with the greatest difference in evolvability between pairs of matrices. There are significant mutational effects on 19 of 21 possible aspects of wing form, consistent with the high dimensionality of standing genetic variation for wing shape previously identified in D. melanogaster. Mutations have partially recessive effects, consistent with average dominance around 0.25. Sex-specific matrices are relatively similar, although male-specific matrices are slightly larger, as expected due to dosage compensation on the X chromosome. Genotype-specific matrices are quite different. Matrices may differ both because of sampling error based on small samples of mutations with large phenotypic effects, and because of the mutational properties of the genotypes. Genotypic differences are likely to be involved, as the two genotypes have different molecular mutation rates and properties.

Although theory indicates that indirect genetic benefits through mate choice should be widespread, empirical work has often either failed to detect the operation of such benefits or shown a net cost to the presence of sexual selection. We tested whether sexual selection can increase the speed with which a conditionally deleterious allele is removed from a laboratory population of Drosophila melanogaster. The alcohol dehydrogenase null allele (Adh-) confers slightly lower viability than wild-type alleles in the absence of ethanol but is lethal in homozygotes when ethanol comprises 6% of the medium. We tracked the frequency of this allele in artificially constructed populations reared at three different levels of ethanol (0%, 2%, and 4%) that either experienced sexual selection or did not. Loss of the deleterious Adh-allele was more rapid when sexual selection was allowed to act, especially in the presence of ethanol. We also quantified the strength of both nonsexual and sexual selection against the Adh-allele using maximum-likelihood estimation. In contrast to recent experiments employing monogamy/polygamy designs, our results demonstrate a fitness benefit to sexual selection. This is consistent with the operation of good-genes female choice.