Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes.

Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole. Author summary: The mode of reproductive exchange among individuals has a profound effect on genetic diversity. In self-reproducing organisms, absence of genetic interchange between individuals reduces the effective population size and increases linkage among segregating sites at different genes, leading to lower diversity than outcrossing species. Caenorhabditis nematodes offer an exceptional system for studying the genomic effects of different systems of mating. While selfing species such as C. elegans have been studied, we present the first recombination map and genome-wide landscape of polymorphism for an outcrossing member of the genus, C. remanei. We find that, similar to C. elegans, C. remanei has high recombination rates on chromosome arms and low rates in central regions. The genomic diversity landscapes of these species are qualitatively similar, with higher diversity in the regions of higher recombination. However, C. remanei exhibits tenfold greater diversity than C. elegans due to their much larger effective population size and the decreased impact of linked selection as an outcrossing species. We use evolutionary simulations to show the influence of genomic and demographic processes work on these patterns. This work illustrates how understanding complex interactions among genetics, genomics, and reproduction is fundamental to describing patterns of genetic variation within natural populations. [ABSTRACT FROM AUTHOR]