Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes

Abstract

Deleterious mutations are of fundamental importance to all aspects of organismal biology. Evolutionary geneticists have expended tremendous effort to estimate the genome-wide rate of mutation and the effects of new mutations on fitness, but the degree to which genomic mutational properties vary within and between taxa is largely unknown, particularly in multicellular organisms. Beginning with two highly inbred strains from each of three species in the nematode family Rhabditidae (Caenorhabditis briggsae, Caenorhabditis elegans, and Oscheius myriophila), we allowed mutations to accumulate in the relative absence of natural selection for 200 generations. We document significant variation in the rate of decay of fitness because of new mutations between strains and between species. Estimates of the per-generation mutational decay of fitness were very consistent within strains between assays 100 generations apart. Rate of mutational decay in fitness was positively associated with genomic mutation rate and negatively associated with average mutational effect. These results provide unambiguous experimental evidence for substantial variation in genome-wide properties of mutation both within and between species and reinforce conclusions from previous experiments that the cumulative effects on fitness of new mutations can differ markedly among related taxa.Caenorhabditis briggsae ͉ Caenorhabditis elegans ͉ deleterious mutation ͉ mutation accumulation ͉ Oscheius myriophila F ew topics in evolutionary biology have generated as much controversy in recent years as spontaneous mutation, considered at the level of the entire genome (1-4). It is widely accepted that the great majority of new mutations are either neutral or deleterious (refs. 1 and 5-7; also see refs. 3 and 8-13), and the importance of deleterious mutations to a wide variety of biological processes and phenomena is well appreciated (7). The source of the controversy stems from uncertainty in the rate at which new mutations accrue in the genome and the distribution of effects of those mutations on fitness.Beginning in the early 1960s, Mukai, Ohnishi, and their colleagues (14-18) conducted several large mutation accumulation (MA) experiments with Drosophila melanogaster that were designed to estimate the rate and average effect of new mutations on fitness. By the early 1970s, the results seemed clear: averaged over experiments, egg-to-adult viability declined rapidly, on the order of 1% per genome per generation, with the implication that the diploid genomic mutation rate (U) was on the order of 0.6 per generation or greater and the average homozygous effect on fitness of a new mutation (2a ) was Ϸ0.05 or less. The typical newborn fly was thus expected to harbor one new mutation that could be expected to reduce its viability by Ϸ5% when homozygous.Several additional lines of evidence supported the results from the early f ly MA experiments. First, the considerable inbreeding depression in Drosophila implied either a high rate of deleterious mutation or considerable...

Analysis and implications of mutational variation

“…An ML analysis of the fitnesses of MA and control lines gave an estimate for the mean mutational effect on fitness of *20%, and suggested that the DEM for fitness is fairly platykurtic (Vassilieva et al 2000; Table 1). U was estimated to be only about 0.005 per haploid genome per generation, consistent with other spontaneous MA experiments in C. elegans (Keightley and Caballero 1997;Baer et al 2005). However, by direct DNA sequencing of samples of the genome from the MA lines, Denver et al (2004) estimated that about two mutation events per haploid genome per generation had occurred.…”

Temperature, stress and spontaneous mutation in Caenorhabditis briggsae and Caenorhabditis elegans

“…Fitness assays also follow Baer et al [11]; see electronic supplementary material, text S2. Fitness was assayed in two blocks; 30 MA lines from each strain/MA temperature were randomly selected for each block, along with ancestral controls.…”

“…The MA protocol follows Baer et al [11]; see electronic supplementary material, text S1. We initiated two sets of 192 replicate MA lines from the N2 strain of C. elegans and from the PB800 strain of C. briggsae; 96 lines were kept at 188C and 96 at 268C.…”

Abiotic stress does not magnify the deleterious effects of spontaneous mutations

“…After nematodes were visibly gravid (but before they laid eggs) they were transferred individually to fresh, seeded NGM plates and incubated at 20°C for 24 h. After the 24 h, the adult nematodes were removed, and plates were incubated another 24 h at 20°C to allow hatching. Plates were stored at 4°C until stained and counted (Baer et al, 2005) for the purposes of confirming fitness category and to confirm that the assay successfully imposed stress (by definition, 'stressful' environments decrease fitness, Martin and Lenormand, 2006). We analyzed the proportion of nematodes on a plate that survived to Day 3, the first day in which gravid adult nematodes were found on any plate.…”

“…The 10 starting stocks (generation 250) from the Matsuba et al (2012) second order MA experiment and the canonical Baer lab N2 ancestor (Baer et al, 2005) were acquired as live worms at the time that Matsuba et al conducted their fitness assay. All lines were cryopreserved using standard methods.…”