High mutational rates of large-scale duplication and deletion in Daphnia pulex

Abstract

Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10 −9 per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.

Genomic features of parthenogenetic animals

“…pulex, they were estimated to amount to approximately 10 −6 locus −1 generation −1 [27,28,70], in the amazon molly P. formosa to 10 − 8 [17]. Up to 11% of the genome of the nematode D. pachys [32] is suggested to be homozygous as a consequence of gene conversion, and studies have also argued for an important role of gene conversion for genome evolution in root-knot nematodes [37] and rotifers [18,19], although no quantitative estimates are available for these groups.…”

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

“…Given the similar estimates of the base-substitution mutation rate ( u ) derived from mutation-accumulation experiments applied to these two lineages (Keith et al 2016), and given that silent-site diversity estimates the composite quantity 4 N e u , we estimate that the TCO source population has a N e ∼ 10% of that of typical populations in the midwest US.…”

Genomic analyses of population structure reveal metabolism as a primary driver of local adaptation in Daphnia pulex

“…To infer the average effect of natural selection, we examined the mean heterozygosity estimate at sites in different functional categories ( Figure 2). The heterozygosity estimate is the highest at silent sites followed by restricted intron (internal positions 8 to 34 from both ends; Using the mutation rate estimate u = 5.69 × 10 −9 per site per generation from Keith et al (2016) and the means of the heterozygosity estimates π at silent and restricted intron sites, which we found to be essentially under neutral evolution in the analysis of one of the populations , we estimated the effective size N e of each population by equating π with 4N e u (TABLE 2). The estimated effective population sizes of the analyzed populations are relatively large and similar to each other (the mean = 640,000 with the standard error = 31,000).…”