Detecting differential copy number variation between groups of samples

Abstract

We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned on the mappability and GC-content of all reads that occur at a given base position. In this model, the read depth within a region is a mixture of binomials, which in simulations matches the read depth more closely than the often-used negative binomial distribution. The method analyzes all samples simultaneously, preserving uncertainty as to the breakpoints and magnitude of CNVs present in an individual when it identifies CNVs differentially present between the two groups. We apply this method to identify CNVs that are recurrently associated with postglacial adaptation of marine threespine stickleback () to freshwater. We identify 6664 regions of the stickleback genome, totaling 1.7 Mbp, which show consistent copy number differences between marine and freshwater populations. These deletions and duplications affect both protein-coding genes and -regulatory elements, including a noncoding intronic telencephalon enhancer of The functions of the genes near or included within the 6664 CNVs are enriched for immunity and muscle development, as well as head and limb morphology. Although freshwater stickleback have repeatedly evolved from marine populations, we show that freshwater stickleback also act as reservoirs for ancient ancestral sequences that are highly conserved among distantly related teleosts, but largely missing from marine stickleback due to recent selective sweeps in marine populations.

Adaptation via pleiotropy and linkage: Association mapping reveals a complex genetic architecture within the sticklebackEdalocus

“…S6). This region includes two indels from this study: LP3621 and Cnv770, which encode a 16 bp and a 107 bp deletion in the freshwater and marine haplotypes, respectively (Lowe et al 2018). Genetic manipulations are now underway to test whether this intronic region contains one or more enhancers active near developing lateral plates or neuromasts, and if so, to test which SNPs or indels may alter the activity of these enhancers and drive the phenotypic differences in plate number, neuromast number, and neuromast patterning.…”

“…2005; Lowe et al. 2018) (See Table S1 for details of PCR primers and genotyping assays). Fish were also genotyped for a marker in the 3′ UTR (untranslated region) of the isocitrate dehydrogenase gene ( Idh ) that distinguishes males from females (Peichel et al.…”

“…We also looked at insertions or deletions (indels) on the freshwater haplotype, as these may play an important role in phenotypic evolution (Lowe et al. 2018). The raw reads from the Jones dataset were used to confirm putative indels.…”

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

“…S8). Notably, TG-repeats are enriched in other loci that have undergone recurrent ecotypic deletions during marine-freshwater stickleback evolution (31) (table S2, fig. S9), and near DNA breakage sites in humans (fig.…”

Threespine Stickleback: A Model System For Evolutionary Genomics

“…In this example, the occurrence of a deletion at this fragile site was estimated to be approximately 10 4 times more likely than a point mutation and thus may point to a type of alternative mechanism to standing genetic variation for repeated and rapid freshwater adaptation, though a genomic survey of the general importance of this type of mutation has been hampered by difficulties in sequencing through repetitive regions (and thus is an area where future long-read sequencing may prove particularly useful). Similarly, dynamic copy number variation and movement of transposable elements may provide another pathway for repeated freshwater adaptation (31), and Lowe et al (94) found consistent differences in copy number variation between oceanic and freshwater ecotypes using the same stickleback genomes sequenced by Jones et al (84). However, the extent to which such variation actually contributes to repeated stickleback adaptation as opposed to neutrally hitchhiking on adaptive haplotypes is still uncertain.…”