Starvation-Associated Genome Restructuring Can Lead to Reproductive Isolation in Yeast

<div><p>Knowledge of the mechanisms that lead to reproductive isolation is essential for understanding population structure and speciation. While several models have been advanced to explain post-mating reproductive isolation, experimental data supporting most are indirect. Laboratory investigations of this phenomenon are typically carried out under benign conditions, which result in low rates of genetic change unlikely to initiate reproductive isolation. Previously, we described an experimental system using the yeast <i>Saccharomyces cerevisiae</i> where starvation served as a proxy to any stress that decreases reproduction and/or survivorship. We showed that novel lineages with restructured genomes quickly emerged in starved populations, and that these survivors were more fit than their ancestors when re-starved. Here we show that certain yeast lineages that survive starvation have become reproductively isolated from their ancestor. We further demonstrate that reproductive isolation arises from genomic rearrangements, whose frequency in starving yeast is several orders of magnitude greater than an unstarved control. By contrast, the frequency of point mutations is less than 2-fold greater. In a particular case, we observe that a starved lineage becomes reproductively isolated as a direct result of the stress-related accumulation of a single chromosome. We recapitulate this result by demonstrating that introducing an extra copy of one or several chromosomes into naïve, i.e. unstarved, yeast significantly diminishes their fertility. This type of reproductive barrier, whether arising spontaneously or via genetic manipulation, can be removed by making a lineage euploid for the altered chromosomes. Our model provides direct genetic evidence that reproductive isolation can arise frequently in stressed populations via genome restructuring without the precondition of geographic isolation.</p></div

Sporulation frequencies of backcrosses and self-crosses.

<p>Crosses were made using haploid derivatives of starved isolates from four starved cultures. A – unstarved diploid control. Light grey bars are self crosses, dark grey bars are backcrosses. “*” denote significant differences between the corresponding self-cross and backcross sporulation frequencies (Bonferroni-corrected (n = 17), two-tailed Fisher's exact test at 95% confidence). “‡” denotes isolate (75a) whose self-cross lost the ability to sporulate. Sporulation frequencies among unstarved isolates backcrossed to the ancestor were indistinguishable from the diploid ancestor's (data not shown).</p

The sporulation defect of starved isolate 62a and chromosome fragment-containing strains is cured by tetraploidization.

<p><b>A</b>. Light grey: sporulation frequencies of unstarved diploid control (BY4743), selfed starved isolate 62a and the unstarved BY4743 containing a Chromosome fragment of Chromosome I (CF1); dark grey: their tetraploid derivatives. <b>B</b>. Sporulation frequencies of a diploid SK1 derivative strain containing CF1 (MKCF1) and its control euploid (diploid) strain (MK2N). Error bars are 95% Wilson's binomial CI.</p

Extra chromosomes decrease (A) sporulation frequency and (B) spore viability, which are cured by tetraploidization to different extents (see text).

<p>Light grey, 2N – diploid strain and its derivatives containing one or several supernumerary chromosomes, as indicated. Dark grey, 4N – tetraploid derivatives. Error bars are 95% Wilson's binomial CI.</p

Array-Comparative Genome Hybridization of starved isolates and their shared ancestor.

<p>aCGH of the ancestral diploid BY4743, four starved isolates displaying lower fertility in backcross (61, 62, 65, 68), two starved isolates with high fertility in backcross (71, 73), and two unstarved isolates (42 and 45). Roman numerals represent chromosome numbers. Grey vertical lines separate chromosomes. Red denotes copy number increase, green copy number decrease. Genes are represented according to their position from left to right on each chromosome. Isolate 62 displays duplicated Chromosome I. The apparent subtelomeric amplifications are artifacts of DNA preparation. Note that BY4743 is a diploid strain, whereas all isolates are haploid.</p