Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes.
Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes.
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DOI：
10.1093/molbev/msac248
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发表时间：
2022-12-05
影响因子：
10.7
通讯作者：
Long, Anthony D.
中科院分区：
文献类型：
--
作者：
Linder, Robert A.;Zabanavar, Behzad;Majumder, Arundhati;Hoang, Hannah Chiao-Shyan;Delgado, Vanessa Genesaret;Tran, Ryan;La, Vy Thoai;Leemans, Simon William;Long, Anthony D.
我们进行了200代的进化和重测序（E&R）实验，从远交二倍体重组18路合成基础群体开始。重复群体以大的有效群体规模（>105个个体）进化，在12周的进化中暴露于几种不同的化学挑战，并对全基因组进行重新测序。每周一次的强迫异交导致相邻基因间每细胞分裂的平均重组率为0.0008。尽管我们试图强迫每周做爱，但大约有一半的人进化成了骗子，而且似乎是无性进化的。专注于7种化学应激源和55个保持性的进化种群，我们观察到了大的适应性增益和高度可重复的全基因组单倍型变化模式，在化学挑战中，化学处理的可重复性水平有限。适应似乎是高度多基因的，几乎整个基因组显示出显着的和一致的模式的单倍型变化，很少有证据表明，在一个子集的人口，我们测序的单倍体克隆的长距离连锁不平衡。也就是说，几乎整个基因组都在选择或起草与选定的网站。在任何给定的基因座适应几乎总是占主导地位的18个创始人的等位基因之一，该等位基因在空间上和治疗之间的变化，这表明选择主要作用于罕见的变异私有的创始人或单倍型块窝藏多个突变。
We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.
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DOI：
10.1534/g3.117.043349
发表时间：
2017-07-05
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Barghi N;Tobler R;Nolte V;Schlötterer C
通讯作者：
Schlötterer C
压力改变白色念珠菌中杂合性丧失的速率和类型。
影响因子：
6.4
作者：
Forche A;Abbey D;Pisithkul T;Weinzierl MA;Ringstrom T;Bruck D;Petersen K;Berman J
通讯作者：
Berman J
影响因子：
16.6
作者：
Gerstein, A. C.;Kuzmin, A.;Otto, S. P.
通讯作者：
Otto, S. P.
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
0.8
作者：
Akhmetov, Azat;Laurent, Jon M.;Marcotte, Edward M.
通讯作者：
Marcotte, Edward M.