Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.
Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.
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DOI：
10.1093/molbev/msac048
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发表时间：
2022-03-02
影响因子：
10.7
通讯作者：
Obbard DJ
中科院分区：
文献类型：
--
作者：
Fields PD;McTaggart S;Reisser CMO;Haag C;Palmer WH;Little TJ;Ebert D;Obbard DJ
水蚤是一种成熟的生态和进化模式，大水蚤及其微寄生虫之间的相互作用被广泛认为是宿主-寄生虫共同进化过程的典范。像其他被充分研究的节肢动物，如黑腹果蝇和冈比亚按蚊一样，大鼠是一个小的、广泛分布的、数量丰富的物种，因此预计会显示出长期的大种群规模和高适应性蛋白质进化率。然而，与其他物种不同的是，D. magna是周期性无性生殖，生活在高度结构化的环境（池塘和湖泊）中，分散程度中等，这两种环境都预测会影响长期有效种群规模和适应性蛋白质进化。为了研究适应性蛋白固定的模式，我们从整个欧洲范围（西部古北）取样了36个D. magna克隆的完整编码基因组，以及近亲D. similis和D. lumholtzi的草图序列，作为外群。我们分析了全基因组的适应性固定模式，特别关注那些具有先验预期高固定率的基因，如那些可能介导免疫反应、RNA干扰病毒和转座因子的基因，以及那些具有强烈男性偏向性表达模式的基因。我们发现，正如预期的那样，D. magna显示出高度的多样性，而且这种多样性在种群中是高度结构化的。然而，与果蝇相比，我们发现D. magna蛋白似乎具有高比例的弱有害变异，并且没有显示出在其整个范围内普遍存在适应性固定的证据。整个基因组都是如此，假定的“军备竞赛”基因在其他物种中也经常表现出更高水平的适应性替代。除了广泛的、先前有文献记载的局部适应可能产生的影响外，我们推测这些发现可能反映了与周期性无性繁殖相关的选择效率降低。
Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.
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影响因子：
13.8
作者：
Czech B;Hannon GJ
通讯作者：
Hannon GJ
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
DOI：
10.1126/science.1197761
发表时间：
2011-02-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Colbourne JK;Pfrender ME;Gilbert D;Thomas WK;Tucker A;Oakley TH;Tokishita S;Aerts A;Arnold GJ;Basu MK;Bauer DJ;Cáceres CE;Carmel L;Casola C;Choi JH;Detter JC;Dong Q;Dusheyko S;Eads BD;Fröhlich T;Geiler-Samerotte KA;Gerlach D;Hatcher P;Jogdeo S;Krijgsveld J;Kriventseva EV;Kültz D;Laforsch C;Lindquist E;Lopez J;Manak JR;Muller J;Pangilinan J;Patwardhan RP;Pitluck S;Pritham EJ;Rechtsteiner A;Rho M;Rogozin IB;Sakarya O;Salamov A;Schaack S;Shapiro H;Shiga Y;Skalitzky C;Smith Z;Souvorov A;Sung W;Tang Z;Tsuchiya D;Tu H;Vos H;Wang M;Wolf YI;Yamagata H;Yamada T;Ye Y;Shaw JR;Andrews J;Crease TJ;Tang H;Lucas SM;Robertson HM;Bork P;Koonin EV;Zdobnov EM;Grigoriev IV;Lynch M;Boore JL
通讯作者：
Boore JL
影响因子：
10.7
作者：
Castellano, David;Coronado-Zamora, Marta;Eyre-Walker, Adam
通讯作者：
Eyre-Walker, Adam
影响因子：
1.8
作者：
Downing, Tim;Cormican, Paul;Lloyd, Andrew T
通讯作者：
Lloyd, Andrew T