A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria
A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria
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在适应结构化和非结构化种群中观察到的龟兔模式表明细菌具有崎岖的适应性景观
DOI：
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发表时间：
2015
影响因子：
11.1
通讯作者：
B. Kerr
中科院分区：
文献类型：
--
作者：
Joshua R. Nahum;P. Godfrey‐Smith;Brittany N. Harding;Joseph H. Marcus;Jared Carlson;B. Kerr
意义“适应景观”的特点基因型和健身之间的关系。随着地形变得更加崎岖，进化可能会变得更加受限。在现代进化综合过程中，对适应过程的不同看法反映了对景观地形学的不同假设，这激发了对生物系统适应性景观的经验评估。在这里，我们描述了实验种群内的进化模式如何产生有关景观地形的信息。具体而言，大肠杆菌的集合种群在不同的迁移模式下进化。我们发现细菌达到更高的健身和积累更多的突变限制迁移比无限制迁移，这是符合崎岖的地形。通过这种方式，对种群结构的实验操作可以深入了解基本的进化约束。在赖特的适应性景观的背景下，遗传上位性可以产生一个多峰或“崎岖”的地形。在非结构化群体中，预期具有选择性访问多个峰的谱系快速固定在一个峰上，该峰可能不是最高峰。另一方面，在空间结构化的群体中，有益的突变需要更长的时间才能传播。这种减速使遥远的部分人口能够半独立地探索景观。这样的群体可以同时发现多个峰，并且预期在最高发现峰处的基因型最终占主导地位。因此，结构化群体牺牲了适应的初始速度，以换取搜索的广度。就像龟兔赛跑的寓言故事一样，结构化种群（乌龟）开始时相对较慢，但最终在平均适应度上超过了非结构化种群（兔子）。相反，在缺乏上位性的单峰景观上，所有上坡路径都会收敛。考虑到这种“平滑”的地形，搜索的广度被贬低，结构化种群在平均适应度上只落后于非结构化种群（最终收敛）。因此，龟兔图案是坚固性的指标。在验证这些预测的模拟人口的耐用性是可操纵的，我们探讨平均健身大肠杆菌的集合种群。与崎岖的地形一致，我们发现了龟兔图案。此外，我们发现结构化群体积累了更多的突变，这表明遥远的峰值更高。这种方法可以用来揭开景观地形在其他系统中，我们讨论了它的应用抗生素耐药性，工程问题，赖特的平衡过程中的元素。
Significance The “adaptive landscape” characterizes the relationship between genotype and fitness. As the landscape becomes more rugged, evolution can become more constrained. During the modern evolutionary synthesis, different views about the process of adaptation reflected different assumptions about landscape topography, which motivated the empirical assessment of adaptive landscapes in biological systems. Here, we describe how evolutionary patterns within experimental populations can yield information about landscape topography. Specifically, metapopulations of Escherichia coli are evolved under different patterns of migration. We find bacteria reach higher fitness and accumulate more mutations under restricted migration than unrestricted migration, which is consistent with a rugged topography. In this way, experimental manipulation of population structure can provide insight into fundamental evolutionary constraints. In the context of Wright’s adaptive landscape, genetic epistasis can yield a multipeaked or “rugged” topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to fix rapidly on one, which may not be the highest peak. In a spatially structured population, on the other hand, beneficial mutations take longer to spread. This slowdown allows distant parts of the population to explore the landscape semiindependently. Such a population can simultaneously discover multiple peaks, and the genotype at the highest discovered peak is expected to dominate eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the fable of the tortoise and the hare, the structured population (tortoise) starts relatively slow but eventually surpasses the unstructured population (hare) in average fitness. In contrast, on single-peak landscapes that lack epistasis, all uphill paths converge. Given such “smooth” topography, breadth of search is devalued and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the tortoise–hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we explore average fitness in metapopulations of Escherichia coli. Consistent with a rugged landscape topography, we find a tortoise–hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright’s shifting balance process.
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DOI：
10.1017/s0016672300034418
发表时间：
1995-08
期刊：
Genetical research
影响因子：
--
作者：
A. Bergman;D. Goldstein;K. Holsinger;M. Feldman
通讯作者：
A. Bergman;D. Goldstein;K. Holsinger;M. Feldman
影响因子：
1.4
作者：
Weissman, Daniel B.;Desai, Michael M.;Fisher, Daniel S.;Feldman, Marcus W.
通讯作者：
Feldman, Marcus W.
DOI：
10.1007/978-1-4939-0554-6_12
发表时间：
2014
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
通讯作者：
--
细菌的补偿性突变、抗生素耐药性和适应性进化的群体遗传学。
影响因子：
3.3
作者：
Levin,BR;Perrot,V;Walker,N
通讯作者：
Walker,N