Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis.
Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis.
复制标题
结核分枝杆菌暴发中的多重合并遗传学。
DOI：
10.1093/molbev/msaa179
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发表时间：
2021-01-04
影响因子：
10.7
通讯作者：
Freund F
中科院分区：
文献类型：
--
作者：
Menardo F;Gagneux S;Freund F
金曼聚结及其发展通常被认为是过去几十年群体遗传学中最重要的进展之一。基于聚结理论的人口统计学推断已被用于重建几种物种的种群动态和进化历史，包括结核分枝杆菌（MTB），一种重要的人类结核病病原体。金曼聚结的一个关键假设是，不同个体的后代数量变化不大，违反这一假设可能会导致模型错误规范造成的严重偏差。由于宿主免疫系统和抗生素治疗的压力，MTB可能处于不断的选择中，MTB在从一个宿主传播到另一个宿主时经历了反复的种群瓶颈，并且3)一些宿主的传播率比平均水平高得多（超级传播者），因此预计MTB的个体谱系在繁殖成功率方面存在很大差异。在这里，我们使用近似贝叶斯计算方法来测试多重合并聚结（multiple-merger coalescents， MMC）是否是更适合研究结核分枝杆菌种群的模型。MMC是一类允许在世系之间繁殖成功率存在较大差异的模型。我们考虑了11个公开的全基因组序列数据集，这些数据集来自当地MTB人群和暴发，发现MMC与Kingman聚结法相比，在11个数据集中有10个数据集具有更好的拟合性。这些结果表明，应该重新评估分析结核分枝杆菌暴发的零模型，并且需要重新审视过去基于金曼凝聚的发现。
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
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影响因子：
64.8
作者：
Bos KI;Harkins KM;Herbig A;Coscolla M;Weber N;Comas I;Forrest SA;Bryant JM;Harris SR;Schuenemann VJ;Campbell TJ;Majander K;Wilbur AK;Guichon RA;Wolfe Steadman DL;Cook DC;Niemann S;Behr MA;Zumarraga M;Bastida R;Huson D;Nieselt K;Young D;Parkhill J;Buikstra JE;Gagneux S;Stone AC;Krause J
通讯作者：
Krause J
DOI：
10.1073/pnas.1611283113
发表时间：
2016-11-29
影响因子：
11.1
作者：
Eldholm, Vegard;Pettersson, John H. -O.;Balloux, Francois
通讯作者：
Balloux, Francois
影响因子：
16.6
作者：
Eldholm, Vegard;Monteserin, Johana;Rieux, Adrien;Lopez, Beatriz;Sobkowiak, Benjamin;Ritacco, Viviana;Balloux, Francois
通讯作者：
Balloux, Francois
影响因子：
3.9
作者：
Bainomugisa, Arnold;Lavu, Evelyn;Coin, Lachlan
通讯作者：
Coin, Lachlan
影响因子：
3.3
作者：
Der, Ricky;Epstein, Charles;Plotkin, Joshua B.
通讯作者：
Plotkin, Joshua B.