Identification of Hidden Population Structure in Time-Scaled Phylogenies.
Identification of Hidden Population Structure in Time-Scaled Phylogenies.
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DOI：
10.1093/sysbio/syaa009
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发表时间：
2020-09-01
影响因子：
6.5
通讯作者：
Didelot X
中科院分区：
文献类型：
--
作者：
Volz EM;Carsten W;Grad YH;Frost SDW;Dennis AM;Didelot X
人口结构影响系谱模式，然而，有关人口结构的数据往往是不可用或无法直接观察。群体结构的推断在分子流行病学中非常重要，其中病原体遗传学越来越多地用于推断传播模式和检测爆发。观察到的和理想化的系谱之间的差异，如那些由合并过程产生的，可以量化，并在显着的差异发生，可能会揭示自然选择的作用，宿主种群结构，或其他人口和流行病学的异质性。我们已经开发了一个快速的非参数统计检验的时间尺度系统发育树中的隐藏的人口结构的检测。该测试是基于对比估计的cumbergenies与理论上预期的cumberdynamic订购的共同祖先在两个分支内的合并框架。这些统计测试也激发了算法的发展，该算法可用于快速筛选可能共享不同人口统计学或流行病学历史的进化枝的系统发育树。流行病学的应用包括鉴定脆弱宿主群体中的暴发或具有适应性优势的基因型的快速扩展。为了证明这些方法在爆发检测中的实用性，我们将新方法应用于从数千个HIV-1部分pol序列重建的大型同源性。这揭示了分支的存在，这些分支在最近的过去迅速增长，并显著集中在年轻男性中，表明该群体中最近和快速的传播。此外，为了证明这些方法在抗菌素耐药性研究中的实用性，我们将新方法应用于从全基因组淋病奈瑟菌序列重建的大型同源性。我们发现，使用这些方法检测到的人口结构与赋予抗菌素耐药性的突变的出现和扩展密切重叠。[抗菌素耐药性;聚结;艾滋病毒;人口结构。]
Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealized genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance. [Antimicrobial resistance; coalescent; HIV; population structure.]
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影响因子：
64.8
作者：
Lam, Tommy Tsan-Yuk;Zhou, Boping;Zhu, Huachen
通讯作者：
Zhu, Huachen
DOI：
10.1038/nrmicro.2015.13
发表时间：
2016-03
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
--
影响因子：
10.7
作者：
Mostowy R;Croucher NJ;Andam CP;Corander J;Hanage WP;Marttinen P
通讯作者：
Marttinen P
影响因子：
1.5
作者：
Dennis AM;Volz E;Frost ASMSDW;Hossain M;Poon AFY;Rebeiro PF;Vermund SH;Sterling TR;Kalish ML
通讯作者：
Kalish ML
影响因子：
1.9
作者：
NOTOHARA, M
通讯作者：
NOTOHARA, M