Predicting Environmental and Ecological Drivers of Human Population Structure.
Predicting Environmental and Ecological Drivers of Human Population Structure.
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预测人口结构的环境和生态驱动因素。
DOI：
10.1093/molbev/msad094
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发表时间：
2023-05-02
影响因子：
10.7
通讯作者：
Henn, Brenna M.
中科院分区：
文献类型：
--
作者：
Pless, Evlyn;Eckburg, Anders M.;Henn, Brenna M.
景观、气候和文化都可以构成人类种群，但现有的方法很少能同时在解释遗传模式时解开大量变量的纠缠。我们开发了一种机器学习方法，用于识别最能解释迁移率的变量，这些变量是由基于聚结器的程序MAPS测量的，该程序使用共享的相同的下降道来推断感兴趣区域的空间迁移。我们将我们的方法应用于东非30个具有高密度单核苷酸多态性阵列数据的人群。该地区种族、语言和环境的显著多样性为探索塑造移民和遗传结构的变量提供了独特的机会。我们探索了20多个空间变量与景观，气候和采采蝇的存在。完整的模型解释了过去56代中迁移率方差的40%。降水量、最冷月的最低温度和海拔是影响最大的变量。在三组采采蝇中，影响最大的是传播牲畜锥虫的褐蝇。我们还测试了埃塞俄比亚人群对高海拔的适应。我们没有发现与高海拔相关的已知基因，但我们确实发现了与代谢和疾病相关的正选择特征。我们的结论是，环境影响了东非人口的迁移和适应;剩余的结构差异可能部分是由于我们的模型中没有捕捉到的文化或其他因素。
Landscape, climate, and culture can all structure human populations, but few existing methods are designed to simultaneously disentangle among a large number of variables in explaining genetic patterns. We developed a machine learning method for identifying the variables which best explain migration rates, as measured by the coalescent-based program MAPS that uses shared identical by descent tracts to infer spatial migration across a region of interest. We applied our method to 30 human populations in eastern Africa with high-density single nucleotide polymorphism array data. The remarkable diversity of ethnicities, languages, and environments in this region offers a unique opportunity to explore the variables that shape migration and genetic structure. We explored more than 20 spatial variables relating to landscape, climate, and presence of tsetse flies. The full model explained ∼40% of the variance in migration rate over the past 56 generations. Precipitation, minimum temperature of the coldest month, and elevation were the variables with the highest impact. Among the three groups of tsetse flies, the most impactful was fusca which transmits livestock trypanosomiasis. We also tested for adaptation to high elevation among Ethiopian populations. We did not identify well-known genes related to high elevation, but we did find signatures of positive selection related to metabolism and disease. We conclude that the environment has influenced the migration and adaptation of human populations in eastern Africa; the remaining variance in structure is likely due in part to cultural or other factors not captured in our model.
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影响因子：
64.8
作者：
Gurdasani, Deepti;Carstensen, Tommy;Tekola-Ayele, Fasil;Pagani, Luca;Tachmazidou, Ioanna;Hatzikotoulas, Konstantinos;Karthikeyan, Savita;Iles, Louise;Pollard, Martin O.;Choudhury, Ananyo;Ritchie, GrahamR. S.;Xue, Yali;Asimit, Jennifer;Nsubuga, Rebecca N.;Young, Elizabeth H.;Pomilla, Cristina;Kivinen, Katja;Rockett, Kirk;Kamali, Anatoli;Doumatey, Ayo P.;Asiki, Gershim;Seeley, Janet;Sisay-Joof, Fatoumatta;Jallow, Muminatou;Tollman, Stephen;Mekonnen, Ephrem;Ekong, Rosemary;Oljira, Tamiru;Bradman, Neil;Bojang, Kalifa;Ramsay, Michele;Adeyemo, Adebowale;Bekele, Endashaw;Motala, Ayesha;Norris, Shane A.;Pirie, Fraser;Kaleebu, Pontiano;Kwiatkowski, Dominic;Tyler-Smith, Chris;Rotimi, Charles;Zeggini, Eleftheria;Sandhu, Manjinder S.
通讯作者：
Sandhu, Manjinder S.
影响因子：
2.9
作者：
Bigham, Abigail W.;Wilson, Megan J.;Shriver, Mark D.
通讯作者：
Shriver, Mark D.
影响因子：
16.6
作者：
Beyer RM;Krapp M;Eriksson A;Manica A
通讯作者：
Manica A
影响因子：
4.5
作者：
Alkorta-Aranburu G;Beall CM;Witonsky DB;Gebremedhin A;Pritchard JK;Di Rienzo A
通讯作者：
Di Rienzo A
影响因子：
3.7
作者：
Getz, Wayne M.;Fortmann-Roe, Scott;Wilmers, Christopher C.
通讯作者：
Wilmers, Christopher C.