Shirani Sahar, Hellweger Ferdi L
Department of Civil & Environmental Engineering, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA.
Microb Ecol. 2017 Aug;74(2):416-426. doi: 10.1007/s00248-017-0963-5. Epub 2017 Mar 16.
Molecular observations reveal substantial biogeographic patterns of cyanobacteria within systems of connected lakes. An important question is the relative role of environmental selection and neutral processes in the biogeography of these systems. Here, we quantify the effect of genetic drift and dispersal limitation by simulating individual cyanobacteria cells using an agent-based model (ABM). In the model, cells grow (divide), die, and migrate between lakes. Each cell has a full genome that is subject to neutral mutation (i.e., the growth rate is independent of the genome). The model is verified by simulating simplified lake systems, for which theoretical solutions are available. Then, it is used to simulate the biogeography of the cyanobacterium Microcystis aeruginosa in a number of real systems, including the Great Lakes, Klamath River, Yahara River, and Chattahoochee River. Model output is analyzed using standard bioinformatics tools (BLAST, MAFFT). The emergent patterns of nucleotide divergence between lakes are dynamic, including gradual increases due to accumulation of mutations and abrupt changes due to population takeovers by migrant cells (coalescence events). The model predicted nucleotide divergence is heterogeneous within systems, and for weakly connected lakes, it can be substantial. For example, Lakes Superior and Michigan are predicted to have an average genomic nucleotide divergence of 8200 bp or 0.14%. The divergence between more strongly connected lakes is much lower. Our results provide a quantitative baseline for future biogeography studies. They show that dispersal limitation can be an important factor in microbe biogeography, which is contrary to the common belief, and could affect how a system responds to environmental change.
分子观测揭示了连通湖泊系统中蓝藻的显著生物地理格局。一个重要问题是环境选择和中性过程在这些系统生物地理学中的相对作用。在这里，我们通过使用基于主体的模型（ABM）模拟单个蓝藻细胞来量化遗传漂变和扩散限制的影响。在模型中，细胞生长（分裂）、死亡并在湖泊之间迁移。每个细胞都有一个完整的基因组，该基因组会发生中性突变（即生长速率与基因组无关）。通过模拟具有理论解的简化湖泊系统对模型进行了验证。然后，它被用于模拟包括五大湖、克拉马斯河、亚哈拉河和查塔胡奇河在内的一些实际系统中铜绿微囊藻的生物地理学。使用标准生物信息学工具（BLAST、MAFFT）分析模型输出。湖泊之间核苷酸差异的出现模式是动态的，包括由于突变积累导致的逐渐增加以及由于迁移细胞的种群接管（合并事件）导致的突然变化。模型预测的核苷酸差异在系统内是异质的，对于连接较弱的湖泊，差异可能很大。例如，苏必利尔湖和密歇根湖预计平均基因组核苷酸差异为8200 bp或0.14%。连接较强的湖泊之间的差异要低得多。我们的结果为未来的生物地理学研究提供了一个定量基线。它们表明扩散限制可能是微生物生物地理学中的一个重要因素，这与普遍看法相反，并且可能影响一个系统对环境变化的响应方式。
