Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes
Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes
复制标题
DOI：
10.1093/evolut/qpad158
复制
发表时间：
2023-09-06
期刊：
影响因子：
3.3
通讯作者：
Katz，Laura A.
中科院分区：
文献类型：
--
作者：
Weiner，Agnes K. M.;Sehein，Taylor;Katz，Laura A.
许多微生物真核生物巨大的种群规模和广泛的生物地理分布决定了种内遗传变异水平很高的预期。然而，调查原生生物种群的研究仍然很少，主要是因为有限的组学数据。相反，到目前为止，大多数微真核生物的遗传学研究都依赖于单基因座，这可能具有误导性，而且不容易检测到重组，这是有性繁殖的标志。在这里，我们分析了来自两个变形虫种-乳突透明藻和优雅透明藻-的72个单细胞转录本中的40个基因，以评估在四年多的时间里从新英格兰沼泽收集的样本的遗传多样性。我们根据我们的多位点数据集确认了神秘物种的存在，这提供了神秘物种内部重组和高度分化的证据。与此同时，神秘物种内的遗传多样性总水平很低，这表明这些丰富的生物的有效种群规模较小，可能是由于灭绝和重新种群事件加上有效的扩散模式。这项研究是利用转录组学数据研究不可培养的异养原生生物种群遗传学的第一个研究之一，并有助于理解非模式微真核生物的神秘物种。
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited ‘omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies—Hyalosphenia papilioandHyalosphenia elegans—of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.