Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta
Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta
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DOI：
10.1111/mec.13417
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发表时间：
2015-11-01
影响因子：
4.9
通讯作者：
Taylor, John W.
中科院分区：
文献类型：
--
作者：
Gladieux, Pierre;Wilson, Benjamin A.;Taylor, John W.
划定微生物种群，发现生态相关的表型和识别迁移者，杂交种或混合个体长期以来一直被证明是非常困难的，从而限制了我们对微生物物种多样化过程中起作用的进化力量的理解。然而，最近的进展，在测序和计算方法，使一个公正的方法，即初期物种和物种形成的遗传相关性，可以通过检查模式的基因组变异内和之间的谱系。在这里，我们提出了一个种群基因组研究的一个系统发育的物种在离散脉孢菌物种复杂的，基于全基因组（类似于37 Mb）的重测序的52个真菌菌株从9个网站在三大洲。人口结构分析显示，在东南亚有两个不同的谱系，在北美/欧洲有三个谱系，具有广泛的纵向和横向范围，谱系之间的混合有限。基因组扫描的选择性扫描和比较的多样性和重组的基因组景观提供了没有支持的作用，选择在基因组异质性的连锁位点之间的分歧谱系。然而，人口统计学推断表明，所观察到的基因组异质性的分歧是由不同的基因流的谱系之间经过一段时间的隔离。已经发现了许多假定的情况下，遗传多样性不同的真菌谱系之间的遗传物质交换，我们的工作突出了数量的重要性，更密切相关的类群之间的遗传交换真菌基因组的进化。我们的研究还支持了异域隔离作为腐殖微生物多样化驱动因素的作用。
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (similar to 37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.