The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA.
The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA.
Am J Bot. 2018 Sep;105(9):1556-1567. doi: 10.1002/ajb2.1150. Epub 2018 Aug 29.
Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome-wide recombination.
Whole-genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single-nucleotide polymorphisms for further analyses.
We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating-type locus was found. Hindcast species distribution models and the distribution of genetic diversity support C. linearis having a larger range during the Last Glacial Maximum in the southern portion of its current extent.
Our findings contribute to the understanding of factors that shape genetic diversity in C. linearis and in fungi more broadly. Because all populations are highly genetically differentiated, the extirpation of any population would mean the loss of unique genetic diversity; therefore, our results support the continued conservation of this species.
地衣真菌在进化上具有多样性，在生态上也很重要，但人们对驱动其多样化和遗传分化的过程知之甚少。通常认为，分布完全是由生态需求决定的，而不是由扩散限制决定的。此外，尽管可以观察到无性和有性生殖结构，但由于缺乏有关重组率的信息，使得对生殖策略的推断变得困难。我们研究了北美东部阿巴拉契亚南部濒临灭绝的地衣 Cetradonia linearis 的种群基因组，以检验环境和地理距离在塑造遗传结构方面的相对贡献，并描述交配系统和全基因组重组。
进行全基因组鸟枪法测序，为 32 个 C. linearis 个体生成数据。组装了一个参考基因组，并将所有样本的读取对齐，生成了一组单核苷酸多态性，用于进一步分析。
我们发现重组率低，存在距离隔离，但不存在环境隔离的证据。鉴于只发现了一个交配型基因座，该物种被假定为单性繁殖。回溯物种分布模型和遗传多样性的分布支持 C. linearis 在其当前分布范围的南部，在末次冰期时有更大的范围。
我们的研究结果有助于了解影响 C. linearis 及其更广泛真菌遗传多样性的因素。由于所有种群的遗传分化程度都很高，因此任何种群的灭绝都意味着独特遗传多样性的丧失；因此，我们的研究结果支持继续保护该物种。
