Whole exome sequencing identifies the potential for genetic rescue in iconic and critically endangered Panamanian harlequin frogs
Whole exome sequencing identifies the potential for genetic rescue in iconic and critically endangered Panamanian harlequin frogs
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DOI：
10.1111/gcb.15405
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发表时间：
2020-11-04
影响因子：
11.6
通讯作者：
Rosenblum, Erica Bree
中科院分区：
文献类型：
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作者：
Byrne, Allison Q.;Richards-Zawacki, Corinne L.;Rosenblum, Erica Bree
在快速变化的环境中避免灭绝通常依赖于一个物种面对极端选择压力快速适应的能力。在巴拿马，两种亲缘关系密切的小丑蛙物种(Atelopus varus和Atelopus zeteki)由于真菌病原体Batrachochytrium endrobatidis(Bd)而面临灭绝的威胁。曾经被认为几乎从巴拿马灭绝的A.varus，最近在其历史范围内的多个地方被重新发现；然而，A.zeteki很可能在野外灭绝了。通过利用在巴拿马Bd爆发之前和之后收集的186个Atelopus组织样本的独特收集，我们描述了这些濒临灭绝的物种的持久性遗传学。我们对转录组进行了测序，并开发了一种外显子组捕获分析来对Atelopus基因组的编码区进行测序。利用这些遗传数据，我们评估了历史种群的遗传结构，描述了遗传多样性随时间的变化，评估了当代和历史个体之间的关系，并检验了一些种群已经快速进化来抵抗或耐受Bd感染的假设。我们发现，当代(与历史上的)变异紫云英种群的遗传多样性显著减少。我们没有发现Bd抗性基因的定向等位基因频率改变或选择的强有力证据，但我们发现了一组值得进一步研究的候选基因。此外，我们在巴拿马最大的持续种群之一中发现了最近迁徙和基因流动的初步证据，表明在这个系统中进行遗传拯救的潜力。最后，我们建议修改以前的保护单位，因为在当地种群水平上不存在明显的遗传突变。我们的数据为基因保护奠定了基础，并促进了我们对如何将濒危物种从灭绝中拯救出来的理解。
Avoiding extinction in a rapidly changing environment often relies on a species' ability to quickly adapt in the face of extreme selective pressures. In Panama, two closely related harlequin frog species (Atelopus varius and Atelopus zeteki) are threatened with extinction due to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Once thought to be nearly extirpated from Panama, A. varius have recently been rediscovered in multiple localities across their historical range; however, A. zeteki are possibly extinct in the wild. By leveraging a unique collection of 186 Atelopus tissue samples collected before and after the Bd outbreak in Panama, we describe the genetics of persistence for these species on the brink of extinction. We sequenced the transcriptome and developed an exome-capture assay to sequence the coding regions of the Atelopus genome. Using these genetic data, we evaluate the population genetic structure of historical A. varius and A. zeteki populations, describe changes in genetic diversity over time, assess the relationship between contemporary and historical individuals, and test the hypothesis that some A. varius populations have rapidly evolved to resist or tolerate Bd infection. We found a significant decrease in genetic diversity in contemporary (compared to historical) A. varius populations. We did not find strong evidence of directional allele frequency change or selection for Bd resistance genes, but we uncovered a set of candidate genes that warrant further study. Additionally, we found preliminary evidence of recent migration and gene flow in one of the largest persisting A. varius populations in Panama, suggesting the potential for genetic rescue in this system. Finally, we propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the local population level. Our data lay the groundwork for genetically informed conservation and advance our understanding of how imperiled species might be rescued from extinction.