Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.
Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA.
Glob Chang Biol. 2021 Jan;27(1):50-70. doi: 10.1111/gcb.15405. Epub 2020 Nov 4.
Avoiding extinction in a rapidly changing environment often relies on a species' ability to quickly adapt in the face of extreme selective pressures. In Panamá, 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 Panamá, 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 Panamá, 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.
在快速变化的环境中避免灭绝通常依赖于物种在面对极端选择压力时快速适应的能力。在巴拿马，两种密切相关的小丑蛙（Atelopus varius 和 Atelopus zeteki）由于真菌病原体蛙壶菌（Batrachochytrium dendrobatidis，Bd）而面临灭绝的威胁。曾经被认为几乎从巴拿马灭绝的 A. varius 最近在其历史分布范围内的多个地点被重新发现；然而，A. zeteki 可能在野外已经灭绝。利用在巴拿马 Bd 爆发前后收集的 186 个 Atelopus 组织样本的独特集合，我们描述了这些濒临灭绝物种的持续生存的遗传学。我们对转录组进行了测序，并开发了外显子组捕获测定法来对 Atelopus 基因组的编码区域进行测序。使用这些遗传数据，我们评估了历史 A. varius 和 A. zeteki 种群的种群遗传结构，描述了随时间变化的遗传多样性变化，评估了当代和历史个体之间的关系，并检验了一些 A. varius 种群已经迅速进化以抵抗或耐受 Bd 感染的假设。我们发现，当代（与历史相比）A. varius 种群的遗传多样性显著降低。我们没有发现强烈的定向等位基因频率变化或对 Bd 抗性基因选择的证据，但我们发现了一组候选基因，值得进一步研究。此外，我们在巴拿马最大的一个持续存在的 A. varius 种群中发现了最近迁移和基因流动的初步证据，这表明该系统中可能存在遗传拯救的潜力。最后，我们提出，以前的保护单位应该进行修改，因为在当地种群水平之外不存在明显的遗传断裂。我们的数据为遗传信息丰富的保护奠定了基础，并提高了我们对受威胁物种如何从灭绝中拯救的理解。
