Seychelles paradise flycatcher (Terpsiphone corvina) genome sequencing

High genetic diversity is often a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the IUCN Red List in 2020. By comparing historical, pre-bottleneck (130+ years old), and modern genomes, we uncovered a 10-fold loss of genetic diversity. We show that the proportion of severely deleterious mutations has reduced in modern individuals, but mildly deleterious mutations have remained unchanged. Computer simulations suggest that the Seychelles paradise flycatcher avoided extinction and recovered due to its long-term small Ne. However, we also show that the chronically small Ne and the severe bottleneck resulted in very low genetic diversity in the modern population. This is likely to reduce the species adaptive potential when faced with environmental change, compromising its long-term population viability.

高遗传多样性通常是预测种群长期存续能力的可靠指标，但部分物种即便遗传多样性水平较低，仍得以存续繁衍。本研究聚焦塞舌尔寿带鸟（Terpsiphone corvina）的基因组退化过程——该物种种群在20世纪60年代锐减至28只个体，险些走向灭绝。该物种未受人工干预便自行恢复至1990年代的250余只个体，并于2020年在世界自然保护联盟（IUCN）红色名录中从极危（Critically Endangered）等级下调至易危（Vulnerable）等级。通过对比瓶颈期前（距今130余年）的历史基因组与现代基因组，本研究发现种群遗传多样性下降了一个数量级。研究显示，现代个体中严重有害突变的占比有所降低，但轻度有害突变的占比未发生明显变化。计算机模拟结果表明，塞舌尔寿带鸟得以避免灭绝并实现种群恢复，得益于其长期维持的较小有效种群大小（Ne）。但本研究同时发现，长期偏小的有效种群大小与严重的种群瓶颈事件，导致现代种群的遗传多样性处于极低水平。这或会降低该物种应对环境变化的适应潜力，进而损害其长期种群存续能力。