Lu Chia-Wei, Yao Cheng-Te, Hung Chih-Ming
Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan.
Mol Ecol. 2022 Feb;31(3):752-766. doi: 10.1111/mec.16277. Epub 2021 Nov 25.
Domesticated species are valuable models to examine phenotypic evolution, and knowledge on domestication history is critical for understanding the trajectories of evolutionary changes. Sequentially Markov Coalescent models are often used to infer domestication history. However, domestication practices may obscure the signal left by population history, affecting demographic inference. Here we assembled the genomes of a recently domesticated species-the society finch-and its parent species-the white-rumped munia-to examine its domestication history. We applied genomic analyses to two society finch breeds and white-rumped munias to test whether domestication of the former resulted from inbreeding or hybridization. The society finch showed longer and more runs of homozygosity and lower genomic heterozygosity than the white-rumped munia, supporting an inbreeding origin in the former. Blocks of white-rumped munia and other ancestry in society finch genomes showed similar genetic distance between the two taxa, inconsistent with the hybridization origin hypothesis. We then applied two Sequentially Markov Coalescent models-psmc and smc++-to infer the demographic histories of both. Surprisingly, the two models did not reveal a recent population bottleneck, but instead the psmc model showed a specious, dramatic population increase in the society finch. Subsequently, we used simulated genomes based on an array of demographic scenarios to demonstrate that recent inbreeding, not hybridization, caused the distorted psmc population trajectory. Such analyses could have misled our understanding of the domestication process. Our findings stress caution when interpreting the histories of recently domesticated species inferred by psmc, arguing that these histories require multiple analyses to validate.
驯化物种是研究表型进化的宝贵模型，而驯化历史的知识对于理解进化变化的轨迹至关重要。顺序马尔可夫合并模型常用于推断驯化历史。然而，驯化实践可能会掩盖种群历史留下的信号，影响人口统计学推断。在这里，我们组装了一种最近被驯化的物种——梅花雀——及其亲本物种——白腰文鸟——的基因组，以研究其驯化历史。我们对两个梅花雀品种和白腰文鸟进行了基因组分析，以测试前者的驯化是否源于近亲繁殖或杂交。与白腰文鸟相比，梅花雀显示出更长且更多的纯合子片段以及更低的基因组杂合度，支持前者源于近亲繁殖。梅花雀基因组中白腰文鸟和其他祖先的片段在两个分类群之间显示出相似的遗传距离，这与杂交起源假说不一致。然后，我们应用了两个顺序马尔可夫合并模型——psmc和smc++——来推断两者的种群历史。令人惊讶的是，这两个模型并没有揭示近期的种群瓶颈，相反，psmc模型显示梅花雀种群出现了看似急剧的增长。随后，我们基于一系列人口统计学情景使用模拟基因组来证明，近期的近亲繁殖而非杂交导致了psmc种群轨迹的扭曲。这样的分析可能会误导我们对驯化过程的理解。我们的研究结果强调，在解释由psmc推断出的近期驯化物种的历史时要谨慎，认为这些历史需要多次分析来验证。
