PDF(Pubmed)
Abstract：
It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3 to 3.4 × 10-4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (Lates calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction.
摘要：
众所周知，尽管一些濒危物种的有效种群规模很小，遗传多态性水平也很低，但它们已经持续了数千年。为了了解受威胁物种长期持续存在的遗传机制，我们确定了阿卡梅（Latesjaponicus）的全基因组序列，它以极低的遗传变异存活了很长时间。阿卡梅的全基因组杂合度估计为3.3-3.4×10-4/bp，硬骨鱼中最小的值之一。对人口历史的分析表明，从30,000年前到最近的过去，阿卡梅的有效人口规模约为1,000。阿卡梅中非同义与同义杂合性的相对较高比率表明遗传负荷增加。然而,对Akame基因组遗传多样性的详细分析表明，多个基因组区域，包括参与免疫的基因，突触发育，和嗅觉系统，保留了相对较高的核苷酸多态性。这意味着Akame基因组通过平衡选择保留了功能性遗传变异，以避免生存能力的降低和适应潜力的丧失。对同义和非同义核苷酸取代率的分析已在许多akame基因中发现了正选择的迹象，表明在阿卡梅及其近亲物种形成后，温带水域的适应性进化，barramundi(L.calcarifer）。我们的结果表明，功能性遗传多样性可能通过避免种群规模减少的有害影响而导致该物种的长期持续存在。
