Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.

尽管类群辐射演化拥有极其丰富的表型变异，但当遗传变化与快速的物种多样化速率不相匹配时，其系统发育关系往往难以解析。古多倍体赋予的基因组潜力，以及适应、随机漂变和杂交在遗传变异分配中的相对作用，仍是尚未被充分阐明的关键因素。本研究以全球物种最为丰富的木本植物属——蒲桃属（Syzygium）作为类群辐射演化的模式类群，对上述问题展开探讨。本研究以海苹果（Syzygium grande）的染色体级参考基因组为参照，对182个明确物种及58个未鉴定类群的基因组进行比较分析。结果显示，尽管蒲桃属与其他桃金娘目（Myrtales）类群共享一次古老的基因组加倍事件，但未发现近期多倍化事件的显著证据。系统基因组学分析证实，蒲桃属起源于澳大利亚-新几内亚地区，并通过多轮迁移事件实现物种多样化：向东扩散至太平洋区域，向西扩散至印度与非洲区域，其物种形成爆发事件在系统发育树上表现为分辨率较低的分支。此外，部分亚支系展现出与成种事件相契合的基因组梯度特征，表明作为中性过程的逐步地理成种在蒲桃属的物种多样化进程中发挥了重要作用。

搜集汇总

背景与挑战

背景概述

该数据集提供了对世界上最大的树属Syzygium快速物种形成的基因组学见解，包括182个物种和58个未分类类群的基因组数据，并与参考基因组Syzygium grande进行比较。研究揭示了Syzygium起源于澳大利亚-新几内亚地区，并通过多次迁移事件进行多样化，其中快速物种形成事件表现为系统发育树上的分支分辨率较低。数据集包含基因组、形态学和生物地理学相关文件，总大小约为389.78 MB，支持对物种辐射、古多倍体事件和地理分布模式的分析。