Interspecific plastome recombination in Picea (Pinaceae) reveals ancient reticulate evolution​

Plastid sequences are a cornerstone in plant evolutionary inference and their interpretation is often guided by strong assumptions. Biparental inheritance, heteroplasmy, and sexual recombination appear rare, but detecting exceptions to these rules requires extensive taxon sampling and abundant sequence data. Utilizing advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ~35 coniferous forest trees, to test for violations of canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for plastomes generated by interspecific hybridization and sexual recombination in the clade comprising Norway spruce (P. abies) and ten other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results resolve conflicting plastid-based phylogenies reported in previous studies and strengthen the inference of reticulate evolution in Picea. Given the relatively high frequency of biparental plastid inheritance and hybridization in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

质体序列（plastid sequences）是植物演化推断研究的基石，其解析通常依赖一系列强假设。尽管双亲遗传（biparental inheritance）、异质性（heteroplasmy）与有性重组被认为较为罕见，但要检测这些规律的例外情况，需要广泛的类群采样与充足的序列数据。依托高通量测序（high-throughput sequencing）技术的发展，我们对约35种针叶林树木所属云杉属（Picea）的65份种质材料的完整质体基因组（whole plastomes）进行了分析，以验证是否存在违背经典质体基因组演化模式的情况。通过互补的假说驱动与数据驱动检验方法，我们在包含欧洲云杉（P. abies）及其余10个物种的演化支（clade）中，发现了由种间杂交（interspecific hybridization）与有性重组产生质体基因组的证据。在控制序列饱和（sequence saturation）、正选择（positive selection）以及潜在比对误差（alignment artifacts）的影响后，种间重组的支持信号依然显著。本研究解决了既往研究中基于质体序列构建的系统发育树存在的冲突问题，进一步支持云杉属存在网状演化（reticulate evolution）的推断。鉴于植物中双亲质体遗传与杂交事件的发生频率相对较高，我们认为种间质体基因组重组的分布范围可能比当前认知更为广泛，且可能是既往报道的质体系统发育树（plastid phylogenies）不一致现象的潜在成因。