Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

Premise
Bryophytes, land plants defined by a free-living gametophyte and an unbranched sporophyte, form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, highlighting extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, and the degree to which the observed homoplasy represents error or biological processes, remain poorly resolved.
Methods
Using the GoFlag probe set, we sampled 405 exons representing 228 nuclear genes for 531 species from 51 of the 53 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.
Results
The phylogeny resolves many relationship...

1. 研究背景
苔藓植物（Bryophytes）是一类以独立生活的配子体（gametophyte）和不分枝的孢子体（sporophyte）为典型特征的陆生植物，是陆生植物生物量的重要组成部分，构建了所有生物群区的生态群落。基于分子数据的推断极大地重塑了我们对角苔类（hornworts）、地钱类（liverworts）和藓类（mosses）演化历史的认知，揭示了各类性状中广泛存在的同塑性（homoplasy）以及多轮爆发式物种分化事件。然而，系统发育中关键事件的发生时间，以及观测到的同塑性究竟代表分析误差还是真实生物学过程，目前仍未得到清晰解析。
2. 研究方法
本研究采用GoFlag探针集（GoFlag probe set），对苔藓植物53个目中的51个目下的531个物种进行取样，获取了代表228个核基因（nuclear genes）的405个外显子（exons）。我们通过串联法与溯祖分析法（coalescence approaches）开展基因树分析，以此推断物种系统发育关系，评估基因冲突情况，并基于29个化石校准点（fossil calibrations）估算物种分化时间。
3. 研究结果
本研究的系统发育分析厘清了诸多类群间的亲缘关系……