Orthotrichum Hedw. s.l. and Ulota Mohr s.l. are two of the most speciose genera of the xerophytic moss family Orthotrichaceae. We reconstructed the phylogeny of these two genera using three data matrices: (i) organellar genomes and 33 taxa; (ii) six loci from three genomes and 144 taxa; and (iii) two plastid loci and 163 taxa. The present phylogeny, based on the maximum sampling of genes or taxa to date, generally confirms the new classification of Orthotrichum and Ulota, and indicated that all Ulota species, except Ulota phyllantha Brid., form a clade and three lineages comprise the cryptoporous Orthotrichum clade. We provided new morphological characters that support the present division of the two genera. Ancestral state reconstruction of stoma indicates that superficial stomata in Orthotrichum represent a plesiomorphic character and semi-immersed stomata were derived from immersed stomata. The results also suggest that immersed stomata independently arose once in Orthotrichum, whereas semi-immersed stomata probably arose more than once. Molecular dating analysis reveals that the occurrence of immersed stomata is probably related to arid environments during the early Oligocene to late Miocene, whereas the appearance of semi-immersed stomata might be associated with the mesic–xeric or semiarid environments during the middle Miocene to Pliocene. Ancestral state reconstruction of habitat indicates that the saxicolous habitat is apomorphic and independently evolved multiple times in Orthotrichum and Ulota, which supports the former hypothesis. Considering morphological statistics, the development of the cryptopore in Orthotrichum could provide increased resilience to dry habitats, and might promote their habitat shift during evolution.

中文翻译：

---

Orthotrichum sl 和 Ulota sl（Orthotrichaceae, Bryophyta）的系统发育：气孔进化的见解

Orthotrichum Hedw。sl 和Ulota Mohr sl 是旱生苔藓科 Orthotrichaceae 中最特殊的两个属。我们使用三个数据矩阵重建了这两个属的系统发育：（i）细胞器基因组和 33 个分类群；(ii) 来自三个基因组和 144 个分类群的六个基因座；(iii) 两个质体基因座和 163 个分类群。目前的系统发育，基于迄今为止对基因或分类群的最大采样，普遍证实了Orthotrichum和Ulota的新分类，并表明除Ulota phyllantha Brid. 之外的所有Ulota物种形成一个进化枝，三个谱系包括隐孔Orthotrichum进化枝。我们提供了新的形态特征来支持目前两个属的划分。气孔的祖先状态重建表明，Orthotrichum的浅表气孔代表了拟形特征，半浸入式气孔来源于浸入式气孔。结果还表明，浸没的气孔曾经在Orthotrichum中独立出现过一次。，而半浸式气孔可能不止一次出现。分子测年分析表明，沉水气孔的出现可能与早渐新世至晚中新世的干旱环境有关，而半沉水气孔的出现可能与中新世中期至上新世的中干或半干旱环境有关。栖息地的祖先状态重建表明，在Orthotrichum和Ulota中，saxicolous栖息地是无形的并且独立地多次进化，这支持了前一种假设。考虑到形态统计，Orthotrichum隐孔的发育可以提高对干旱栖息地的恢复力，并可能促进它们在进化过程中的栖息地转变。