Higher systematics and evolutionary history of Protobranchia, a subclass of Bivalvia, have long been controversial due to paucity of prominent shell characters and difficulties in collecting live material for diverse taxa. Here, we evaluate the reliability of shell microstructure for protobranch higher systematics by reconstructing a molecular phylogeny of the subclass. Relationships were assessed using the nuclear (18S rRNA, 28S rRNA and histone H3) and mitochondrial (16S rRNA and cytochrome c oxidase subunit 1) gene sequences from 89 in‐group species. Maximum likelihood reconstruction with the nuclear markers recognized five superfamilies (Nuculoidea, Solemyoidea, Manzanelloidea, Nuculanoidea and Sareptoidea) as the in‐group clades of the monophyletic Protobranchia. Sareptoidea is herein redefined to comprise Sarepta and Setigloma in the sole family Sareptidae, whereas Pristigloma and its monotypic Pristiglomidae are transferred from this superfamily to Nuculanoidea, both in the order Nuculanida. Mapping of shell microstructure characters on the tree confirmed their conservativeness at superfamily level when only living species were taken into account. The Nuculoidea have shells with the outer prismatic and middle/inner nacreous structures; Solemyoidea are characterized by either the radially elongate simple prismatic structure or the reticulate structure in the outer shell layer; Manzanelloidea, Nuculanoidea and Sareptoidea have shells of homogeneous, fibrous prismatic and/or fine complex crossed lamellar structures, all of which lack large structural units. Our Bayesian time calibration, on the contrary, suggested frequent loss of nacre in the Paleozoic and Mesozoic history of Protobranchia, at least once each in Nuculoidea, Manzanelloidea, Solemyoidea and Sareptoidea in the Paleozoic, and perhaps multiple times in Nuculanoidea by the Mesozoic.

中文翻译：

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原分支双壳类的分子系统发育及其壳微结构的系统意义

由于缺乏突出的壳特征和难以为不同分类群收集活体材料，原鳃亚纲（双壳纲的一个亚纲）的高等系统学和进化史长期以来一直存在争议。在这里，我们通过重建亚类的分子系统发育来评估壳微结构对原枝高等系统学的可靠性。使用来自 89 个组内物种的核（18S rRNA、28S rRNA 和组蛋白 H3）和线粒体（16S rRNA 和细胞色素 c 氧化酶亚基 1）基因序列评估关系。使用核标记的最大似然重建将五个超科（核总科、Solemyoidea、Manzanelloidea、Nuculanoidea 和 Sareptoidea）识别为单系原鳃亚纲的群内进化枝。Sareptoidea 在本文中被重新定义为包括 Sareptidae 唯一家族中的 Sarepta 和 Setigloma，而 Pristigloma 及其单型 Pristiglomidae 则从这个超科转移到 Nuculanoidea，两者都在 Nuculanida 目中。当仅考虑活物种时，树上壳微结构特征的映射证实了它们在超科水平上的保守性。Nuculoidea 的外壳具有外棱柱形和中/内珍珠质结构；Solemyoidea 的特征是外壳层中的径向细长的简单棱柱结构或网状结构；Manzanelloidea、Nuculanoidea 和 Sareptoidea 具有均质、纤维状棱柱状和/或精细复杂交叉层状结构的壳，所有这些壳都缺乏大的结构单元。相反，我们的贝叶斯时间校准