Arcidae is a diverse group of ark shells with over 260 described species. The phylogenetic relationships and the evolution of the mitochondrial genomes in this family were poorly understood. Comparisons of mitogenomes have been widely used to explore the phylogenetic relationship among animal taxa. We described the complete mitogenomes of Arca navicularis, Scapharca gubernaculum and one nearly complete mitogenome of Anadara consociata. The mitogenome of A. navicularis (18,103 bp) is currently the smallest known Arcidae mitogenome, while the mitogenomes of S. gubernaculum (45,697 bp) and A. consociata (44,034 bp) are relatively large. The mitochondrial gene orders of the three taxa were substantially different from each other, as well as the patterns found in other ark shells. The relationships among Arcidae species recovered from different mitochondrial characters (nucleotide sequence versus gene order) were in disagreement. The phylogeny based on nucleotide sequences did not support the monophyly of Arcidae, as Cucullaea labiata (Cucullaeidae) appeared as a subgroup within Arcinae, rather than sister group to the family Arcidae. In addition, we presented the first time-calibrated evolutionary tree of Arcidae based on mitochondrial DNA (mtDNA) sequences, which placed the deepest divergence within Arcidae at 342.36 million years ago (Mya), around the Carboniferous (360–300 Mya).

ida科是一个由超过260种描述的物种组成的方舟贝壳类。对该家族的线粒体系统发育关系和进化了解甚少。有丝分裂基因组的比较已广泛用于探索动物类群之间的系统发育关系。我们描述了Arca navicularis，Scapharca gubernaculum的一个完整的有丝分裂基因组和Anadara consociata的一个几乎完整的有丝分裂基因组。Nav。A. navicularis（18,103 bp）的有丝分裂基因组是目前已知的最小的弧菌有丝分裂基因组，而S. gubernaculum（45,697 bp）和A. consociata的有丝分裂基因组（44034 bp）相对较大。这三个类群的线粒体基因顺序以及其他方舟壳中的模式都存在很大差异。从不同的线粒体特征（核苷酸序列与基因顺序）中恢复的Arc科物种之间的关系存在分歧。基于核苷酸序列的系统发育不支持Arcidae的单亲，因为唇形目Cucullaea labiata（Cucullaeidae）作为Arcinae的一个亚组出现，而不是Arcidae家族的姊妹组。此外，我们提出了基于线粒体DNA（mtDNA）序列的第一代经过时间校准的Arcidae进化树，该树在342,360万年前（Mya）的石炭纪（360-300 Mya）周围将Arcidae内的最深差异。