Giant clams are conspicuous bivalves inhabiting Indo-Pacific reefs. Since Rosewater’s seminal paper in 1965, the number of giant clam species described or resurrected has exactly doubled. The increased number of species reported and accessibility to genetic material of rare or uncommon species therefore call for a reappraisal of the phylogenetic relationships within the Tridacninae subfamily. Here, we aim to reconstruct the evolutionary relationships among all 12 extant species by performing a comprehensive phylogenetic analysis of mitochondrial genome and nuclear 18S rRNA data from a combination of genome skimming, Sanger sequencing and previously published sequences. Comparing the mitogenomes among Tridacninae species, we report two new findings: (1) the T. crocea mitogenome length obtained here (18,266 bp) is shorter than previously known, and (2) the mitochondrial gene order in T. crocea and T. squamosa differs from the other species. Our phylogeny based on a concatenated 16-gene dataset (15 mitochondrial markers and nuclear 18S rRNA) reveals highly supported relationships within and between the three subgenera, Tridacna (Tridacna), Tridacna (Persikima) and Tridacna (Chametrachea). Overall, the inclusion of new molecular markers greatly improves the confidence and support for the subfamily’s phylogeny. The availability of this comprehensive phylogenetic dataset serves as the foremost baseline of Tridacninae relationships to support future studies examining giant clam systematics, ecology and conservation.

蛤lam是居住在印度太平洋礁石上的显眼双壳类动物。自1965年罗斯沃特（Rosewater）发表开创性的论文以来，描述或复活的巨型蛤species种类的数量就已经增加了一倍。报告的物种数量增加，稀有或罕见物种获得遗传材料的机会增加，因此需要重新评估Tridacninae亚科内的系统发育关系。在这里，我们旨在通过对脱氧核糖核酸，Sanger测序和先前发表的序列相结合的线粒体基因组和18S rRNA核数据进行全面的系统发育分析，从而重建所有12种现存物种之间的进化关系。比较旋毛虫科中的有丝分裂基因组，我们报告了两个新发现：（1）T。番红花此处获得的有丝分裂基因组长度（18,266 bp）比以前已知的短，并且（2）T中的线粒体基因顺序。大黄鱼和Ť。鳞片不同于其他物种。我们基于串联的16个基因数据集（15个线粒体标记和18S rRNA核）的系统发育研究揭示了Tridacna（Tridacna），Tridacna（Persikima）和Tridacna（Chametrachea）这三个亚属之间以及它们之间的高度支持的关系。）。总体而言，包含新的分子标记可大大提高对亚科系统发育的信心和支持。这个综合的系统发育数据集的可用性是三角龙科关系的最基本的基线，以支持未来研究巨型蛤的系统性，生态学和保护性的研究。