Parham James F, Feldman Chris R, Boore Jeffrey L
Department of Evolutionary Genomics, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA.
BMC Evol Biol. 2006 Feb 7;6:11. doi: 10.1186/1471-2148-6-11.
The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.
We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles.
Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, including Platysternon.
东亚的大头龟（Platysternon megacephalum）是一个研究较少的龟类谱系（平胸龟科）中唯一现存的代表。它没有现存的近亲，其在龟类中的系统发育位置是龟类系统学中一个突出的争议点。基于对其形态和线粒体（mt）DNA的一些研究，平胸龟传统上被认为与鳄龟（鳄龟科）关系密切，然而，其他关于形态和核（nu）DNA的研究并不支持这一假设。
我们对平胸龟的完整线粒体基因组以及另外两种相关龟类的近乎完整的线粒体基因组进行了测序，并将它们与文献中的龟类线粒体基因组进行比较，以形成迄今为止用于解决该问题的最大分子数据集。由此产生的系统发育树有力地否定了平胸龟与鳄龟科的分类关系，而是表明它是曲颈龟亚目（Testudinoidea）的成员，曲颈龟亚目是一个多样的、几乎全球分布的类群，包括水龟和陆龟。我们还发现平胸龟线粒体DNA存在大规模的基因重排，并且拥有两个几乎相同的控制区，这些特征使其与所有其他研究过的龟类区分开来。
我们的研究有力地确定了平胸龟的系统发育位置，并提供了一个解析良好的主要龟类谱系轮廓，同时证明了比较大量线粒体序列比短片段具有显著更强的解析能力。早期将平胸龟与鳄龟科归为一类的系统发育研究需要化石记录中的一个时间间隔，而现在这个间隔已不再必要。平胸龟线粒体DNA的重复控制区和基因重排可能是由于基因组的部分复制以及随后冗余基因的丢失所致。虽然拥有两个控制区可能具有一些优势，这可以解释为什么控制区会保留而一些重复基因却被淘汰，但这种情况很少见。到目前为止，仅在包括平胸龟在内的12个后生动物类群的线粒体基因组中报道过重复控制区。
