Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs
Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs
复制标题
无尾目 mtDNA 的高效测序以及青蛙系统发育和进化的线粒体基因组学探索
DOI：
10.1093/molbev/mst091
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发表时间：
2013-08-01
影响因子：
10.7
通讯作者：
Cannatella, David C.
中科院分区：
文献类型：
--
作者：
Zhang, Peng;Liang, Dan;Cannatella, David C.
无尾目（青蛙和蟾蜍）占两栖动物多样性的88%以上，但关于它们的生殖和进化的许多重要问题仍然没有解决。在这项研究中，我们开发了一种有效的方法测序无尾两栖类线粒体DNA（mtDNA）扩增线粒体基因组中的12个重叠片段，使用蛙特异性通用引物集。基于这种方法，我们产生了47个几乎完整的，新的无尾两栖类线粒体基因组，并发现了9个新的基因排列。通过结合新的数据和已发表的无尾两栖类线粒体基因组，我们组装了一个大型的线粒体基因组数据集（11，007 nt），包括90种青蛙，代表53个公认的无尾两栖类家族中的39个，以研究它们的系统发育关系和进化历史。由此产生的树强有力地支持一个并系排列的古蟾类（=nonneobatrachian）青蛙，Leiopelmatoidea分支第一，其次是Discoglossoidea，Pipoidea，Pelobatoidea。在Neobatrachia中，南非的Heleophrynidae是所有其他Neobatrachia青蛙的姐妹分类群，而Seychelles特有的Sooglossidae被恢复为Ranoidea的姐妹分类群。这些系统发育关系与许多核基因研究一致。利用两种贝叶斯松弛钟方法（MultiDivTime和BEAST）得到的年代图表明，现代蛙类（Anura）起源于早三叠世约244 Ma，新蛙类（Neobatrachia）出现于晚侏罗世约163 Ma。两个物种丰富的超科Hyloidea和Ranoidea的最初的多样化开始110和133 Ma，分别。这些时间比其他一些估计要早大约30-40 My。与核数据相比，mtDNA对深节点（>150 Ma）的时间估计是一致的，但对浅节点的估计显然更早。我们的研究表明，虽然mtDNA进化相对较快，表现得更像一个单一的位点，但它在系统发育和分化时间推断方面表现良好，将为青蛙的系统发育和进化提供重要的参考假设。
Anura (frogs and toads) constitute over 88% of living amphibian diversity but many important questions about their phylogeny and evolution remain unresolved. For this study, we developed an efficient method for sequencing anuran mitochondrial DNAs (mtDNAs) by amplifying the mitochondrial genome in 12 overlapping fragments using frog-specific universal primer sets. Based on this method, we generated 47 nearly complete, new anuran mitochondrial genomes and discovered nine novel gene arrangements. By combining the new data and published anuran mitochondrial genomes, we assembled a large mitogenomic data set (11,007 nt) including 90 frog species, representing 39 of 53 recognized anuran families, to investigate their phylogenetic relationships and evolutionary history. The resulting tree strongly supported a paraphyletic arrangement of archaeobatrachian (=nonneobatrachian) frogs, with Leiopelmatoidea branching first, followed by Discoglossoidea, Pipoidea, and Pelobatoidea. Within Neobatrachia, the South African Heleophrynidae is the sister-taxon to all other neobatrachian frogs and the Seychelles-endemic Sooglossidae is recovered as the sister-taxon to Ranoidea. These phylogenetic relationships agree with many nuclear gene studies. The chronogram derived from two Bayesian relaxed clock methods (MultiDivTime and BEAST) suggests that modern frogs (Anura) originated in the early Triassic about 244 Ma and the appearance of Neobatrachia took place in the late Jurassic about 163 Ma. The initial diversifications of two species-rich superfamilies Hyloidea and Ranoidea commenced 110 and 133 Ma, respectively. These times are older than some other estimates by approximately 30-40 My. Compared with nuclear data, mtDNA produces compatible time estimates for deep nodes (>150 Ma), but apparently older estimates for more shallow nodes. Our study shows that, although it evolves relatively rapidly and behaves much as a single locus, mtDNA performs well for both phylogenetic and divergence time inferences and will provide important reference hypotheses for the phylogeny and evolution of frogs.