The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies.
The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies.
复制标题
Arvicolinae啮齿动物的进化辐射（田鼠和诱饵）：核和线粒体DNA系统发育的相对贡献。
DOI：
10.1186/1471-2148-6-80
复制
发表时间：
2006-10-09
影响因子：
3.4
通讯作者：
Douzery, Emmanuel J. P.
中科院分区：
文献类型：
--
作者：
Galewski, Thomas;Tilak, Marie-ka;Sanchez, Sophie;Chevret, Pascale;Paradis, Emmanuel;Douzery, Emmanuel J. P.
在分子系统学中，线粒体基因和核基因通常被用于不同的目的，前者用于解决最近进化的群体之间的关系，后者用于更深层次的系统发育研究。在快速和最近的进化辐射的情况下，像细胞色素b(Cyb)这样的线粒体基因在解决系统发育关系方面往往效率低下。最好的例子之一是Arvicolinae啮齿动物(啮齿目；鼠科)，这是北半球最令人印象深刻的哺乳动物辐射，它产生了田鼠、旅鼠和麝鼠。在这里，我们比较了核标记-生长激素受体(GHR)基因外显子10-与线粒体CyB的相对贡献，以推断Arvicoline啮齿动物主要谱系之间的系统发育关系。GHR序列的分析提高了Arvicolinae系统发育的整体分辨率。我们的结果表明，高加索长爪田鼠(Prometheomys Schaposnikowi)是一种基本的腹足类，并证实了真旅鼠(Lemmus)和衣狐猴(DMicro Stonix)并不像形态学所暗示的那样密切相关。红背田鼠(Myodini)是包括水田鼠(Arvicola)、雪田鼠(Chionomys)和草甸田鼠(Microtus及其盟友)的一个分支的姐妹群。在后者中，没有恢复对Blanfordimys、Lasiopoomys、Neodon和Phaiomys的属级识别的支持，这一点从形态上来看是正确的。对分支长度、碱基组成、位点间异质性和GTR相对替换率的参数估计的比较表明，CyB序列在密码子位置之间始终表现出比GHR更大的异质性。通过分析每个密码子的位置对节点分辨率的贡献，我们发现GHR的效率明显较高是由于它们的第三个密码子位置。虽然我们关注的是跨越过去1000万年(MyR)的物种形成事件，但CyB序列显示了与核外显子相反的高度饱和的密码子位置。最后，可变长度Bootstrap预测，通过对比GHR外显子10大三到五倍的核数据进行测序，可以显著提高Arvicoline系统发育的分辨率。我们的调查提供了Arvicolinae的第一个已解析的基因树。CyB和GHR系统发育效率的比较支持了最近的断言，即核基因有助于解决最近进化的动物的关系。核外显子的优势可能在于(I)不同位点之间的异质性较低，以及(Ii)在第三密码子位置上存在信息丰富的位点，这些位点进化得足够快，可以积累突触，但足够慢，可以避免替代饱和。
Mitochondrial and nuclear genes have generally been employed for different purposes in molecular systematics, the former to resolve relationships within recently evolved groups and the latter to investigate phylogenies at a deeper level. In the case of rapid and recent evolutionary radiations, mitochondrial genes like cytochrome b (CYB) are often inefficient for resolving phylogenetic relationships. One of the best examples is illustrated by Arvicolinae rodents (Rodentia; Muridae), the most impressive mammalian radiation of the Northern Hemisphere which produced voles, lemmings and muskrats. Here, we compare the relative contribution of a nuclear marker – the exon 10 of the growth hormone receptor (GHR) gene – to the one of the mitochondrial CYB for inferring phylogenetic relationships among the major lineages of arvicoline rodents. The analysis of GHR sequences improves the overall resolution of the Arvicolinae phylogeny. Our results show that the Caucasian long-clawed vole (Prometheomys schaposnikowi) is one of the basalmost arvicolines, and confirm that true lemmings (Lemmus) and collared lemmings (Dicrostonyx) are not closely related as suggested by morphology. Red-backed voles (Myodini) are found as the sister-group of a clade encompassing water vole (Arvicola), snow vole (Chionomys), and meadow voles (Microtus and allies). Within the latter, no support is recovered for the generic recognition of Blanfordimys, Lasiopodomys, Neodon, and Phaiomys as suggested by morphology. Comparisons of parameter estimates for branch lengths, base composition, among sites rate heterogeneity, and GTR relative substitution rates indicate that CYB sequences consistently exhibit more heterogeneity among codon positions than GHR. By analyzing the contribution of each codon position to node resolution, we show that the apparent higher efficiency of GHR is due to their third positions. Although we focus on speciation events spanning the last 10 million years (Myr), CYB sequences display highly saturated codon positions contrary to the nuclear exon. Lastly, variable length bootstrap predicts a significant increase in resolution of arvicoline phylogeny through the sequencing of nuclear data in an order of magnitude three to five times greater than the size of GHR exon 10. Our survey provides a first resolved gene tree for Arvicolinae. The comparison of CYB and GHR phylogenetic efficiency supports recent assertions that nuclear genes are useful for resolving relationships of recently evolved animals. The superiority of nuclear exons may reside both in (i) less heterogeneity among sites, and (ii) the presence of highly informative sites in third codon positions, that evolve rapidly enough to accumulate synapomorphies, but slow enough to avoid substitutional saturation.
登录
查看更多内容
影响因子：
4.1
作者：
Adkins, RM;Walton, AH;Honeycutt, RL
通讯作者：
Honeycutt, RL
影响因子：
4.9
作者：
Conroy, CJ;Cook, JA
通讯作者：
Cook, JA
影响因子：
4.9
作者：
Da Silva, MNF;Patton, JL
通讯作者：
Patton, JL
影响因子：
64.8
作者：
Baker, RJ;VanDenBussche, RA;Chesser, RK
通讯作者：
Chesser, RK
影响因子：
4.1
作者：
Cook, JA;Runck, AM;Conroy, CJ
通讯作者：
Conroy, CJ