Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes.
Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes.
复制标题
DOI：
10.1186/1741-7007-2-3
复制
发表时间：
2004-03-11
期刊：
影响因子：
5.4
通讯作者：
Miyata T
中科院分区：
文献类型：
--
作者：
Kikugawa K;Katoh K;Kuraku S;Sakurai H;Ishida O;Iwabe N;Miyata T
基于线粒体序列的有颌类脊椎动物系统发育分析往往导致混乱的推论，这显然与公认的树不一致。特别是在Rasmussen和Arnason基于线粒体树的假设中，软骨鱼类在硬骨鱼的并系群中具有终端位置。以前没有基于核DNA编码基因的分析可以显着拒绝有颌脊椎动物的线粒体树。我们已经从13种脊椎动物中克隆并测序了7个核DNA编码基因。这些序列，连同从数据库中获得的序列，包括来自8个主要群体（软骨鱼类，bichir，chondrosteans，加尔，弓鳍，硬骨鱼，肺鱼和四足动物）和外群（圆口鱼和文昌鱼）的13种有颌脊椎动物，已进行系统发育分析的基础上的最大似然法。软骨鱼类被推断为其他有颌脊椎动物的基础，这与普遍接受的观点一致。最大似然树与不支持软骨鱼类基底位置的树之间的最小对数似然差为18.3 ± 13.1。Rasmussen和Arnason的假设被显著拒绝，最小对数似然差为123 ± 23.3。我们的树还表明，活的全骨类，包括弓鳍鱼和雀鳝，形成一个单系群，这是硬骨鱼的姐妹群。这与以前流行的脊椎动物分类观点一致，尽管与目前基于形态学和基于线粒体序列的树不一致。此外，bichir已被证明是基底鳍鱼。四足动物和肺鱼已经形成了一个单系集群的树推断从串联对齐，与目前流行的观点一致。也有可能四足动物与鳍鱼的关系比肺鱼更密切。
Phylogenetic analyses of jawed vertebrates based on mitochondrial sequences often result in confusing inferences which are obviously inconsistent with generally accepted trees. In particular, in a hypothesis by Rasmussen and Arnason based on mitochondrial trees, cartilaginous fishes have a terminal position in a paraphyletic cluster of bony fishes. No previous analysis based on nuclear DNA-coded genes could significantly reject the mitochondrial trees of jawed vertebrates. We have cloned and sequenced seven nuclear DNA-coded genes from 13 vertebrate species. These sequences, together with sequences available from databases including 13 jawed vertebrates from eight major groups (cartilaginous fishes, bichir, chondrosteans, gar, bowfin, teleost fishes, lungfishes and tetrapods) and an outgroup (a cyclostome and a lancelet), have been subjected to phylogenetic analyses based on the maximum likelihood method. Cartilaginous fishes have been inferred to be basal to other jawed vertebrates, which is consistent with the generally accepted view. The minimum log-likelihood difference between the maximum likelihood tree and trees not supporting the basal position of cartilaginous fishes is 18.3 ± 13.1. The hypothesis by Rasmussen and Arnason has been significantly rejected with the minimum log-likelihood difference of 123 ± 23.3. Our tree has also shown that living holosteans, comprising bowfin and gar, form a monophyletic group which is the sister group to teleost fishes. This is consistent with a formerly prevalent view of vertebrate classification, although inconsistent with both of the current morphology-based and mitochondrial sequence-based trees. Furthermore, the bichir has been shown to be the basal ray-finned fish. Tetrapods and lungfish have formed a monophyletic cluster in the tree inferred from the concatenated alignment, being consistent with the currently prevalent view. It also remains possible that tetrapods are more closely related to ray-finned fishes than to lungfishes.
登录
查看更多内容
DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
2.5
作者：
Arnason, U;Gullberg, A;Janke, A
通讯作者：
Janke, A
影响因子：
64.8
作者：
GORR, T;KLEINSCHMIDT, T;FRICKE, H
通讯作者：
FRICKE, H
DOI：
10.1266/jjg.70.687
发表时间：
1995-12-01
期刊：
JAPANESE JOURNAL OF GENETICS
影响因子：
--
作者：
Iwabe, N;Kuma, K;Miyata, T
通讯作者：
Miyata, T
影响因子：
3.9
作者：
Nikoh, N;Iwabe, N;Miyata, T
通讯作者：
Miyata, T