基于高速双倍自助法对蒙古马系统发育树的研究

doi:10.11843/j.issn.0366-6964.2018.09.007

畜牧兽医学报 ›› 2018, Vol. 49 ›› Issue (9): 1861-1869.doi: 10.11843/j.issn.0366-6964.2018.09.007

基于高速双倍自助法对蒙古马系统发育树的研究

任爱珍¹, 白东义², 赵一萍², 侯娜¹, 芒来^2*

1. 内蒙古农业大学理学院, 呼和浩特 010018;
2. 内蒙古农业大学动物科学学院内蒙古自治区蒙古马遗传资源保护及马产业工程实验室, 呼和浩特 010018

收稿日期:2018-01-22 出版日期:2018-09-23 发布日期:2018-09-23
通讯作者: 芒来,博导,教授,主要从事马属动物遗传育种与繁殖研究,E-mail:dmanglai@163.com
作者简介:任爱珍(1974-),女,蒙古族,内蒙古呼和浩特人,博士,副教授,主要从事统计模型信赖度研究及其应用,Tel:0471-4306727,E-mail:1620594116@qq.com
基金资助:
内蒙古农业大学博士科研启动基金（BJ2014-14）；内蒙古自治区自然科学基金（2017ZD06；2018MS01006）；内蒙古自治区科学技术厅项目（201603002）；国家自然科学基金（31472070）

Phylogenetic Tree Analysis of Mongolian Horses Using the Speedy Double Bootstrap Method

REN Ai-zhen¹, BAI Dong-yi², ZHAO Yi-ping², HOU Na¹, DUGARJAVIIN Mang-lai^2*

1. College of Science, Inner Mongolia Agricultural University, Hohhot 010018, China;
2. Inner Mongolia Autonomous Region Mongolian Horse Genetic Resources Protection and Horse Industry Engineering Laboratory, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China

Received:2018-01-22 Online:2018-09-23 Published:2018-09-23

摘要/Abstract

摘要：

旨在利用高速双倍自助法研究蒙古马系统发育树的问题。本研究选用30匹蒙古马的mtDNA D-loop区碱基序列，其中包括5个蒙古马类群（巴尔虎马、三河马、乌审马、乌珠穆沁马、锡尼河马）各6匹，对其所有105个可能系统树（普氏野马作为外群，6匹）进行分析，利用生物信息学软件Mega6和PAMAL4.9，以最大似然法估计蒙古马的最大似然系统树。最后利用生物信息软件CONSEL、R3.0中的SDBP包等计算105个候补系统树的基于高速双倍自助法的可靠度（speedy double bootstrap P-value，SDBP）。结果表明，SDBP值最大的蒙古马系统树共有3个分支，巴尔虎马与乌审马合并为一个分支，具有较近的遗传关系；乌珠穆沁马与锡尼河马具有较近的遗传关系；三河马独立于其他4种蒙古马，构成一个系统发育分支。SDBP值最大的蒙古马系统树与三河马和其他4类蒙古马具有较远的预测血缘关系是一致的，同时此结果的系统树也具有最大似然值。本研究结果还表明，采用最大似然法结合SDBP值分析蒙古马的系统拓扑关系是较最大似然法结合渐近无偏（approximately unbiased，AU）值以及结合自助（bootstrap P-value，BP）值分析蒙古马系统拓扑关系更有效。同时也比非加权组平均法（unweighted pair-group method with arithmetic means，UPGMA）有效，而与邻接法（neighbor joining，NJ）得到了相近的结论。上述结果提示，我们的研究结果使蒙古马的进化理论奠定在更坚实的遗传学基础上，可推动蒙古马的进化理论进一步发展与完善。

Abstract:

The aim of this study was to analyze the phylogenetic tree of Mongolian horses using the speedy double bootstrap method. The mitochondrial DNA D-loop base sequences of 30 modern horses were used, which included 5 Mongolian horse subspecies (Baerhu, Sanhe, Wushen, Ujimqin and Xinihe horses) 6 for each subspecies and 6 Przewalski's horse as the outgroup, and all 105 possible phylogenetic trees were analyzed. Mega6 and PAMAL4.9 were used, and maximum likelihood phylogenetic tree of Mongolian horse were estimated by maximum likelihood method. Finally, the 3^rd order accurate P-value (speedy double bootstrap P-value, SDBP) of the 105 phylogenetic trees was calculated with the CONSEL, SDBP packages in R3.0. The phylogenetic tree of Mongolian horse with the largest SDBP value had 3 branches; Baerhu and Wushen horses were clustered together, Ujimqin and Xinihe horses were clustered together, and Sanhe horse formed an independent branch which was sister to all other Mongolian subspecies. The Mongolian horse phylogenetic tree with the largest SDBP value was consistent with the predicted relationship between Sanhe and the other 4 Mongolian horse subspecies, and this topological tree also had the highest likelihood value. The results of this study also showed that it was more effective to analyze the topological relationships of Mongolian horses using the maximum likelihood method combined with the SDBP value than using the maximum likelihood method combined with the approximately unbiased (AU) value and the bootstrap P-value (BP) value. Additionally, this approach was more effective than the unweighted pair-group method with arithmetic means (UPGMA), and had similar results to the neighbor joining (NJ) method. The results of this study provided robust genetic data which would produce a more complete picture of Mongolian horse evolution.

中图分类号:

S821.2

任爱珍, 白东义, 赵一萍, 侯娜, 芒来. 基于高速双倍自助法对蒙古马系统发育树的研究[J]. 畜牧兽医学报, 2018, 49(9): 1861-1869.

REN Ai-zhen, BAI Dong-yi, ZHAO Yi-ping, HOU Na, DUGARJAVIIN Mang-lai. Phylogenetic Tree Analysis of Mongolian Horses Using the Speedy Double Bootstrap Method[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(9): 1861-1869.

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基于高速双倍自助法对蒙古马系统发育树的研究

Phylogenetic Tree Analysis of Mongolian Horses Using the Speedy Double Bootstrap Method

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