The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies.
The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies.
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第一组用于鸟类系统发育和群体遗传学研究的通用核蛋白编码位点标记
DOI：
10.1038/s41598-018-33646-x
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发表时间：
2018-10-24
影响因子：
4.6
通讯作者：
Li SH
中科院分区：
文献类型：
--
作者：
Liu Y;Liu S;Yeh CF;Zhang N;Chen G;Que P;Dong L;Li SH
多个核标记为分子系统学和群体遗传学研究提供遗传多态性数据。基于合并的分析尤其需要它们，可用于准确估计物种树并推断种群人口统计历史。然而，在鸟类进化研究中，这些基于聚结的强大方法因缺乏足够数量的标记而受到阻碍。在这项研究中，我们设计了 PCR 引物，通过扫描已发表的红原鸡 (Gallus gallus) 和斑马雀 (Taeniopygia guttata) 基因组来扩增 136 个核蛋白编码位点 (NPCL)。为了测试它们的实用性，我们在代表 23 个鸟纲的 41 种鸟类中扩增了这些基因座。基于高 PCR 成功率，选择了 63 个表现最好的 NPCL，它们具有不同的突变率，并且均匀分布在 17 条禽类常染色体和 Z 染色体上。为了测试这些标记的系统发育解析能力，我们使用源自 48 个鸟类全基因组的 63 个串联 NPCL 标记进行了新鸟类系统发育分析。由此产生的系统发育拓扑在很大程度上与之前的全基因组数据解析的结果一致。为了测试这些标记的种内多态性水平，我们检查了肯特鸻 (Charadrius alexandrinus) 四个种群在随机选择的 17 个 NPCL 标记上的遗传多样性。我们的结果表明，这些 NPCL 标记表现出与线粒体基因座相当的多态性水平。因此，这套泛鸟类核蛋白编码位点具有促进鸟类系统发育和群体遗传学研究的巨大潜力。
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
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影响因子：
10.7
作者：
Drummond, Alexei J.;Suchard, Marc A.;Rambaut, Andrew
通讯作者：
Rambaut, Andrew
影响因子：
3.5
作者：
Chojnowski, Jena L.;Kimball, Rebecca T.;Braun, Edward L.
通讯作者：
Braun, Edward L.
DOI：
10.1073/pnas.032662799
发表时间：
2002-02-05
影响因子：
11.1
作者：
Bapteste, E;Brinkmann, H;Philippe, H
通讯作者：
Philippe, H
影响因子：
4.1
作者：
Ericson, Per G. P.;Zuccon, Dario;Prum, Richard O.
通讯作者：
Prum, Richard O.
DOI：
10.2307/2412923
发表时间：
1978-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FELSENSTEIN, J
通讯作者：
FELSENSTEIN, J