From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).
From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).
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DOI：
10.1093/sysbio/syu071
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发表时间：
2015-01
影响因子：
6.5
通讯作者：
Jakobsen KS
中科院分区：
文献类型：
--
作者：
Marcussen T;Heier L;Brysting AK;Oxelman B;Jakobsen KS
在许多真核生物谱系中，异源多倍体化在物种形成事件中占有重要地位。然而，现有的系统发育和定年方法需要树形拓扑结构，无法处理含有异源多倍体的谱系的网络状系统发育关系。到目前为止，还没有明确的框架来评估相互竞争的网络拓扑结构，也很少有人尝试确定系统发育网络的日期。本文采用四步法建立了世界性被子植物堇菜属（堇菜科）的多倍体物种网络。该属包含约600种，包括最近的（新）和更古老的（中）多倍体谱系，分布在16个剖面上。首先，我们获得了来自42个物种的所有16个部分的三个低拷贝核基因和一个叶绿体区域的DNA序列。其次，我们获得了每个核基因标记的化石校准计时表。第三，我们确定了最简约的多标记基因组树及其相应的网络，在片段（而不是物种）水平上解决。重建一组多倍体的“正确”网络依赖于恢复这些多倍体中的所有同源物，即所有亚基因组。假设存在未被核基因系统发育检测到的紫堇亚基因组谱系（“幽灵亚基因组谱系”）显著减少了推断的多倍体事件的数量。我们从一组不同的同源灭绝和谱系分类解释的五种竞争情景中确定了最简约的网络拓扑，基于(i)最少可能的鬼亚基因组谱系，（ii）最少可能的多倍体化事件，以及（iii）从相关多倍体分类群的可用染色体计数推断的预期倍性最小可能的偏差。最后，我们估计了最简约网络的同倍体和多倍体物种形成时间。通过基因树节点年龄的聚结分析估计同倍体的物种形成时间。多倍体形成时间是通过比较有和没有倍性转移的谱系的分支长度和物种形成率来估计的。我们的分析认为Viola是一个古老的属（树冠年龄31 Ma），其进化史受到异源多倍体的深刻影响。16 ~ 21个异源多倍体化是解释紫堇16个主要谱系（区段）多样化的必要条件，这表明异源多倍体化在这一水平的物种形成事件中占了很高的比例——67% ~ 88%。本文提出的理论和方法方法(i)构建网络和（ii）确定网络内物种形成事件的年代，对发生异源多倍体的群体的系统发育研究具有普遍适用性。他们明确地利用迄今为止尚未开发的来自染色体计数的倍性信息来源，以帮助解决不完整序列数据阻碍网络推断的系统发育案例。重要的是，本文使用的基于聚结的方法绕过了大多数确定物种形成事件年代的技术所要求的树状进化假设。
Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the “correct” network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies (“ghost subgenome lineages”) significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage—between 67% and 88%—of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events.
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影响因子：
3.4
作者：
Cai D;Rodríguez F;Teng Y;Ané C;Bonierbale M;Mueller LA;Spooner DM
通讯作者：
Spooner DM
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
DOI：
10.1109/tcbb.2011.137
发表时间：
2012-03-01
影响因子：
4.5
作者：
Chen, Zhi-Zhong;Wang, Lusheng
通讯作者：
Wang, Lusheng
影响因子：
9.8
作者：
Dehal P;Boore JL
通讯作者：
Boore JL
影响因子：
7
作者：
Cui, Liying;Wall, P. Kerr;dePamphilis, Claude W.
通讯作者：
dePamphilis, Claude W.