生物多样性 ›› 2024, Vol. 32 ›› Issue (4): 23400. DOI: 10.17520/biods.2023400 cstr: 32101.14.biods.2023400
吕燕文1,2(), 王子韵1,2(), 肖钰1,2(), 何梓晗1,2(), 吴超1,2(), 胡新生1,2,*()()
收稿日期:
2023-10-22
接受日期:
2024-02-20
出版日期:
2024-04-20
发布日期:
2024-03-28
通讯作者:
* E-mail: 基金资助:
Yanwen Lv1,2(), Ziyun Wang1,2(), Yu Xiao1,2(), Zihan He1,2(), Chao Wu1,2(), Xinsheng Hu1,2,*()()
Received:
2023-10-22
Accepted:
2024-02-20
Online:
2024-04-20
Published:
2024-03-28
Contact:
* E-mail: 摘要:
谱系分选为理解物种形成机制提供了一个途径, 常被划分为复系、并系及单系3个阶段, 对应着不同的基因树与物种树关系。本文首先系统地探讨了不同进化属性(中性和选择性)的基因组位点在祖先群体中如何传递到子代群体中的相关理论, 分析了可能的基因树与物种树关系。其次探讨了基于中性序列谱系分选分析方法, 包括在不完全谱系分选下物种树构建和系统发育网络分析。进一步探讨了选择对谱系分选的影响, 基于基因树和物种树途径检测选择的方法, 包括定向选择和平衡选择检测。最后, 探讨了植物交配系统对谱系分选的影响, 不完全谱系分选检测存在的问题以及在花粉流和种子流及不完全谱系分选的综合条件下系统发育网络分析方法, 澄清这些问题有助于深度理解植物种的谱系分选过程。
吕燕文, 王子韵, 肖钰, 何梓晗, 吴超, 胡新生 (2024) 谱系分选理论与检测方法的研究进展. 生物多样性, 32, 23400. DOI: 10.17520/biods.2023400.
Yanwen Lv, Ziyun Wang, Yu Xiao, Zihan He, Chao Wu, Xinsheng Hu (2024) Advances in lineage sorting theories and their detection methods. Biodiversity Science, 32, 23400. DOI: 10.17520/biods.2023400.
图1 两个物种的谱系分选过程: (a)复系; (b)并系; (c)单系。图中的蓝色粗线表示物种树(A和B物种), 黑色细线为物种A的等位基因, 红色细线为物种B的等位基因。
Fig. 1 Lineage sorting process of two species: (a) Polyphyly; (b) Paraphyly; (c) Monophyly. The blue bold lines in the figure indicate the tree of species A and B. The thin black lines represent the alleles of species A. The thin red lines represent the alleles of species B.
图2 两个子代物种(物种1, 物种2)在t世代前溯祖。种内所有基因来自单一祖先, 两直系基因回溯到物种分化前的祖先群体中(T世代)。在中性假设下, 两个子代物种直系同源基因间自物种分化后的突变数等于2μt。红点表示突变, 字母a、b表示两个直系同源基因。
Fig. 2 Two progeny species (species 1 and 2) descend from an ancestral population at t generations ago. All the genes within a species descend from a single lineage. Two orthologous genes coalesce to a single lineage in the ancestral population at T generations ago. Under the neutrality hypothesis, the two orthologous genes differ from each other by 2μt mutations since speciation. The red dots indicate mutations. Letters a and b indicate two orthologous genes.
祖先群体中选择类型 Selection type at a locus in the ancestral population | 子代物种间基因平均溯祖时间 Mean coalescent time between orthologous genes from descent species |
---|---|
定向选择 Directional selection | 近似于在祖先群体时溯祖时间, 或长于物种分化时间 Approximate to the coalescent time in the ancestral population, or longer than the species divergence time |
平衡选择 Balancing selection | 远远大于物种分化时间 Much longer than the species divergence time |
歧化选择 Disruptive selection | 近似于物种分化时间 Approximate to the species divergence time |
正频率依赖选择 Positive frequency-dependent selection | 近似于在祖先群体时的溯祖时间 Approximate to the coalescent time in the ancestral population |
负频率依赖选择 Negative frequency-dependent selection | 远远大于物种分化时间 Much longer than the species divergence time |
随机选择 Stochastic selection | 近似于子代物种中性基因间溯祖时间, 大于物种分化时间 Approximate to the coalescent time of neutral genes in decent species but is longer than the species divergence time |
表1 在祖先群体中位点的选择类型及其在子代种间两直系同源基因的基因树与物种树的可能关系
Table 1 The type of selection at a locus in the ancestral population and the potential relationship between the gene tree of two orthologous genes and the descent species tree
祖先群体中选择类型 Selection type at a locus in the ancestral population | 子代物种间基因平均溯祖时间 Mean coalescent time between orthologous genes from descent species |
---|---|
定向选择 Directional selection | 近似于在祖先群体时溯祖时间, 或长于物种分化时间 Approximate to the coalescent time in the ancestral population, or longer than the species divergence time |
平衡选择 Balancing selection | 远远大于物种分化时间 Much longer than the species divergence time |
歧化选择 Disruptive selection | 近似于物种分化时间 Approximate to the species divergence time |
正频率依赖选择 Positive frequency-dependent selection | 近似于在祖先群体时的溯祖时间 Approximate to the coalescent time in the ancestral population |
负频率依赖选择 Negative frequency-dependent selection | 远远大于物种分化时间 Much longer than the species divergence time |
随机选择 Stochastic selection | 近似于子代物种中性基因间溯祖时间, 大于物种分化时间 Approximate to the coalescent time of neutral genes in decent species but is longer than the species divergence time |
类型 Type | 输入/输出 Input/output | 方法 Method | 参考文献 References |
---|---|---|---|
汇总法 Summary method | 无根基因树/无根物种树 UGT/UST | NJst | Liu & Yu, |
无根基因树/无根物种树 UGT/UST | wQMC | Avni et al, | |
无根基因树/无根物种树 UGT/UST | ASTRAL | Mirarab et al, | |
无根基因树/无根物种树 UGT/UST | ASTRAL-II | Mirarab & Warnow, | |
无根基因树/无根物种树 UGT/UST | ASTRID | Vachaspati & Warnow, | |
无根基因树/无根物种树 UGT/UST | DISTIQUE | Sayyari & Mirarab, | |
无根基因树/无根物种树 UGT/UST | ASTRAL-III | Zhang et al, | |
无根基因树/无根物种树 UGT/UST | USTAR/FastME | Allman et al, | |
无根基因树/无根物种树 UGT/UST | wQFM | Mahbub et al, | |
无根基因树/无根物种树 UGT/UST | ASTER | Zhang & Mirarab, | |
无根基因树/无根物种树 UGT/UST | TREE-QMC | Han & Molloy, | |
无根基因树/无根物种树 UGT/UST | Asteroid | Morel et al, | |
无根基因树/无根物种树 UGT/UST | wASTRID | Liu & Warnow, | |
有根基因树/有根物种树 RGT/RST | STEM | Kubatko et al, | |
有根基因树/有根物种树 RGT/RST | STAR/STEAC | Liu et al, | |
有根基因树/有根物种树 RGT/RST | MP-EST | Liu et al, | |
有根基因树/有根物种树 RGT/RST | STELLS | Wu, | |
有根基因树/有根物种树 RGT/RST | METAL | Dasarathy et al, | |
有根基因树/有根物种树 RGT/RST | STELLS2 | Pei & Wu, | |
有根基因树/有根物种树 RGT/RST | QR-STAR | Tabatabaee et al, | |
有根基因树/无根物种树 RGT/UST | STELAR | Islam et al, | |
共同估计法 Co-estimation of gene and species trees | 多序列比对/有根物种树和基因树分布 MSA/DRSGT | BEST | Liu, |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | *BEAST | Heled & Drummond, | |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | SNAP | Bryant et al, | |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | BPP | Yang, | |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | StarBEAST2 | Ogilvie et al, | |
基于位点法 Site-based method | 多位点比对/无根物种树 Multi-site alignments/UST | SVDquartets | Chifman & Kubatko, |
多位点比对/无根物种树 Multi-site alignments/UST | SVDquest | Vachaspati & Warnow, | |
独立溯祖位点/有根物种树 ICS/RST | Lily | Richards & Kubatko, |
表2 多物种溯祖模型下的物种树估计方法
Table 2 Methods for estimating species tree under multispecies coalescent model (MSC)
类型 Type | 输入/输出 Input/output | 方法 Method | 参考文献 References |
---|---|---|---|
汇总法 Summary method | 无根基因树/无根物种树 UGT/UST | NJst | Liu & Yu, |
无根基因树/无根物种树 UGT/UST | wQMC | Avni et al, | |
无根基因树/无根物种树 UGT/UST | ASTRAL | Mirarab et al, | |
无根基因树/无根物种树 UGT/UST | ASTRAL-II | Mirarab & Warnow, | |
无根基因树/无根物种树 UGT/UST | ASTRID | Vachaspati & Warnow, | |
无根基因树/无根物种树 UGT/UST | DISTIQUE | Sayyari & Mirarab, | |
无根基因树/无根物种树 UGT/UST | ASTRAL-III | Zhang et al, | |
无根基因树/无根物种树 UGT/UST | USTAR/FastME | Allman et al, | |
无根基因树/无根物种树 UGT/UST | wQFM | Mahbub et al, | |
无根基因树/无根物种树 UGT/UST | ASTER | Zhang & Mirarab, | |
无根基因树/无根物种树 UGT/UST | TREE-QMC | Han & Molloy, | |
无根基因树/无根物种树 UGT/UST | Asteroid | Morel et al, | |
无根基因树/无根物种树 UGT/UST | wASTRID | Liu & Warnow, | |
有根基因树/有根物种树 RGT/RST | STEM | Kubatko et al, | |
有根基因树/有根物种树 RGT/RST | STAR/STEAC | Liu et al, | |
有根基因树/有根物种树 RGT/RST | MP-EST | Liu et al, | |
有根基因树/有根物种树 RGT/RST | STELLS | Wu, | |
有根基因树/有根物种树 RGT/RST | METAL | Dasarathy et al, | |
有根基因树/有根物种树 RGT/RST | STELLS2 | Pei & Wu, | |
有根基因树/有根物种树 RGT/RST | QR-STAR | Tabatabaee et al, | |
有根基因树/无根物种树 RGT/UST | STELAR | Islam et al, | |
共同估计法 Co-estimation of gene and species trees | 多序列比对/有根物种树和基因树分布 MSA/DRSGT | BEST | Liu, |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | *BEAST | Heled & Drummond, | |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | SNAP | Bryant et al, | |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | BPP | Yang, | |
多序列比对/有根物种树和基因树分布 MSA/DRSGT | StarBEAST2 | Ogilvie et al, | |
基于位点法 Site-based method | 多位点比对/无根物种树 Multi-site alignments/UST | SVDquartets | Chifman & Kubatko, |
多位点比对/无根物种树 Multi-site alignments/UST | SVDquest | Vachaspati & Warnow, | |
独立溯祖位点/有根物种树 ICS/RST | Lily | Richards & Kubatko, |
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