Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella.
Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella.
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DOI：
10.1371/journal.pgen.1003754
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发表时间：
2013
期刊：
影响因子：
4.5
通讯作者：
Coop G
中科院分区：
文献类型：
--
作者：
Brandvain Y;Slotte T;Hazzouri KM;Wright SI;Coop G
从异交到自花受精的转变是有花植物中最常见的进化转变之一。然而，直到最近，由于缺乏适当的数据和缺乏适当的群体基因组方法来解释这些数据，这种转变的全基因组观点一直模糊不清。在这里，我们提出了一种新的人口基因组分析，详细说明了自交物种，红铃兰，最近从它的异交姐妹，大花荠菜分裂的起源。由于最近的分裂，大部分的变化在C。风疹也存在于C.大花。因此，我们可以确定两个C。风疹个体遗传了存在于C.风疹的创始人。在此基础上，我们证明了C.风疹是由来自与现存C. grandiflora，漂移和选择已经迅速同质化的大部分，这种祖先的变化，因为C。风疹的建立，以及在这段时间内积累的一些新的变异。尽管大量的祖先变异的损失，大约25%的基因组，其中两个C。风疹个体遗传了不同的基础单倍型，构成了它们之间大约90%的遗传变异。为了扩展这些发现，我们开发了一个合并模型，利用推断的频率建立单倍型和变异内建立单倍型估计，C。风疹是由50至100 kya之间的潜在大量个体引起的，随后其有效种群规模减少了20倍。随着越来越多的异交/自交对的群体基因组数据的产生，像这里开发的一个分析将有助于对向自交过渡的进化和人口影响进行精细的观察。虽然许多植物需要另一个个体的花粉来结种子，但在某些物种中，自花授粉是正常的。这种从异交到自花受精的进化转变是显花植物中最常见的转变之一。在这里，我们使用密集的基因组序列数据，以确定在基因组中的两个人继承了相同或不同的片段的祖先的多样性存在于创始人的自交物种，荠菜风疹，以获得一个全基因组的观点，这一转变。这种单倍型的鉴定使我们能够将突变划分为发生在C.风疹分离自其异交祖先，C.大花。通过这种划分，我们估计C.风疹分离自C. grandiflora之间50和100 kya.在这个相对较短的时间内，C的极端减少。风疹的人口规模与遗传变异的大量丧失和有害的多型性的相对比例的增加有关。
The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants. Until recently, however, a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present a novel population genomic analysis detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella's founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella's founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for which two C. rubella individuals have inherited different founding haplotypes makes up roughly 90% of the genetic variation between them. To extend these findings, we develop a coalescent model that utilizes the inferred frequency of founding haplotypes and variation within founding haplotypes to estimate that C. rubella was founded by a potentially large number of individuals between 50 and 100 kya, and has subsequently experienced a twenty-fold reduction in its effective population size. As population genomic data from an increasing number of outcrossing/selfing pairs are generated, analyses like the one developed here will facilitate a fine-scaled view of the evolutionary and demographic impact of the transition to self-fertilization. While many plants require pollen from another individual to set seed, in some species self-pollination is the norm. This evolutionary shift from outcrossing to self-fertilization is among the most common transitions in flowering plants. Here, we use dense genome sequence data to identify where in the genome two individuals have inherited the same or different segments of ancestral diversity present in the founders of the selfing species, Capsella rubella to obtain a genome-wide view of this transition. This identification of founding haplotypes allows us to partition mutations into those that occurred before and after C. rubella separated from its outcrossing progenitor, C. grandiflora. With this partitioning, we estimate that C. rubella split from C. grandiflora between 50 and 100 kya. In this relatively short time frame, an extreme reduction in C. rubella's population size is associated with a massive loss of genetic variation and an increase in the relative proportion of putatively deleterious polymorphisms.
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影响因子：
4.5
作者：
Gutenkunst RN;Hernandez RD;Williamson SH;Bustamante CD
通讯作者：
Bustamante CD
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
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作者：
通讯作者：
--
影响因子：
3.3
作者：
Glemin, Sylvain
通讯作者：
Glemin, Sylvain
影响因子：
3.3
作者：
Adams, AM;Hudson, RR
通讯作者：
Hudson, RR
影响因子：
10.7
作者：
Cutter, AD;Payseur, BA
通讯作者：
Payseur, BA