Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling random ..., The data described in Árnason et al. 2023 are unfolded site frequency spectra of two populations of Atlantic cod (Gadus morhua) from Iceland. The site frequency spectra are estimated from whole-genome sequence results using ANGSD (Korneliussen et. al 2014). The estimation uses genotype likelihood (Samtools likelihood, gl1, and GATK likelihood, gl2) and returns 100 bootstrap estimates. An estimate is provided for each of the 23 chromosomes. Pacific cod (G. macrocephalus) was used as an outgroup to polarize the variation at sites.
Reference
Árnason E, Koskela J, Halldórsdóttir K, and Eldon B. 2023. Sweepstakes reproductive success via pervasive and recurrent selective sweeps. eLife 2023;12:e80781. DOI: https://doi.org/10.7554/eLife.80781.
Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics. 2014 nov; 15(1). http://dx.doi.org/10.1186/s12859-014-0356-4, doi: 10.1186/s12859-014-0356-4., The data are presented as zipped archives of plain text files of site frequency spectrum and 100 bootstrap values for each chromosome and both likelihoods. The data are readable, for example, with R.Â

自然界中广泛存在高早期死亡率的高繁殖力自然种群，但我们对其种群补充动态的认知仍较为粗浅。这一认知缺口，制约了我们对高繁殖力种群的遗传变异、种群连通性、局部适应以及恢复力的理解。抽奖式繁殖成功（sweepstakes reproductive success）这一概念提出，个体繁殖产出存在显著的方差与偏斜，是阐释个体繁殖成功分布的核心框架。然而，我们仍未明确高繁殖力生物是否采用抽奖式繁殖模式繁衍，若确实如此，中性抽奖与选择性抽奖各自的相对作用也有待厘清。

本研究通过对种群基因组数据开展基于溯祖（coalescent）的统计分析，证实选择性抽奖模式或可解释高繁殖力大西洋鳕的种群补充动态。研究表明，Kingman溯祖（模拟无抽奖式繁殖）与Xi-Beta溯祖（模拟随机……）

Árnason等人2023年研究中所描述的数据，为冰岛海域两个大西洋鳕（*Gadus morhua*）种群的展开型位点频率频谱（unfolded site frequency spectrum）。该位点频率频谱通过ANGSD（Korneliussen等人2014年开发的工具）从全基因组测序结果中估算得到，估算过程采用基因型似然值（Samtools似然值gl1与GATK似然值gl2），并生成100次自举（bootstrap）估算结果，且为大西洋鳕的23条染色体分别提供了位点频率频谱估算值。本研究以太平洋鳕（*G. macrocephalus*）作为外类群，对位点处的遗传变异进行极化处理。

参考文献：
1. Árnason E, Koskela J, Halldórsdóttir K, Eldon B. 2023. 基于广泛且反复发生的选择性清除的抽奖式繁殖成功. eLife 2023;12:e80781. DOI: https://doi.org/10.7554/eLife.80781.
2. Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD：下一代测序数据分析工具. BMC Bioinformatics. 2014年11月;15(1). http://dx.doi.org/10.1186/s12859-014-0356-4, doi: 10.1186/s12859-014-0356-4.

本数据集以压缩归档形式提供，内含各染色体、两种基因型似然值对应的位点频率频谱及100次自举值的纯文本文件，可通过R语言等工具读取。