Efficient summary statistics for detecting lineage fusion from phylogeographic datasets
Efficient summary statistics for detecting lineage fusion from phylogeographic datasets
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DOI：
10.1111/jbi.13932
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发表时间：
2020-07-22
影响因子：
3.9
通讯作者：
Arantes, Isis C.
中科院分区：
文献类型：
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作者：
Garrick, Ryan C.;Hyseni, Chaz;Arantes, Isis C.
目的谱系融合（一个物种的两个或两个以上种群合并为一个单一的全混群）是二次接触的一种特殊情况。它有可能抵消多样化和物种形成，或通过创造新的基因型来促进多样化和物种形成。理解谱系融合在自然界中的普遍性需要对其进行可靠的检测，因此需要有效的汇总统计。在这里，我们报告的模拟，其特征在于初始强度和随后的衰减的签名，过去的融合17个汇总统计适用于DNA序列单倍型数据。位置全球。分类群二倍体异交种。方法我们考虑了一系列场景，这些场景可以揭示读段长度与基因座数量（DNA序列数据的排列）的不同组合的影响，以及融合前人群是否经历了与其分歧一致的瓶颈（融合的历史背景）。融合后基因库沿着代表姐妹群体合并后增加的滞后时间的沿着10个连续时间点取样，并且在每个时间点重新计算汇总统计值。结果在1.5N（e）代的抽样滞后时间后，许多汇总统计量都能检测出群体完全合并的特征，但最具信息量的汇总统计量包括两个中立性检验和四个多样性度量，其中Z（nS）（一种基于连锁不平衡的中立性检验）的作用尤为显著。两个中立性测试和两个多样性指标之间的相关性相对较低。许多短（200 bp x 200）基因座明显优于少数长（4 kb x 10）基因座。此外，只有后一种遗传数据集类型显示出在发散期间瓶颈对信息性汇总统计量的影响。主要结论这项工作有助于确定谱系融合的情况下，并通过使更细致入微的重建个别物种，或多个成员的生态群落，对过去的环境变化作出反应，推进生态地理学。
Aim Lineage fusion (merging of two or more populations of a species resulting in a single panmictic group) is a special case of secondary contact. It has the potential to counteract diversification and speciation, or to facilitate it through creation of novel genotypes. Understanding the prevalence of lineage fusion in nature requires reliable detection of it, such that efficient summary statistics are needed. Here, we report on simulations that characterized the initial intensity and subsequent decay of signatures of past fusion for 17 summary statistics applicable to DNA sequence haplotype data. Location Global. Taxa Diploid out-crossing species. Methods We considered a range of scenarios that could reveal the impacts of different combinations of read length versus number of loci (arrangement of DNA sequence data), and whether or not pre-fusion populations experienced bottlenecks coinciding with their divergence (historical context of fusion). Post-fusion gene pools were sampled along 10 successive time points representing increasing lag times following merging of sister populations, and summary statistic values were recalculated at each. Results Many summary statistics were able to detect signatures of complete merging of populations after a sampling lag time of 1.5N(e)generations, but the most informative ones included two neutrality tests and four diversity metrics, withZ(nS)(a linkage disequilibrium-based neutrality test) being particularly powerful. Correlation was relatively low among the two neutrality tests and two of the diversity metrics. There were clear benefits of many short (200-bp x 200) loci over a handful of long (4-kb x 10) loci. Also, only the latter genetic dataset type showed impacts of bottlenecks during divergence upon the number of informative summary statistics. Main conclusions This work contributes to identifying cases of lineage fusion, and advances phylogeography by enabling more nuanced reconstructions of how individual species, or multiple members of an ecological community, responded to past environmental change.