Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro’s current range reflects post-glacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects.

中文翻译：

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仙人掌 (Carnegiea gigantea) 的起源和多样化：种内系统发育分析

在一个物种内重建准确的历史关系带来了许多挑战，尤其是在许多基因流高到足以远远超出物种边界的植物群中。尽管如此，一个物种中树状历史的程度是一个经验问题，现在可以用大量的基因组序列来解决这个问题。我们评估了仙人掌的地理范围内的系统发育结构，仙人掌是仙人掌科的标志性成员，仙人掌是一个以广泛杂交和多孔物种边界而闻名的进化枝。使用来自 10 个地点的 20 个个体的 200 Gb 全基因组重测序数据，我们组装了两个数据集，其中包含来自蛋白质编码序列的 150,000 个双等位基因单核苷酸多态性 (SNP)。从这些我们推断种内树并使用五种不同的推断方法评估它们的重要性和稳健性。尽管序列多样性低、人口普查种群规模大、存在范围广泛的花粉和种子传播剂，但系统发育树在数据集和所有方法中都得到了很好的解析和高度一致。我们推断，根据边际似然比较，最有可能的根源位于墨西哥索诺拉加利福尼亚湾沿岸的遗传多样性最高区域的东部和南部。再加上在北部发现的边际可能性显着下降，这支持了这样的假设，即仙人掌的当前范围反映了其范围南部避难所的冰川后扩张。我们以对物种内系统基因组数据集提出的实际和理论问题的观察结束，其中必须使用基于 SNP 的方法，而不是在序列差异较高时广泛使用的基因树方法。这些包括计算可扩展性、基因流的推断以及在存在连锁效应的情况下对统计支持的适当评估。