Saguaro cactus within-species phylogenomics

Reconstructing accurate historical relationships between populations
within a species poses numerous challenges, not least in many plant groups
in which gene flow can 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 infer a population tree and evaluate its 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, population 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. 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 far south following retreat to refugia
there. 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.