Origin and Diversification of the Saguaro Cactus (Carnegiea gigantea): A Within-Species Phylogenomic Analysis
Por:
Sanderson, Michael J., Burquez, Alberto, Copetti, Dario, McMahon, Michelle M., Zeng, Yichao, Wojciechowski, Martin F.
Publicada:
10 ago 2022
Resumen:
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 postglacial 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. [Phylogenomics; phylogeography; rooting;
Sonoran Desert.]
Filiaciones:
Sanderson, Michael J.:
Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA
Burquez, Alberto:
Univ Nacl Autonoma Mexico, Unidad Hermosillo, Inst Ecol, Hermosillo, Sonora, Mexico
Copetti, Dario:
Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ USA
McMahon, Michelle M.:
Univ Arizona, Sch Plant Sci, Tucson, AZ 85721 USA
Zeng, Yichao:
Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA
Wojciechowski, Martin F.:
Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA
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