10.5061/DRYAD.5HQBZKH2R
Rose, Jeffrey
0000-0001-5598-7584
University of Wisconsin-Madison
Toledo, Cassio
State University of Campinas
Lemmon, Emily
Florida State University
Lemmon, Alan
Florida State University
Sytsma, Kenneth
University of Wisconsin-Madison
Data from: Out of sight, out of mind: Widespread nuclear and
plastid-nuclear discordance in the flowering plant genus Polemonium
(Polemoniaceae) suggests widespread historical gene flow despite limited
nuclear signal
Dryad
dataset
2020
Polemoniaceae
Polemonium
cyto-nuclear discordance
plastid capture
phylogenetic networks
Reticulations
2020-07-30T00:00:00Z
2020-07-30T00:00:00Z
en
https://doi.org/10.1093/sysbio/syaa049
8101402 bytes
9
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Phylogenomic data from a rapidly increasing number of studies provide new
evidence for resolving relationships in recently radiated clades, but they
also pose new challenges for inferring evolutionary histories. Most
existing methods for reconstructing phylogenetic hypotheses rely solely on
algorithms that only consider incomplete lineage sorting as a cause of
intra- or inter-genomic discordance. Here, we utilize a variety of
methods, including those to infer phylogenetic networks, to account for
both incomplete lineage sorting and introgression as a case for nuclear
and cytoplasmic-nuclear discordance using phylogenomic data from the
recently radiated flowering plant genus Polemonium (Polemoniaceae), an
ecologically diverse genus in Western North America with known and
suspected gene flow between species. We find evidence for widespread
discordance among nuclear loci that can be explained by both incomplete
lineage sorting and reticulate evolution in the evolutionary history of
Polemonium. Furthermore, the histories of organellar genomes show strong
discordance with the inferred species tree from the nuclear genome.
Discordance between the nuclear and plastid genome is not completely
explained by incomplete lineage sorting, and only one case of discordance
is explained by detected introgression events. Our results suggest that
multiple processes have been involved in the evolutionary history of
Polemonium and that results from the plastid genome do not accurately
reflect species relationships. We discuss several potential causes for
this cytoplasmic-nuclear discordance, which emerging evidence suggests is
more widespread across the Tree of Life than previously thought.