Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do
not necessarily share the same evolutionary history due to widespread
Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary
relationships of prokaryotes as bifurcating trees has long been
controversial. However, studies reporting conflicts among gene trees
derived from phylogenomic datasets have shown that these conflicts can be
the result of artifacts or evolutionary processes other than HGT, such as
incomplete lineage sorting, low phylogenetic signal, and systematic errors
due to substitution model misspecification. Here, we present the results
of an extensive exploration of phylogenetic conflicts in the
cyanobacterial order Nostocales, for which previous studies have inferred
strongly supported conflicting relationships when using different
concatenated phylogenomic datasets. We found that most of these conflicts
are concentrated in deep clusters of short internodes of the Nostocales
phylogeny, where the great majority of individual genes have low resolving
power. We then inferred phylogenetic networks to detect HGT events while
also accounting for incomplete lineage sorting. Our results indicate that
most conflicts among gene trees are likely due to incomplete lineage
sorting linked to an ancient rapid radiation, rather than to HGTs.
Moreover, the short internodes of this radiation fit the expectations of
the anomaly zone, i.e., a region of the tree parameter space where a
species tree is discordant with its most likely gene tree. We demonstrated
that concatenation of different sets of loci can recover up to 17 distinct
and well-supported relationships within the putative anomaly zone of
Nostocales, corresponding to the observed conflicts among well-supported
trees based on concatenated datasets from previous studies. Our findings
highlight the important role of rapid radiations as a potential cause of
strongly conflicting phylogenetic relationships when using phylogenomic
datasets of bacteria. We propose that polytomies may be the most
appropriate phylogenetic representation of these rapid radiations that are
part of anomaly zones, especially when all possible genomic markers have
been considered to infer these phylogenies.