Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance

Despite the obstacles facing marine colonists, most lineages of aquatic
organisms have colonized and diversified in freshwaters repeatedly. These
transitions can trigger rapid morphological or physiological change and,
on longer timescales, lead to increased rates of speciation and
extinction. Diatoms are a lineage of ancestrally marine microalgae that
have diversified throughout freshwater habitats worldwide. We generated a
phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to
resolve freshwater transitions in one lineage, the Thalassiosirales.
Although most parts of the species tree were consistently resolved with
strong support, we had difficulties resolving a Paleocene radiation, which
affected the placement of one freshwater lineage. This and other parts of
the tree were characterized by high levels of gene tree discordance caused
by incomplete lineage sorting and low phylogenetic signal. Despite
differences in species trees inferred from concatenation versus summary
methods and codons versus amino acids, traditional methods of ancestral
state reconstruction supported six transitions into freshwaters, two of
which led to subsequent species diversification. Evidence from gene trees,
protein alignments, and diatom life history together suggest that habitat
transitions were largely the product of homoplasy rather than hemiplasy, a
condition where transitions occur on branches in gene trees not shared
with the species tree. Nevertheless, we identified a small set of
putatively hemiplasious genes, many of which have been associated with
shifts to low salinity, indicating that hemiplasy played a small but
potentially important role in freshwater adaptation. Accounting for
differences in evolutionary outcomes, in which some taxa became locked
into freshwaters while others were able to return to the ocean or become
salinity generalists, might help further distinguish different sources of
adaptive mutation in freshwater diatoms.