Data from: Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

Understanding the genetic basis of reproductive isolation is a
long-standing goal of speciation research. In recently diverged
populations, genealogical discordance may reveal genes and genomic regions
that contribute to the speciation process. Previous work has shown that
conspecific colonies of Acropora that spawn in different seasons (spring
and autumn) are associated with highly diverged lineages of the
phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide
polymorphisms to generate a genome-wide phylogeny and compared it with
gene genealogies from the PaxC intron and the mtDNA Control Region in 20
species of Acropora, including three species with spring- and
autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn
and spring spawners into different genetic clusters in all three species;
however, this pattern was not supported in two of the three species at the
genome level, suggesting a selective connection between PaxC and
reproductive timing in Acropora corals. This genome-wide phylogeny
provides an improved foundation for resolving phylogenetic relationships
in Acropora and, combined with PaxC, provides a fascinating platform for
future research into regions of the genome that influence reproductive
isolation and speciation in corals.