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

Raw DArT-seq data:
DArT-seq genotypes for 86 individuals of Acropora. These data include the raw sequences (~100 bp) for each of 10,034 loci, and show the position and variation of each single nucleotide polymorphism (SNP).

PaxC sequence alignment:
Aligned DNA sequences from PaxC 46/47 intron, including indels, for 85 individuals of Acropora from Western Australia. Sequence length ~ 1067 bp. File is in FASTA format.

Control Region (mtDNA) sequence alignment:
Aligned sequences of the mtDNA Control Region, including indels, for 84 individuals of Acropora from Western Australia. Sequence length ~1255 bp. File is in FASTA format.

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.