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.

原始DArT-seq数据：
包含86株鹿角珊瑚（Acropora）个体的DArT-seq基因型数据。该数据集涵盖10034个基因座的原始序列（长度约100 bp），并标注了每个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）的位置与变异情况。

PaxC序列比对数据集：
涵盖采自西澳大利亚的85株鹿角珊瑚个体的PaxC 46/47内含子比对DNA序列，包含插入缺失（indels）变异。序列长度约1067 bp，文件格式为FASTA。

线粒体DNA（mtDNA）控制区序列比对数据集：
涵盖采自西澳大利亚的84株鹿角珊瑚个体的mtDNA控制区比对序列，包含插入缺失（indels）变异。序列长度约1255 bp，文件格式为FASTA。

解析生殖隔离的遗传基础是物种形成研究长期以来的核心目标。在新近分化的种群中，基因谱系冲突可揭示参与物种形成过程的基因及基因组区域。既往研究表明，鹿角珊瑚中于不同季节（春季与秋季）产卵的同种群落，其系统发育标记PaxC的谱系分化程度极高。本研究利用10034个单核苷酸多态性（SNP）构建全基因组系统发育树，并将其与20种鹿角珊瑚的PaxC内含子及mtDNA控制区的基因谱系进行比对分析，其中包含3个同时拥有春季与秋季产卵群的物种。结果显示，PaxC系统发育树可将这3个物种的同种群落按产卵季节区分为不同遗传簇；然而在全基因组水平上，该模式仅在其中1个物种中得到支持，提示PaxC与鹿角珊瑚的繁殖时间存在选择性关联。本研究构建的全基因组系统发育树为解析鹿角珊瑚的系统发育关系提供了更完善的研究基础，结合PaxC标记，可为未来探索珊瑚生殖隔离与物种形成相关的基因组区域提供极具价值的研究平台。