Data from: Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation-related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi-complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time-calibrated species tree based on whole-genome sequences and provide strong evidence for incomplete lineage sorting in the early phases of diversification and multiple introgression events affecting different stages. Importantly, we find that the Neolamprologus chromosomes show centre-to-periphery biases in nucleotide diversity, sequence divergence, GC content, incomplete lineage sorting and rates of introgression, which are likely modulated by recombination density and linked selection. The detection of heterogeneous genomic landscapes has strong implications on the genomic mechanisms involved in speciation. Collinear chromosomal regions can be protected from gene flow and harbour incompatibility genes if they reside in lowly recombining regions, and coupling can evolve between nonphysically linked genomic regions (chromosome centres in particular). Simultaneously, higher recombination towards chromosome peripheries makes these more dynamic, evolvable regions where adaptation polymorphisms have a fertile ground. Hence, differences in genome architecture could explain the levels of taxonomic and phenotypic diversity seen in taxa with collinear genomes and might have contributed to the spectacular cichlid diversity observed today.

基因组变异如何转化为生物多样性，以及新物种的起源机制，长期以来都是进化生物学领域的核心未解之谜。非洲慈鲷（African cichlid fishes）凭借其极为丰富的分类学与表型多样性，以及该过程中基因流可能发挥的作用，成为研究物种形成相关问题的首选模式系统。本研究借助全基因组测序与系统基因组学分析，探讨了坦噶尼喀湖萨氏新亮丽鲷复合群（Neolamprologus savoryi-complex，又称“公主慈鲷”）中，不完全谱系分选、基因渐渗与杂交物种形成的相对影响。我们构建了基于全基因组序列的时间校准物种树，并为多样化早期阶段的不完全谱系分选，以及影响不同演化阶段的多起基因渐渗事件提供了强有力的证据。值得注意的是，我们发现新亮丽鲷属（Neolamprologus）的染色体在核苷酸多样性、序列分化、GC含量、不完全谱系分选以及基因渐渗速率上均呈现出从染色体中心到外围的梯度偏倚，这种偏倚很可能受重组密度与连锁选择的调控。对异质性基因组景观的检测，为理解物种形成涉及的基因组机制提供了重要启示。若共线性染色体区域位于低重组区域，则可免受基因流的影响，并容纳不相容性基因；同时，非物理连锁的基因组区域（尤其是染色体中心区域）之间可演化出耦合关联。与此同时，染色体外围区域的重组率更高，使其成为更具动态性、可演化性的区域，为适应性多态性提供了理想的演化温床。因此，基因组结构的差异或许可以解释具有共线性基因组的类群所呈现的分类学与表型多样性水平，也可能促成了当今我们所见的惊人慈鲷物种多样性。