Phylogenomic conflict coincides with rapid morphological innovation
Phylogenomic conflict coincides with rapid morphological innovation
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DOI：
10.1101/2020.11.04.368902
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发表时间：
2020-11
期刊：
影响因子：
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通讯作者：
C. Parins-Fukuchi;Gregory W. Stull;Stephen A. Smith
中科院分区：
文献类型：
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作者：
C. Parins-Fukuchi;Gregory W. Stull;Stephen A. Smith
意义我们证明，在哺乳动物，鸟类和几个主要的植物分支的高基因树冲突（基因间的系统发育信号不一致）的情况下，对应于形态创新率的增加。我们认为，在维管植物、哺乳动物和鸟类的主要分支中，基因树冲突和快速的表型变化往往是同时发生的种群过程的结果（例如，种群规模的变化、快速物种形成和不完全谱系分类）。对这些一致模式的仔细研究将有助于更好地理解表型模式出现背后的微进化动力学，这些表型模式通常只能在很长一段时间内观察到。我们的研究结果表明，基因树冲突的模式，发生在整个生命之树，提供了线索，了解人口水平的过程驱动主要的进化转变。进化生物学家长期以来一直着迷于主要谱系出现背后的快速表型创新。虽然我们对这些事件的环境和生态背景的理解已经稳步增加，但仍然不清楚人口过程如何促成新兴的宏观进化模式。从生物基因组学中得到的一个启示是，基因树冲突通常是由种群水平的过程引起的，在主要谱系的起源过程中往往很猖獗。由于了解到基因组冲突往往是由复杂的人口过程驱动的，我们假设，如果两种模式都来自相同的过程，那么高冲突和表型创新率升高的情况之间可能存在直接的对应关系。我们评估了这一假设在六个分支跨越脊椎动物和植物。我们发现，这六个分支中冲突最丰富的地区也往往经历最高的表型创新率，这表明塑造表型和基因组进化的人口过程可能会在较深的时间尺度上留下签名。更深入地研究基因组冲突的生物学意义，可能会改善微观进化和宏观进化之间的联系，并增加我们对生命之树中主要谱系起源过程的理解。
Significance We demonstrate that instances of high gene-tree conflict (discordance in phylogenetic signal across genes) in mammals, birds, and several major plant clades correspond to rate increases in morphological innovation. We suggest that gene-tree conflict and rapid phenotypic change across major clades of vascular plants, mammals, and birds are often the result of coincident population processes (e.g., changes in population size, rapid speciation, and incomplete lineage sorting). Closer examination of these coincident patterns will contribute to a stronger understanding of the microevolutionary dynamics underlying the emergence of phenotypic patterns typically only observable over deep time. Our findings indicate that patterns of gene-tree conflict, occurring episodically across the Tree of Life, offer clues toward understanding the population-level processes driving major evolutionary transitions. Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between instances of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.