Resolving deep animal phylogeny with irreversible and unrepeatable genomic changes

通过不可逆和不可重复的基因组变化解决深层动物系统发育

• 批准号: EP/Y023668/1
• 负责人: Maximilian Telford
• 金额: $ 25.55万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FY023668%2F1
• 关键词: Resolving; deep; animal; phylogeny; irreversible

Resolving the animal tree of life is essential to understand the origin and evolution of complex traits such as muscles, guts, and a nervous system. Sequence-based phylogenomics has not met expectations- replacing old problems in animal phylogenetics with new ones. Different datasets and phylogenetic models routinely produce strongly supported but incompatible trees. A key driver of this is convergent evolution of the same nucleotide or amino acid character state at a given position in distantly related sequences by reverse or parallel substitutions. This is prevalent, given the few possible alternative nucleotide (4) or amino acid (20) states, and can produce incorrect trees. Despite substantial effort, adequate and tractable solutions to this and related problems continue to evade us, confounding understanding of animal evolution. An alternative is rare genomic changes, e.g. presence/absence of genes, indels, introns, gene clusters, protein domain architecture etc. Such complex characters are very unlikely to have evolved convergently and their presence/absence is a binary character uniting species. Despite the potential and growing use of such methods, it is already clear that like phylogenomics, they can be misled; character loss can be convergent and is indistinguishable from primary absence. To circumvent this, we will build computational tools for systematic genome-wide identification of a special class of rare genomic changes that employ 'irreversible', 'unrepeatable' characters. These characters are never absent and take two equally and highly complex conserved states-one ancestral (present in non-animals and some animals) and one derived (present in the remaining animals)-making reverse or parallel evolution vanishingly unlikely (e.g. gene adjacency relationships, 'conserved-but-different' genes). This will produce a new, confidently-resolved animal phylogeny allowing us to trace the history of animal trait evolution in ancient Precambrian oceans.

解决生命的动物树对于了解肌肉，胆量和神经系统等复杂性状的起源和演变至关重要。基于序列的系统基因学尚未达到预期 - 用新动物的系统发育中的旧问题取代了旧问题。不同的数据集和系统发育模型通常会产生强烈支持但不兼容的树木。这样的关键驱动力是通过反向或平行取代在给定位置处相同核苷酸或氨基酸特征状态的收敛演化。考虑到少数可能的替代核苷酸（4）或氨基酸（20）状态，这很普遍，并且会产生不正确的树木。尽管付出了巨大的努力，但对此问题和相关问题的适当和可牵持的解决方案仍在逃避我们，这使人们对动物的进化感到困惑。另一种是罕见的基因组变化，例如存在/不存在基因，indels，内含子，基因簇，蛋白质结构结构等。这种复杂的特征不太可能趋于融合，并且它们的存在/不存在是二进制特征统一物种。尽管这种方法的使用潜力和日益增长的使用，但已经很明显，像系统基因组一样，它们可能会被误导。角色丧失可以是收敛的，并且与原发性缺失没有区别。为了避免这种情况，我们将构建用于全基因组的系统识别的计算工具，以识别采用“不可逆”，“难以重复”字符的特殊罕见基因组变化。这些字符永远不存在，并采取两个平等且高度复杂的保守状态，是一个祖先（存在于非动物和某些动物中），一个衍生（存在于其余动物中） - 制造反向或平行的进化消失了（例如，基因邻接关系，'保守的'but distrent'基因）。这将产生一种新的，确信的动物系统发育，使我们能够追踪古代前寒武纪海洋中动物特质进化的历史。