Data from: The phylogenetic origins and evolutionary history of holocentric chromosomes

In eukaryotes, we can recognize two kinds of chromosomes, based on the location of the kinetochores. The majority of eukaryotes have monocentric chromosomes, in which kinetochoric activity is concentrated in a single locus. In several unrelated eukaryotic lineages, chromosomes are holocentric, having diffuse centromeric / kinetochoric activity along the length of the chromosome. Whether holocentric chromosomes are derived or ancestral is still under debate. This study uses the phylogenetic tree from Time Tree of Life project, comprising more than 50,000 sampled species, to reconstruct the evolution of holocentry. Asymmetrical two-state Markov (Mk2) models were compared with BiSSE models to assess sensitivity of our conclusions to possible effects of holocentry on lineage diversification rates. Our analyses based on Mk2 and BiSSE models inferred that the rate of transition from holocentric to monocentric chromosomes is two orders of magnitude higher than the reverse direction. The ancestral state of all eukaryotes is ambiguous depending on the model, inferred to be either monocentric (Mk2) or holocentric (BiSSE). Whatever the direction, the multiple transitions and high diversity of centromere organization across the tree of life are what we would expect if there are selective advantages to both chromosome types. Understanding those selective advantages is key to understanding how genetic information is organized and transmitted from one generation to the next, and why these major evolutionary transitions in centromere organization have occurred in the first place.

在真核生物中，我们可根据动粒（kinetochores）的位置区分两类染色体。多数真核生物拥有单着丝粒染色体（monocentric chromosomes），其动粒活性集中于单个基因座。在多个互不相关的真核生物演化支中，染色体为全着丝粒染色体（holocentric chromosomes），其着丝粒/动粒活性沿染色体全长呈弥散分布。全着丝粒染色体究竟属于衍生性状还是祖先性状，目前仍存在争议。本研究借助生命时间树（Time Tree of Life）项目构建的包含超5万个采样物种的系统发育树，重构全着丝粒性状（holocentry）的演化历程。本研究通过对比不对称双态马尔可夫（Mk2）模型与BiSSE模型，评估我们的结论是否会因全着丝粒性状对演化支分化速率的潜在影响而出现偏差。基于Mk2与BiSSE模型的分析结果显示，全着丝粒染色体向单着丝粒染色体的转换速率较反向转换速率高出两个数量级。所有真核生物的祖先性状状态因所用模型不同而存在歧义：基于Mk2模型推断为单着丝粒，基于BiSSE模型则推断为全着丝粒。无论转换方向如何，若两类染色体均存在选择优势，那么生命之树中着丝粒组织形式的多次演化转换与高度多样性便符合我们的预期。解析这些选择优势，是理解遗传信息如何组织并传递给后代，以及着丝粒组织形式这类重大演化转换最初为何会发生的关键。