Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan.
PLoS Genet. 2021 Apr 16;17(4):e1009502. doi: 10.1371/journal.pgen.1009502. eCollection 2021 Apr.
Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the "karyograph", which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.
核型，包括染色体和臂数，是所有生物的基本遗传特征，长期以来一直被用作物种诊断特征。此外，核型进化在趋异适应和物种形成中起着重要作用。着丝粒融合和裂变改变染色体数量，而着丝粒在染色体内部的移动，如臂内倒位，改变臂数。尚未建立同时包含染色体和臂数的概率模型。在这里，我们基于“核型图”构建了核型进化的概率模型，将核型进化视为代表染色体和臂数的二维空间上的行走。该模型可以分析具有稳定核型的任何给定参数的平稳分布。在使用模拟数据评估其性能后，我们将我们的模型应用于鱼类的两个大分类群，即板鳃亚纲和真骨鱼亚纲，以对过渡率进行最大似然估计，并重建核型的进化历史。这两个分类群在臂数的进化上存在显著差异。包括物种形成和灭绝率表明，在这两个群体中，除了最典型核型之外的核型的物种可能具有较高的灭绝率。最后，我们构建了一个包含多倍体形成率的模型，并将其应用于一个小型植物群。因此，使用这种概率模型可以帮助更好地理解核型进化的时间和模式及其在物种形成和灭绝中的可能作用。
