Gorbunov K Iu, Liubetskiĭ V A
Mol Biol (Mosk). 2009 Sep-Oct;43(5):946-58.
A model and algorithm are proposed to infer evolution of a gene family, given the gene tree, with respect to species evolution, given the species tree. The model describes such evolution using the "nested tree" concept. Performance of the algorithm is verified on several orthologous protein groups. The evolutionary events inferred are: speciation, gene duplication and loss, horizontal gene transfer retaining the original gene copy. A transfer event with the loss of original gene copy is considered a combination of gene transfer and loss. The model maps gene evolution events onto the species phylogeny.
提出了一种模型和算法，在已知物种树的情况下，根据基因树推断基因家族相对于物种进化的演变。该模型使用“嵌套树”概念来描述这种演变。在几个直系同源蛋白质组上验证了该算法的性能。推断出的进化事件包括：物种形成、基因复制和丢失、保留原始基因拷贝的水平基因转移。原始基因拷贝丢失的转移事件被视为基因转移和丢失的组合。该模型将基因进化事件映射到物种系统发育树上。
