A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.

ABSTRACT: Models of tree evolution have mostly focused on capturing the cladogenesis processes behind speciation. Processes that derive the evolution of genomic elements, such as repeats, are not necessarily captured by these existing models. In this article, we design a model of tree evolution that we call the dual-birth model, and we show how it can be useful in studying the evolution of short Alu repeats found in the human genome in abundance. The dual-birth model extends the traditional birth-only model to have two rates of propagation, one for active nodes that propagate often, and another for inactive nodes, that with a lower rate, activate and start propagating. Adjusting the ratio of the rates controls the expected tree balance. We present several theoretical results under the dual-birth mod

SUBMITTER: Moshiri N 

PROVIDER: S-EPMC5920319 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature