Data from: A two-state model of tree evolution and its applications to alu retrotransposition

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 paper, 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 model, introduce parameter estimation techniques, and study the properties of the model in simulations. We then use the dual-birth model to estimate the number of active Alu elements and their rates of propagation and activation in the human genome based on a large phylogenetic tree that we build from close to one million Alu sequences.现有树状演化模型大多聚焦于刻画物种形成背后的分支演化（cladogenesis）过程，而这类经典模型往往无法捕捉重复序列等基因组元件的演化进程。 本文提出一种名为双起源模型（dual-birth model）的树状演化模型，并展示其可用于研究人类基因组中大量富集的短Alu重复序列（Alu repeats）的演化规律。 双起源模型对传统纯出生模型（birth-only model）进行了拓展，引入两类增殖速率：一类对应高频增殖的活跃节点，另一类对应以较低速率激活并启动增殖的非活跃节点。调整两类速率的比值可调控预期的树状结构平衡性。 本文给出双起源模型框架下的若干理论结果，提出参数估计技术，并通过模拟实验分析该模型的各项特性。 最后，本文基于从近百万条Alu序列构建的大型系统发育树（phylogenetic tree），利用双起源模型估算人类基因组中活跃Alu元件的数量，以及它们的增殖与激活速率。