Supplementary material for: Intermittent migration can induce pulses of speciation in a two-island system

Geographic barriers can come and go depending on natural conditions. These fluctuations cause population cycles of expansion and contraction, introducing intermittent migrations that may not hinder speciation but rather promote diversification. Here, we study a neutral two-island speciation model with intermittent migration driven by sea-level fluctuations. Seabed depth modulates isolation and connection periods between the islands, with migration occurring during connection periods with a certain probability. Mating is restricted to genetically compatible individuals on the same island, and offspring inherit genomes from both parents through recombination. We observe speciation pulses that would not occur under strict isolation or continuous migration, with infrequent, temporary increases in species richness happening at different times depending on the combination of geographic settings and migration probability. The resulting dynamic patterns of richness exhibit contrasting behavior ..., , , # Supplementary Material for \"Intermittent migration can induce pulses of speciation in a two-island system\"

**supplementary.pdf** contains the Supplementary Information to the manuscript.

We provide one code, written in FORTRAN: **\"Program\_intermittent.f90\"**
This program has one input file, **\"input\_sea.txt\"**, and one output, **\"Temporal.txt\"**:

```
a) The input\_sea.txt provides in the first line five parameters (the values in the parentheses refer to the values in the file):
a.1) Number of iterations (2000)
a.2) Initial migration probability (0.4)
a.3) Number of repetitions for the set of parameters (1)
a.4) Mutation rate (0.001)
a.5) Time interval that species identification is made (10 iterations)
The remaining lines provide the step iteration and the value of migration. The migration variation period (written over the subsequent lines) is based on the sea level data assuming a seabed of h=-50m.
```

Other parameters, such as minimal genetic similarity, genome size, and pop...

地理屏障会随自然条件的变化而消长。此类波动会引发种群的扩张与收缩周期，带来间歇性迁徙——这类迁徙或许不会阻碍物种形成（speciation），反而会推动物种多样化。
本研究针对由海平面波动驱动间歇性迁徙的中性两岛物种形成模型展开分析。海底深度调控岛屿间的隔离与连通时段，连通时段内种群以特定概率发生迁徙。交配仅允许同一岛屿上遗传兼容性匹配的个体进行，后代通过基因重组（recombination）继承双亲的基因组。
我们观测到，在严格隔离或持续迁徙的条件下不会出现的物种形成脉冲现象：即物种丰富度（species richness）会随地理环境设置与迁徙概率的组合不同，在不同时段出现零星、短暂的提升。由此产生的物种丰富度动态模式呈现出迥异的行为特征……
# 题为《间歇性迁徙可在两岛系统中诱发物种形成脉冲》（Intermittent migration can induce pulses of speciation in a two-island system）的论文补充材料
**supplementary.pdf** 包含该论文的补充信息。
我们提供一段由FORTRAN编写的代码：**"Program_intermittent.f90"**。该程序包含一个输入文件**"input_sea.txt"**与一个输出文件**"Temporal.txt"**：
a) 输入文件input_sea.txt的第一行包含五项参数（括号内数值为示例文件中的取值）：
a.1) 迭代总次数（2000）
a.2) 初始迁徙概率（0.4）
a.3) 参数集重复运行次数（1）
a.4) 突变率（0.001）
a.5) 物种鉴定的时间间隔（以迭代次数计，为10）
剩余行依次给出迭代步长与迁徙概率值。迁徙变化周期基于海床深度h=-50m的海平面数据生成。
其余参数包括最小遗传相似度、基因组大小以及种群……