This repository contains an analysis of the demographic history of the barnacle species Balanus improvisus using MSMC2 and SMC++. These tools estimate the effective population size (Ne) over time, providing insights into the evolutionary history of the species.

• Connor S. Murray
• Date: November 7, 2022

• Mutation rate: 2.76e-08
• Generation time: 1 year

• MSMC2: Multi-Species Coalescent method to infer population size history.
• SMC++: Sequentially Markovian Coalescent method is used to infer population size history.

• QC/: Contains the scripts to check quality control of raw NGS fastqs.
• Scripts/: R and shell scripts used for data processing and analysis in MSMC2 and SMC++.
• Plots/: Outputs of the plots from R.
• README.md: Project overview and instructions.

The analysis results include estimates of the effective population size (Ne) of B. improvisus over time. These results provide insights into the species' demographic history and evolutionary patterns and show evidence for rapid population expansion following the last glacial maximum, which occurred roughly 10-15 kya.

Contributions are welcome! If you have any suggestions or improvements, please open an issue or submit a pull request.

• If you have any questions or need further assistance, please don't hesitate to contact me.