mtDNAcombine

mtDNAcombine compiles and preprocesses mitochondrial DNA (mtDNA) sequence data from multiple independent studies in R to produce datasets suitable for Bayesian Skyline Plot (BSP) demographic reconstructions.

Key Features:

• Data Integration: Systematically combines mtDNA sequences from multiple studies to create consolidated datasets.
• Data Compilation: Aggregates mtDNA sequences from publicly available repositories.
• Quality Control: Implements checks to ensure data integrity and consistency across different studies.
• Bayesian Skyline Plot (BSP) Preparation: Specifically prepares compiled mtDNA datasets for Bayesian Skyline Plot demographic reconstructions.
• Handling Multi-study Complexities: Addresses decisions and challenges arising from multi-study sequence data integration, including data extraction and consistency issues.

Scientific Applications:

• Ecology and Evolution: Enables exploration of species' evolutionary histories and ecological relationships using aggregated mtDNA data.
• Conservation Biology: Supports inference of past demographic events to inform conservation strategies and assess impacts of environmental change on species.

Methodology:

Aggregating mtDNA sequences from publicly available repositories; implementing quality-control checks for data integrity and consistency across studies; and preparing compiled datasets for Bayesian Skyline Plot demographic reconstructions.