phylogeographic data aggregation and repurposing

Launch Database

First time users must create an account to access the phylogatR database. Sign up instructions can be found here.

This material is based upon work supported by the National Science Foundation under grant numbers 1910623 and 1911293

Teacher Resources

We are currently developing a PhylogatR companion book as well as educational modules for use in secondary and college level classes. Modules will support interactive analysis of PhylogatR data through R Shiny applications and include documentation for educators to facilitate classroom use and ensure specific learning objectives are met.

You can access a working draft of the PhylogatR book here.

Working drafts of our educational modules can be accessed below.

Module Purpose Link
Checking Your Data Check genetic and geographic data downloaded from PhylogatR through visualization of: i) aligned DNA sequences for all loci present for a particular species in the database and ii) geographic coordinates for all individuals within that species. Checking Your Data
Checking Your Data 2 Check genetic data downloaded from PhylogatR by screening for outliers using measures of genetic diversity. Checking Your Data 2
Genetic Diversity Evaluate the genetic diversity of data downloaded from PhylogatR by: i) looping through all sequence alignments in your PhylogatR download to calculate genetic diversity and sampling range size, and ii) running a regression analysis to ask the question: does the size of the geographic range of sampling predict levels of genetic diversity? Genetic Diversity
Spatial Genetic Structure Explore the spatial genetic structure of data downloaded from PhylogatR by: i) importing your genetic and geographic data, ii) visualizing sample density, and iii) exploring the genetic variation and how it is clustered. Spatial Genetic Structure
Conservation Linking genetic diveristy to IUCN status. This exercise asks the question: Is the IUCN red list designed to help protect species with low genetic diveristy that would put them at a higher risk of extinction? by seeing if genetic diveristy is correlated with conservation status. Conservation