Amaranth-phylogenetics

The master repo for Amaranthus phylogenetic study using 3RAD data

This project includes estimating the phylogeny using different types of methods:

• Genome-wide SNP frequencies, combining relationships between sets of 4 taxa (quartets) to estimate phylogeny for all samples.
• Concatenating all RAD loci and using maximum likelihood to estimate the phylogeny for consensus sequences for each species.
• Species tree estimation from gene trees using the multispecies coalescent.

We tested different length "genes" in the gene tree methods by combining RAD loci aligned to a reference sequence using different size genomic windows. We tested different reference genomes to test for biases in the amopunt of reads aligned across species.

This project also includes node dating (estimating the age of diversification) of Amaranthus using different methods:

• Bayesian MCMC analysis using concatenated loci in MrBayes.
• Bayesian MCMC analysis using gene trees in SuperBPP.

This project also includes investigation of hybridization throughout the genus using different methods:

• Hypothesis testing using a network multispecies coalescent model in Snaq.
• Model fitting using a network multispecies coalescent model in Nanuq.

This work is not yet published.