Building a mitogenome reference tree

Introduction

Phylogenetic trees are more powerful when built with comprehensive data. Mitochondrial genomes allow us to build accurate phylogenetic trees from a set of reference specimens. The previous subsections have demonstrated how we can use these phylogenies; here we work through a rapid and efficient pipeline for building a mitogenome phylogeny.

We will use as our data a combination of novel mitogenomes sequenced from reference specimens from the same study as our example data, along with further data downloaded by GenBank. Data from either source alone would be suitable, but the combination makes our phylogeny more comprehensive and therefore more effective both as a backbone and to aid in later use to assign taxonomy.

As in the previous sections, we would like to stress here that the focus is on exploring the possibilities and potentialities of phylogenetic metabarcoding, but a detailed exploration of phylogenetic methodologies and analysis is beyond the scope of these resources. The broad methodologies presented here cover a general outline of methods for building phylogenies, but the specific alignment and tree-building software employed has been chosen for speed and ease of use, rather than necessarily for optimal phylogenetic reconstruction.

Next Steps

We suggest you work through the 5 tutorials step-by-step, starting with Preparing mitogenome data.