A phylogeny visually represents how different species are evolutionarily related.  However, phylogenies depict hypotheses of evolutionary history to account for extinct species. Even though we don’t have a complete picture of evolutionary history, phylogenies can provide us with a useful tool to test other hypotheses of evolution.  

First, let’s go over how to read a phylogeny.  Follow along using this phylogeny:

A clade considers a group of species and their most recent common ancestor.  The section Lampyridae represents a clade.  A node is a point where species branch off.  The most recent node on this phylogeny is between Aquatica ficta and Asymmetricata circumdata.  Newer species are listed at the tips of each branch, while the ‘root’ of the phylogeny is the oldest in the  phylogeny of consideration. Branch lengths provide information on morphological or genetic differences, not time.  If you want to include more chronological information, a chronogram uses branch lengths to determine the difference between extant and extinct species.  

Traditionally, two species were put in the same clade if they were morphologically similar.  For cases of convergent evolution, scientists used the idea of parsimony. Parsimony hypothesizes that the evolution of a new morphology is an unlikely event.  For example, if researchers found fireflies in North America and Europe, they would be placed underneath a common ancestor on a phylogeny under the assumption that Luciferase, the bioluminescent protein, evolved once when the continents were not separated by an ocean instead of twice.  There are limitations to this method. Since the tree was built on evolutionary principles, you can’t use the tree to study evolution, as this would be circular reasoning.  
Over time, there have been many improvements to the process of building phylogenies. A more modern approach to assembling phylogenies involves the use of genetic data and “likelihood” to put together phylogenies.  Based on the molecular data, each possible phylogeny gets a likelihood score for the chance that this given tree is the correct one. The trees with the highest likelihood score are published in scientific papers. But what about confounding variables such as morphology and resource availability?  Phylogenetic Generalized Least Squares (PGLS) regression is used to account for the confounding variables and put species in their correct relationships with other species.  Genomics revealed that Luciferase has evolved independently at least twice.  By sequencing the genome of an American and a Japanese firefly that diverged over 100 million years ago and a Caribbean firefly, they were able to distinguish genetic markers surrounding each gene for Luciferase.