Modern phylogenetics no longer relies on morphology, but on varying sets of mitochondrial and nuclear DNA sequences, or RNA transcriptomes. When molecular data are incomplete, molecular and morphological data are sometimes combined to propose “total evidence” phylogenies. However, I will not take these hybrid studies into account. 

Introduction

Somatic avian cells contain a single nucleus and numerous mitochondria, both organelles being provided with DNA. While nuclear DNA (nDNA) is complex and distributed over several chromosomes, mitochondrial DNA (mtDNA) contains a limited number of elements that are located on a single double-stranded circular molecule. Mitochondria are uniparentally inherited via egg cells, whereas nuclear DNA is biparentally inherited via sperm and egg cells. As a consequence, only nuclear DNA is diploid and subject to recombination (via meiotic chromosome segregation, meiotic crossing-over, and zygote formation). In the following, the significance of mitochondrial and nuclear DNA in the reconstruction of phylogenetic relationships will be evaluated separately.