Anatomical females carry a Y chromosome only rarely, as a result of genetic defect.
The other linkage group is the mitochondrial DNA (mt DNA).
The process of recombination, if frequent enough, corrupts the ability to create parsimonious trees because of stretches of amino acid subsititions (SNPs).
When looking between distantly related species, recombination is less of a problem since recombination between branches from common ancestors is prevented after true speciation occurs.
Mt DNA, through the process of organelle division, became clonal over time; very little, or often none, of that paternal mt DNA is passed.
Mitochondrial DNA became an area of research in phylogenetics in the late 1970s.
Unlike genomic DNA, it offered advantages in that it did not undergo recombination.
Generally, comparisons are made between sequences, either DNA or protein sequences; however, early studies used comparative serology.