ABSTRACT
The nuclear genome is a veritable treasure trove for deoxyribonucleic acid (DNA) sequence loci yet it has largely remained inaccessible to researchers. The clock-like manner by which substitutions seem to occur in some genomic sites is a useful property for a DNA sequence locus to have. Nuclear loci enjoy important advantages over mitochondrial loci. Besides the sheer variety and number of loci that can be obtained from the nuclear genome, some nuclear loci have the desirable properties of being presumably neutral and genealogically independent of other sampled loci. Numt-contaminated datasets can cause a variety of problems ranging from obtaining poor quality DNA sequences to spurious interpretations of phylogenomic results. Horizontal gene transfer has played a significant role in the evolution of prokaryotic and eukaryotic genomes. Complete genome in silico approaches are generating large datasets consisting of hundreds of independent loci.
