A method of genetically evaluating animals by using mitochondrial DNA is disclosed. Polymorphisms in mitochondrial DNA are detected by isolating, fragmenting, and sequencing the DNA. The restriction patterns and nucleotide sequences of mitochondrial DNA of different animals are correlated to expressed traits in the animals. This may be confirmed by comparing results to expression of the trait in maternal lineages of animals. Further, effects of maternal lineages are determined by partitioning maternal genetic variation from nuclear variation.