![]() It is especially severe when conserved PCR primers preferentially amplify numts instead of authentic mitochondrial fragments. However, nuclear copies of mitochondrial genes (numts) or contamination by exogenous DNAs can produce non-target PCR products. These difficulties make mitochondrial genomes (mitogenomes) a main target for PCR-based aDNA analyses because of their high copy numbers relative to loci in the nuclear genome and the availability of more published references for primer design than for nuclear loci. The small quantity and poor quality of aDNA also result in high rates of PCR failure. However, owing to the highly degraded and fragmented nature of aDNA, researchers need to amplify and sequence numerous overlapping short fragments to assemble sequences of sufficient lengths for analysis. Polymerase chain reaction (PCR) amplification has been widely used to amplify targeted regions from aDNA. For example, results of aDNA analyses suggested an association between the extinction of Beringian steppe bison ( Bison priscus) and the onset of the last glacial cycle. Studies based on aDNA could also be important for conservation by providing insights into the historical demographics of extinct populations or species and possible causes of their extinction. For example, aDNA was used to clarify the phylogenetic relationships among enigmatic extinct dodos ( Raphus cucullatus) and other Columbidae species, to assess whether there were functional differences in mitochondrial DNA leading to different fates between two clades of woolly mammoths ( Mammuthus primigenius), and to estimate the evolutionary rate of base substitutions in the mitochondrial DNA of Adélie penguins ( Pygoscelis adeliae). ![]() Ancient DNA (aDNA) extracted from fossils or museum specimens can provide information to help us position extinct species in the tree of life and investigate evolution of genes directly. Species extinction is a process that prunes the tree of life and eliminates the genetic information harbored by the species.
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