Emilio Rolán-Alvarez has given the perfect answer. Additionally though, there are several drawbacks associated with the use of mtDNA in phylogenetic studies which nuclear loci do not suffer from. The following two papers would be a good start to get an overview of these:
Balloux, F., 2010. The worm in the fruit of the mitochondrial DNA tree. Heredity 104, 419-420.
Galtier, N., Nabholz, B., Glemin, S., Hurst, G.D., 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18, 4541-4550.
All living entities does not have a mitochondrion but has to have a 16S/18S rDNA.
sir i am a fisheries student and all the fishes do have both mitochondrion and nucleus, so, in this case why 16s/18s rdna is more prefered than mitochondrial dna???
It will depend on your question, but there are a bunch of different neutral markers to use. For instance, you can use neutral microsatellites or neutral SNPs...but for a phylogenetic study I will combine it with mitocondrial as well.
Mitochondrial information is more sensitive to short historial periods (as typically it is maternally inherited and therefore the Ne of the population is reduced). However mtDNA actually represent one linked relatively-small segment, and therefore is giving inference about just one locus. Nuclear inference (if based on several genes) is more representative of the organism history, as it is multilocus.
Emilio Rolán-Alvarez has given the perfect answer. Additionally though, there are several drawbacks associated with the use of mtDNA in phylogenetic studies which nuclear loci do not suffer from. The following two papers would be a good start to get an overview of these:
Balloux, F., 2010. The worm in the fruit of the mitochondrial DNA tree. Heredity 104, 419-420.
Galtier, N., Nabholz, B., Glemin, S., Hurst, G.D., 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18, 4541-4550.
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