Organellar DNA continues to provide a rich source of information in the
genomics era
Abstract
The genomics revolution continues to change how ecologists and
evolutionary biologists study the evolution and maintenance of
biodiversity. It is now easier than ever to generate large molecular
data sets consisting of hundreds to thousands of independently evolving
nuclear loci to estimate a suite of evolutionary and demographic
parameters. However, any inferences will be incomplete or inaccurate if
incorrect taxonomic identities and perpetuated throughout the analytical
pipeline. Due to decades of research and comprehensive online databases,
sequencing of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and
select nuclear genes can provide researchers with a cost effective and
simple means to verify the species identity of samples prior to
subsequent phylogeographic and population genomic analysis. The addition
of these sequences to genomic studies can also shed light on other
important evolutionary questions such as explanations for gene
tree-species tree discordance, species limits, sex-biased dispersal
patterns, and mtDNA introgression. Although the mtDNA and cpDNA genomes
often should not be used exclusively to make historical inferences given
their well-known limitations, the addition of these data to modern
genomic studies adds little cost and effort while simultaneously
providing a wealth of useful data that can have significant implications
for both basic and applied research.