Evolutionary Biology and Mitochondrial Genomics: 50 000 Mitochondrial DNA Genomes and Counting

Abstract

Mitochondrial deoxyribonucleic acid (mtDNA) is a small circular piece of deoxyribonucleic acid (DNA) that resides inside of mitochondria in the cytoplasm of most eukaryotic cells. It has been used by evolutionary biologists for nearly four decades as an analytical tool for everything from tracing human lineages and how people moved across the planet to studies about natural selection. More recently, mtDNA has become even more useful in evolutionary biology as a result of the ease with which the entire molecule can be sequenced. Large numbers of fully sequenced mitochondrial genomes have been generated as a result of next‐generation sequencing (NGS) and powerful bioinformatic approaches.

Key Concepts

  • Mitochondrial DNA has been used to study evolutionary biology for nearly four decades.
  • The capacity to sequence whole mitochondrial genomes has become an important part of the expansion of the role of this molecule in evolutionary biology.
  • MtDNA genome information has contributed to the study of human mtDNA haplogroup studies, animal phylogeography and phylogenetic studies, ancient DNA studies, studies of natural selection and studies of nuclear mitochondrial interactions.
  • As of 2017, over 500 ancient human mtDNA genomes have been sequenced.
  • As of 2017, over 100 ancient animal mtDNA genomes have been sequenced.
  • An important new area where mtDNA genomics will contribute in the future is in using DNA sequence analysis of natural history collection specimens.

Keywords: mitochondrial DNA; genomics; natural selection; ancient DNA; evolution; mitonuclear interactions

Figure 1. Global distribution of human paleo mtDNA (mitochondrial deoxyribonucleic acid) genomes. The age of the specimen from which the mtDNA genome was sequences is given in the legend with colours. Each circle represents a single genome from Homo sapiens. Diamonds and squares represent Neanderthal and Denisova, respectively.
Figure 2. Plot of the number of mtDNA genomes in the database for six major groups of animals (orange line). The blue line represents the total number of named described species for the group.
Figure 3. Phylogenetic tree showing the geographic distribution of paleo specimens where mtDNA genomes have been generated. The geographic location is given by the colour of the open circles. The age of the paleo specimen is given by its position in the grid to the right of the tree.
Figure 4. Plots of percentage of sites under selection in 12 protein‐coding genes (listed on the X‐axis) in the mtDNA genome. The percentage of sites under selection were plotted in two ways. The first approach (blue bars) uses the raw number of positions in each gene divided by the number of bases in each gene summed over the 36 animal groups included in the survey. The second approach (orange bars) simply counts the number of animal groups per gene with positively selected sites divided by the number of bases in each gene summed over the 36 animal groups in the survey. The blue dotted box shows the Complex V genes (Atp6 and Atp8) and the red box shows the three Complex I genes (ND2, ND4 and ND5) that are show high levels of positive selection. The green box shows the low‐level positively selected Complex IV genes.
Figure 5. Structure of animal mtDNA genomes. The largest animal mtDNA genomes are circular and more than 40 kb in size, while the smallest are less than 10 kb in size. mtDNA genome linearisation and fragmentations have occurred as a synapomorphy in the Medusozoa but are also found as an exception in some Porifera. With respect to the gene inventory, the most complete mtDNA genomes are found in placozoans, while the derived Ctenophora show the most incomplete genomes. Within the Bilateria, similar secondary fragmentations of the mtDNA genome are observed in some arthropods but with the structure remains circular. Substantial secondary expansions due to duplication events of whole mtDNA genome regions are found in some molluscs. tRNA abbreviations CS (complete set of tRNAs), GCS (generally complete set of tRNAs), IS (incomplete set of tRNAs).
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DeSalle, Rob, and Hadrys, Heike(Jul 2017) Evolutionary Biology and Mitochondrial Genomics: 50 000 Mitochondrial DNA Genomes and Counting. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027270]