Introduction
As known, in humans, mitochondria are transmitted only through the maternal line, because sperm mitochondria are destroyed during fertilization of the egg. It leads to the conclusion that if all modern people have a common female ancestor, then the entire human population has a common mitochondrial ancestor [1].
Due to the fact that mitochondria is an organoid with its own genome that does not undergo recombination, information on substitutions (mutations) in the mitochondrial genome (frequency and quantity) can be used to analyze the phylogenetics of the modern human population, as well as ancestors.
In this work, we estimate the age for a common mitochondrial Eve (a common female ancestor from whom modern people inherited mitochondria) and use this data to calibrate the tree’s molecular clock and assign a date to the root to describe the phylogenetic relationship between Neanderthals, Denisovans, and modern humans. Also, mitochondrial data were used to search for a common first ancestor who came from Africa (the most recent ancestor of all non-Africans) to describe how humans populated the Earth.
Methods
For this study, we used modern human mtDNA [2] and mtDNA of Neanderthal[3] and Denisovan[4].
First, we constructed an evolutionary tree based on modern human mtDNA to investigate the relationship between all of them and calculate the age of ‘mitochondrial Eve’. For this purpose we used the MAFFT web tool with default parameters[5], that is using the MAFFT algorithm[6] for alignment and Neighbour Joining for phylogeny (with bootstrap support value option)[7]. Trees were drawn by web-service phylo.io[11].
Then we calculated the difference between the most distant ‘relatives’ using script (in supplementary) — we calculated the number of single mutations. Assuming that there are 2.67×10−8 substitutions per site per year for the whole molecule of mtDNA[8] and knowing the length of mtDNA and amount of mutations, we can calculate the distance between samples and study the age of our common ancestor.
Using the same manipulations and assuming that Neanderthals, Denisovans were living 40000 years ago[9][10], we can make the same calculations for them and modern humans.
Results
The first part of the investigation has shown that Central African is the most distant from other human populations (pic.1). Then Mozambicans and Susanesians, Moroccans and Yemenis were split from each other. Then there is a big branch with all Asians (+ split Americans) and several branches with Europeans (however they are quite mixed).
Calculations of the common ancestor of all humans: the most distant is Central African mtDNA, so we calculated the average amount of different bases. The amount is 90 (with the length of genome 16567). We can make calculations:
So the age of our common ancestor is 100.000 years.
Then we provided the same manipulations with Neanderthals, Denisovans. The phylogenetic tree is shown in pic.2:
The common ancestors' ages have been calculated:
For humans and Neanderthals:
The average number of different bases between mtDNA of modern humans and Neanderthals is 220 (with the length of genome 16567). We made calculations (with the thought that they lived 40000 years ago (we add it, because we want to bring Neanderthals to our ages)):
So the age of our common ancestor is 270.000 years.
For humans and Denisovans:
The average number of different bases between mtDNA of modern humans and Denisovans is 395 (with the length of genome 16567). We made the same calculations as before:
So the age of our common ancestor is 465.000 years.
Discussion
Since the most distant branch of the human population is Central African, we can assume that our common ancestor was from Africa (and he lived about 100000 years ago). Then humans started moving to the Eurasian continent (through Mesopotamia — the earliest branches after Central Africans are Mozambicans, Susanesians, Moroccans, and Yemenis). After this humans started settling all continents. We can not provide more detailed information, because the bootstrap support value is not high. But this information looks like the truth (due to other investigations[8]).
We also can see that about 465000 years ago our ancestors were split. One of the branches evolved into Denisovans. The other split again about 27000 years ago. One branch evolved into Neanderthals. The other evolved into a modern human ancestor.
References
[1] A. C. Wilson, R. L. Cann, S. M. Carr, M. George Jr., U. B. Gyllensten, K. Helm- Bychowski, R. G. Higuchi, S. R. Palumbi, E. M. Prager, R. D. Sage, and M. Stoneking (1985) «Mitochondrial DNA and two perspectives on evolutionary genetics». Biological Journal of the Linnean Society 26:375–400
[3] Neandertal mtDNA
[4] Denisovan mtDNA
[5] MAFFT web
[6] Kazutaka Katoh, Kazuharu Misawa,Kei-ichi Kuma, and Takashi Miyataa. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
[7] Saitou, N.; Nei, M. (1 July 1987). “The neighbor-joining method: a new method for reconstructing phylogenetic trees”. Molecular Biology and Evolution. 4 (4): 406–425. doi:10.1093/oxfordjournals.molbev.a040454. PMID 3447015.
[8] Qiaomei Fu,Alissa Mittnik, Philip L.F. Johnson,Kirsten Bos,Martina Lari,Ruth Bollongino,Chengkai Sun,Liane Giemsch,Ralf Schmitz,Joachim Burger,Anna Maria Ronchitelli,Fabio Martini,Renata G. Cremonesi,Jiří Svoboda, Peter Bauer,David Caramelli,Sergi Castellano, David Reich, Svante Pääbo, and Johannes Krause. 2016. A revised timescale for human evolution based on ancient mitochondrial genomes
[9] Johannes Krause, Qiaomei Fu, Jeffrey M. Good, Bence Viola, Michael V. Shunkov, Anatoli P. Derevianko & Svante Pääbo. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia
[10] Tom Higham, Katerina Douka, Roger Jacobi. 2014 The timing and spatiotemporal patterning of Neanderthal disappearance.
[11] phylo.io
