Homo habilis is a species of the genus Homo, that lived from about 2.5 million to 1.6 million years ago. Source: Wikimedia Commons.
“Where do we come from?” This has been one of the fundamental questions asked by humans for thousands of years. Physical anthropologists have been providing an answer for over a hundred years by studying morphological characteristics, such as skull shape, of the fossilised remains of our human and proto-human ancestors.
For the last 15 years or so, molecular anthropologists have been comparing the DNA of living humans of diverse origins to build evolutionary trees. Mutations occur in our DNA at a regular rate and will often be passed along to our children. It is these differences (polymorphisms) that, on a genotypic level, make us all unique and analysis of these differences will show how closely we are related. However, different approaches used by molecular and physical anthropologists have led to opposing views on how modern humans evolved from our archaic ancestors.
Two main hypotheses
The two main hypotheses agree that Homo erectus evolved in Africa and spread to the rest of the world around 1 - 2 million years ago; it is regarding our more recent history where they disagree.
1) Multi-regional evolution
- suggests that modern humans evolved from archaic forms (such as Neanderthal and Homo erectus) concurrently in different regions of the world
- supported by physical evidence, such as the continuation of morphological characteristics between archaic and modern humans
- now a minority standpoint
2) Recent African origin
- proposes that modern humans evolved once in Africa between 100 - 200 thousand years ago
- modern humans subsequently colonised the rest of the world without genetic mixing with archaic forms
- supported by the majority of genetic evidence
DNA is present inside the nucleus of every cell of our body but it is the DNA of the cell’s mitochondria that has been most commonly used to construct evolutionary trees.
Mitochondria have their own genome of about 16,500 bp that exists outside of the cell nucleus. Each contains 13 protein coding genes, 22 tRNAs and 2 rRNAs.
They are present in large numbers in each cell, so fewer samples is required.
They have a higher rate of substitution (mutations where one nucleotide is replaced with another) than nuclear DNA making it easier to resolve differences between closely related individuals.
They are inherited only from the mother, which allows tracing of a direct genetic line.
They don’t recombine. The process of recombination in nuclear DNA (except the Y chromosome) mixes sections of DNA from the mother and the father creating a garbled genetic history.
Focusing on the D-loop
Evidence from DNA studies generally supports a recent African origin but these conclusions have been criticised for a lack of statistical support. One possible reason for this is because these studies have focussed mainly on the polymorphisms in a small section of the mitochondrial genome called the D-loop, which comprises around 7% of the mitochondrial genome. The reason for this section’s popularity lies in its particularly high mutation rate, meaning that scientists can analyse this relatively short sequence and still resolve differences between closely related sequences. Unfortunately, it is now becoming increasingly clear that this very high mutation rate is actually obscuring the informative information. Three main problems with data from the D-loop section have been identified:
- back mutation - sites that have already undergone substitution are returned to their original state
- parallel substitution - mutations occur at the same site in independent lineages
- rate heterogeneity - there is a large difference in the rate at which some sites undergo mutation when compared to other sites in the same region; data shows evidence of ‘hot spots’ for mutation
Although the mitochondrial genome is one of the first genomes to be sequenced in its entirety, it was not until recently that the progression of technology allowed sequences of that length to be obtained with relative ease and a study of any appreciable size using whole genomes was undertaken. This study became an important landmark in the field of population genetics and perhaps will be a precedent for a new field, already coined “population genomics.” These researchers (Ingman et al., see references) found that although sequencing the whole genome was considerably more work, it provided some important advantages.
- Although the D-loop was evolving at a much higher rate, the greater length of the complete genome allowed for the analysis of twice as many informative polymorphic sites (sites that show the same polymorphism in at least two sequences).
- The numbers of back- and parallel mutations found outside of the D-loop were practically zero.
- The rate of evolution of the rest of the genome was surprisingly even between different sites, different genes and also between the different gene complexes.
The robust phylogenetic tree reconstructed with this dataset of complete mitochondrial genomes gives strong support to the ‘recent African origin’ theory. By determining the substitution rate of the genomic sequences, it is possible to derive dates for points on the tree and build a chronology of events in the evolution and migration of our species.
- The most important date, in relation to the competing evolutionary theories, is the time when all the sequences coalesce into one — the ‘mitochondrial Eve.’
- From this study, a date of 171,500 years ago was obtained which fits remarkably well with that proposed in the recent African origin hypothesis.
- For us to accept multi-regionality, we would expect a much older date, as it would represent the common ancestor of Homo erectus rather than of Homo sapiens.
This study is only the first and population genomics is in its infancy. The future will provide more studies with ever-increasing numbers of sequences from yet unanalysed populations and perhaps an interface between genetic data from different loci. For example, a recent study of ancient human remains in Australia integrated genetic data with the information collected by physical anthropology. There are many important questions that remain to be resolved such as how and when the Aborigines arrived in Australia and the evolutionary history and relationships of North and South American Indians.
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