Human evolutionary genetics


Human evolutionary genetics studies how one human genome differs from another human genome, the evolutionary past that gave rise to the human genome, and its current effects. Differences between genomes have anthropological, medical, historical and forensic implications and applications. Genetic data can provide important insights into human evolution.

Origin of apes

Biologists classify humans, along with only a few other species, as great apes. The living Hominidae include two distinct species of chimpanzee, two species of gorilla, and two species of orangutan. The great apes with the family Hylobatidae of gibbons form the superfamily Hominoidea of apes.
Apes, in turn, belong to the primate order, along with the Old World monkeys, the New World monkeys, and others. Data from both mitochondrial DNA and nuclear DNA indicate that primates belong to the group of Euarchontoglires, together with Rodentia, Lagomorpha, Dermoptera, and Scandentia. This is further supported by Alu-like short interspersed nuclear elements which have been found only in members of the Euarchontoglires.

Phylogenetics

A phylogenetic tree is usually derived from DNA or protein sequences from populations. Often, mitochondrial DNA or Y chromosome sequences are used to study ancient human demographics. These single-locus sources of DNA do not recombine and are almost always inherited from a single parent, with only one known exception in mtDNA. Individuals from closer geographic regions generally tend to be more similar than individuals from regions farther away. Distance on a phylogenetic tree can be used approximately to indicate:
  1. Genetic distance. The genetic difference between humans and chimpanzees is less than 2%, or three times larger than the variation among modern humans.
  2. Temporal remoteness of the most recent common ancestor. The mitochondrial most recent common ancestor of modern humans is estimated to have lived roughly 160,000 years ago, the latest common ancestors of humans and chimpanzees roughly 5 to 6 million years ago.

    Speciation of humans and the African apes

The separation of humans from their closest relatives, the non-human African apes, has been studied extensively for more than a century. Five major questions have been addressed:
  • Which apes are our closest ancestors?
  • When did the separations occur?
  • What was the effective population size of the common ancestor before the split?
  • Are there traces of population structure preceding the speciation or partial admixture succeeding it?
  • What were the specific events prior to and subsequent to the separation?

    General observations

As discussed before, different parts of the genome show different sequence divergence between different hominoids. It has also been shown that the sequence divergence between DNA from humans and chimpanzees varies greatly. For example, the sequence divergence varies between 0% to 2.66% between non-coding, non-repetitive genomic regions of humans and chimpanzees. The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%. Additionally gene trees, generated by comparative analysis of DNA segments, do not always fit the species tree. Summing up:
  • The sequence divergence varies significantly between humans, chimpanzees and gorillas.
  • For most DNA sequences, humans and chimpanzees appear to be most closely related, but some point to a human-gorilla or chimpanzee-gorilla clade.
  • The human genome has been sequenced, as well as the chimpanzee genome. Humans have 23 pairs of chromosomes, while chimpanzees, gorillas and orangutans have 24. Human chromosome 2 is a fusion of two chromosomes 2a and 2b that remained separate in the other primates.

    Divergence times

The divergence time of humans from other apes is of great interest. One of the first molecular studies, published in 1967 measured immunological distances between different primates. Basically the study measured the strength of immunological response that an antigen from one species induces in the immune system of another species. Closely related species should have similar antigens and therefore weaker immunological response to each other's antigens. The immunological response of a species to its own antigens was set to be 1.
The ID between humans and gorillas was determined to be 1.09, that between humans and chimpanzees was determined as 1.14. However the distance to six different Old World monkeys was on average 2.46, indicating that the African apes are more closely related to humans than to monkeys. The authors consider the divergence time between Old World monkeys and hominoids to be 30 million years ago, based on fossil data, and the immunological distance was considered to grow at a constant rate. They concluded that divergence time of humans and the African apes to be roughly ~5 MYA. That was a surprising result. Most scientists at that time thought that humans and great apes diverged much earlier.
The gorilla was, in ID terms, closer to human than to chimpanzees; however, the difference was so slight that the trichotomy could not be resolved with certainty. Later studies based on molecular genetics were able to resolve the trichotomy: chimpanzees are phylogenetically closer to humans than to gorillas. However, some divergence times estimated later do not substantially differ from the very first estimate in 1967, but a recent paper puts it at 11–14 MYA.

Divergence times and ancestral effective population size

Current methods to determine divergence times use DNA sequence alignments and molecular clocks. Usually the molecular clock is calibrated assuming that the orangutan split from the African apes 12-16 MYA. Some studies also include some old world monkeys and set the divergence time of them from hominoids to 25-30 MYA. Both calibration points are based on very little fossil data and have been criticized.
If these dates are revised, the divergence times estimated from molecular data will change as well. However, the relative divergence times are unlikely to change. Even if we cannot tell absolute divergence times exactly, we can be fairly sure that the divergence time between chimpanzees and humans is about sixfold shorter than between chimpanzees and monkeys.
One study used 15 DNA sequences from different regions of the genome from human and chimpanzee and 7 DNA sequences from human, chimpanzee and gorilla. They determined that chimpanzees are more closely related to humans than gorillas. Using various statistical methods, they estimated the divergence time human-chimp to be 4.7 MYA and the divergence time between gorillas and humans to be 7.2 MYA.
Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be ~100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only ~10,000. If true that means that the human lineage would have experienced an immense decrease of its effective population size in its evolution.
Image:Ancestralsizehuman.svg|thumb|300px|right|A and B are two different loci. In the upper figure they fit to the species tree. The DNA that is present in today's gorillas diverged earlier from the DNA that is present in today's humans and chimps. Thus both loci should be more similar between human and chimp than between gorilla and chimp or gorilla and human. In the lower graph, locus A has a more recent common ancestor in human and gorilla compared to the chimp sequence. Whereas chimp and gorilla have a more recent common ancestor for locus B. Here the gene trees are incongruent to the species tree.
Another study sequenced 53 non-repetitive, intergenic DNA segments from human, chimpanzee, gorilla and orangutan. When the DNA sequences were concatenated to a single long sequence, the generated neighbor-joining tree supported the Homo-''Pan clade with 100% bootstrap. When three species are fairly closely related to each other, the trees obtained from DNA sequence data may not be congruent with the tree that represents the speciation.
The shorter the internodal time span, the more common are incongruent gene trees. The effective population size of the internodal population determines how long genetic lineages are preserved in the population. A higher effective population size causes more incongruent gene trees. Therefore, if the internodal time span is known, the ancestral effective population size of the common ancestor of humans and chimpanzees can be calculated.
When each segment was analyzed individually, 31 supported the Homo-Pan clade, 10 supported the Homo-Gorilla clade, and 12 supported the Pan-Gorilla clade. Using the molecular clock the authors estimated that gorillas split up first 6.2-8.4 MYA and chimpanzees and humans split up 1.6-2.2 million years later 4.6-6.2 MYA. The internodal time span is useful to estimate the ancestral effective population size of the common ancestor of humans and chimpanzees.
A parsimonious analysis revealed that 24 loci supported the Homo-Pan clade, 7 supported the Homo-Gorilla clade, 2 supported the Pan-Gorilla clade and 20 gave no resolution. Additionally they took 35 protein coding loci from databases. Of these 12 supported the Homo-Pan clade, 3 the Homo-Gorilla clade, 4 the Pan-Gorilla'' clade and 16 gave no resolution. Therefore, only ~70% of the 52 loci that gave a resolution support the 'correct' species tree. From the fraction of loci which did not support the species tree and the internodal time span they estimated previously, the effective population of the common ancestor of humans and chimpanzees was estimated to be ~52 000 to 96 000. This value is not as high as that from the first study, but still much higher than present day effective population size of humans.
A third study used the same dataset that Chen and Li used but estimated the ancestral effective population of 'only' ~12,000 to 21,000, using a different statistical method.