Human taxonomy

From Wikipedia, the free encyclopedia

The taxonomic classification of humans following John Edward Gray (1825).

 

Overview of speciation and hybridization within the genus Homo over the last two million years (vertical axis). The rapid "Out of Africa" expansion of H. sapiens is indicated at the top of the diagram, with admixture indicated with Neanderthals, Denisovans, and unspecified archaic African hominins.

 

Homo ("humans") Temporal range: Piacenzian-Present, 2.865–0 Ma PreЄ Є O S D C P T J K Pg N ↓
Scientific classification
Kingdom:	Animalia
Phylum:	Chordata
Class:	Mammalia
Order:	Primates
Suborder:	Haplorhini
Infraorder:	Simiiformes
Family:	Hominidae
Subfamily:	Homininae
Tribe:	Hominini
Genus:	Homo Linnaeus, 1758
Type species
Homo sapiens Linnaeus, 1758
Species
Homo sapiens †Homo erectus other species or subspecies suggested

Human taxonomy is the classification of the human species (systematic name Homo sapiens) within zoological taxonomy. The systematic genus, Homo, is designed to include both anatomically modern humans and extinct varieties of archaic humans.

Since the introduction of systematic names in the 18th century, knowledge of human evolution has increased drastically, and a number of intermediate taxa have been proposed in the 20th to early 21st century. The most widely accepted taxonomy groups takes the genus Homo as originating between two and three million years ago, divided into at least two species, archaic Homo erectus and modern Homo sapiens, with about a dozen further suggestions for species without universal recognition.

The genus Homo is placed in the tribe Hominini alongside Pan (chimpanzees). The two genera are estimated to have diverged over an extended time of hybridization spanning roughly 10 to 6 million years ago, with possible admixture as late as 4 million years ago. A subtribe of uncertain validity, grouping archaic "pre-human" or "para-human" species younger than the Homo-Pan split is Australopithecina (proposed in 1939).

A proposal by Wood and Richmond (2000) would introduce Hominina as a subtribe alongside Australopithecina, with Homo the only known genus within Hominina. Alternatively, following Cela-Conde and Ayala (2003), the "pre-human" or "proto-human" genera of Australopithecus, Ardipithecus, Praeanthropus, and possibly Sahelanthropus may be placed on equal footing alongside the genus Homo. An even more radical view rejects the division of Pan and Homo as separate genera, which based on the Principle of Priority would imply the re-classification of chimpanzees as Homo paniscus (or similar).

History

Human taxonomy on one hand involves the placement of humans within the Taxonomy of the hominids (great apes), and on the other the division of archaic and modern humans into species and, if applicable, subspecies. Modern zoological taxonomy was developed by Carl Linnaeus during the 1730s to 1750s. He named the human species as Homo sapiens in 1758, as the only member species of the genus Homo, divided into several subspecies corresponding to the great races. The Latin noun homō (genitive hominis) means "human being". The systematic name Hominidae for the family of the great apes was introduced by John Edward Gray (1825). Gray also supplied Hominini as the name of the tribe including both chimpanzees (genus Pan) and humans (genus Homo).

The discovery of the first extinct archaic human species from the fossil record dates to the mid 19th century, Homo neanderthalensis, classified in 1864. Since then, a number of other archaic species have been named, but there is no universal consensus as to their exact number. After the discovery of H. neanderthalensis, which even if "archaic" is recognizable as clearly human, late 19th to early 20th century anthropology for a time was occupied with finding the supposedly "missing link" between Homo and Pan. The "Piltdown Man" hoax of 1912 was the (fraudulent) presentation of such a transitional species. Since the mid-20th century, knowledge of the development of Hominini has become much more detailed, and taxonomical terminology has been altered a number of times to reflect this.

The introduction of Australopithecus as a third genus, alongside Homo and Pan, in the Hominini tribe is due to Raymond Dart (1925). Australopithecina as a subtribe containing Australopithecus as well as Paranthropus (Broom 1938) is a proposal by Gregory & Hellman (1939). More recently proposed additions to the Australopithecina subtribe include Ardipithecus (1995) and Kenyanthropus (2001). The position of Sahelanthropus (2002) relative to Australopithecina within Hominini is unclear. Cela-Conde and Ayala (2003) propose the recognition of Australopithecus, Ardipithecus, Praeanthropus, and Sahelanthropus (the latter incertae sedis) as separate genera.

Other proposed genera, now mostly considered part of Homo, include: Pithecanthropus (Dubois, 1894), Protanthropus (Haeckel, 1895), Sinanthropus (Black, 1927), Cyphanthropus (Pycraft, 1928) Africanthropus (Dreyer, 1935), Telanthropus (Broom & Anderson 1949), Atlanthropus (Arambourg, 1954), Tchadanthropus (Coppens, 1965).

The genus Homo has been taken to originate some two millions ago since the discovery of stone tools in Olduvai Gorge, Tanzania, in the 1960s. Homo habilis (Leakey et al., 1964) would be the first "human" species (member of genus Homo) by definition, its type specimen being the OH 7 fossils. However, the discovery of more fossils of this type has opened up the debate on the delineation of H. habilis from Australopithecus. Especially, the LD 350-1 jawbone fossil discovered in 2013, dated to 2.8 Mya, has been argued as being transitional between the two. It is also disputed whether H. habilis was the first hominin to use stone tools, as Australopithecus garhi, dated to c. 2.5 Mya, has been found along with stone tool implements. Fossil KNM-ER 1470 (discovered in 1972, designated Pithecanthropus rudolfensis by Alekseyev 1978) is now seen as either a third early species of Homo (alongside H. habilis and H. erectus) at about 2 million years ago, or alternatively as transitional between Australopithecus and Homo.

Wood and Richmond (2000) proposed that Gray's tribe Hominini ("hominins") be designated as comprising all species after the chimpanzee-human last common ancestor by definition, to the inclusion of Australopithecines and other possible pre-human or para-human species (such as Ardipithecus and Sahelanthropus) not known in Gray's time. In this suggestion, the new subtribe of Hominina was to be designated as including the genus Homo exclusively, so that Hominini would have two subtribes, Australopithecina and Hominina, with the only known genus in Hominina being Homo. Orrorin (2001) has been proposed as a possible ancestor of Hominina but not Australopithecina.

Designations alternative to Hominina have been proposed: Australopithecinae (Gregory & Hellman 1939) and Preanthropinae (Cela-Conde & Altaba 2002);

Species

At least a dozen species of Homo other than Homo sapiens have been proposed, with varying degrees of consensus. Homo erectus is widely recognized as the species directly ancestral to Homo sapiens. Most other proposed species are proposed as alternatively belonging to either Homo erectus or Homo sapiens as a subspecies. This concerns Homo ergaster in particular. One proposal divides Homo erectus into an African and an Asian variety; the African is Homo ergaster, and the Asian is Homo erectus sensu stricto. (Inclusion of Homo ergaster with Asian Homo erectus is Homo erectus sensu lato.) There appears to be a recent trend, with the availability of ever more difficult-to-classify fossils such as the Dmanisi skulls (2013) or Homo naledi fossils (2015) to subsume all archaic varieties under Homo erectus.

Subspecies

Homo sapiens subspecies

1737 painting of Carl von Linné wearing a traditional Sami costume, sometimes named as the lectotype of both H. sapiens and H. s. sapiens.

The recognition or non-recognition of subspecies of Homo sapiens has a complicated history. The rank of subspecies in zoology is introduced for convenience, and not by objective criteria, based on pragmatic consideration of factors such as geographic isolation and sexual selection. The informal taxonomic rank of race is variously considered equivalent or subordinate to the rank of subspecies, and the division of anatomically modern humans (H. sapiens) into subspecies is closely tied to the recognition of major racial groupings based on human genetic variation.

A subspecies cannot be recognized independently: a species will either be recognized as having no subspecies at all or at least two (including any that are extinct). Therefore, the designation of an extant subspecies Homo sapiens sapiens only makes sense if at least one other subspecies is recognized. H. s. sapiens is attributed to "Linnaeus (1758)" by the taxonomic Principle of Coordination. William Stearn (1959) in a "passing remark" argued that Linnaeus "must stand as the type of his Homo sapiens". Since Linnaeus describes H. s. europaeus as having blue/green (caerulus) eyes but himself had brown eyes, he cannot have included himself in H. s. europaeus, Linnaeus would therefore have to be classified as H. sapiens sapiens, as not matching any of the descriptions of his five subspecies, and so would stand as the lectotype both for H. sapiens, and for H. s. sapiens within his own subspecies nomenclature.

During the 19th to mid-20th century, it was common practice to classify the major divisions of extant H. sapiens as subspecies, following Linnaeus (1758), who had recognized H. s. americanus, H. s. europaeus, H. s. asiaticus and H. s. afer as grouping the native populations of the Americas, West Eurasia, East Asia and Sub-Saharan Africa, respectively, besides H. s. ferus (for the "wild" form which he identified with feral children) and two further "wild" forms for reported specimens now considered part of cryptozoology, H. s. monstrosus and H. s. troglodytes.

There were variations and additions to the categories of Linnaeus, such as H. s. tasmanianus for the native population of Australia. Bory de St. Vincent in his Essai sur l'Homme (1825) extended Linné's "racial" categories to as many as fifteen: Leiotrichi ("smooth-haired"): japeticus (with subraces), arabicus, indicus, scythicus, sinicus, hyperboreus, neptunianus, australasicus, columbicus, americanus, patagonicus; Oulotrichi ("crisp-haired"): aethiopicus, cafer, hottentotus, melaninus. Similarly, Georges Vacher de Lapouge (1899) also had categories based on race, such as priscus, spelaeus (etc.).

Homo sapiens neanderthalensis was proposed by King (1864) as an alternative to Homo neanderthalensis. There have been "taxonomic wars" over whether Neanderthals were a separate species since their discovery in the 1860s. Pääbo (2014) frames this as a debate that is unresolvable in principle, "since there is no definition of species perfectly describing the case." Louis Lartet (1869) proposed Homo sapiens fossilis based on the Cro-Magnon fossils.

There are a number of proposals of extinct varieties of Homo sapiens made in the 20th century. Many of the original proposals were not using explicit trinomial nomenclature, even though they are still cited as valid synonyms of H. sapiens by Wilson & Reeder (2005). These include: Homo grimaldii (Lapouge, 1906), Homo aurignacensis hauseri (Klaatsch & Hauser, 1910), Notanthropus eurafricanus (Sergi, 1911), Homo fossilis infrasp. proto-aethiopicus (Giuffrida-Ruggeri, 1915), Telanthropus capensis (Broom, 1917),^[39] Homo wadjakensis (Dubois, 1921), Homo sapiens cro-magnonensis, Homo sapiens grimaldiensis (Gregory, 1921), Homo drennani (Kleinschmidt, 1931), Homo galilensis (Joleaud, 1931) = Paleanthropus palestinus (McCown & Keith, 1932). Rightmire (1983) proposed Homo sapiens rhodesiensis.

By the 1980s, the practice of dividing extant populations of Homo sapiens into subspecies declined. An early authority explicitly avoiding the division of H. sapiens into subspecies was Grzimeks Tierleben, published 1967–1972. A late example of an academic authority proposing that the human racial groups should be considered taxonomical subspecies is John Baker (1974). The trinomial nomenclature Homo sapiens sapiens became popular for "modern humans" in the context of Neanderthals being considered a subspecies of H. sapiens in the second half of the 20th century. Derived from the convention, widespread in the 1980s, of considering two subspecies, H. s. neanderthalensis and H. s. sapiens, the explicit claim that "H. s. sapiens is the only extant human subspecies" appears in the early 1990s. This is only true if the nomenclature derived from Linnaeus is rejected. Based on Linnaeus (1758), there are at least six subspecies, with H. s. sapiens catching those specimens not included in any other.

Since the 2000s, the extinct Homo sapiens idaltu (White et al., 2003) has gained wide recognition as a subspecies of Homo sapiens, but even in this case there is a dissenting view arguing that "the skulls may not be distinctive enough to warrant a new subspecies name". H. s. neanderthalensis and H. s. rhodesiensis continue to be considered separate species by some authorities, but the genetic evidence of archaic human admixture with modern humans discovered in the 2010s has re-opened the details of taxonomy of archaic humans.

Homo erectus ssp.

Homo erectus since its introduction in 1892 has been divided into numerous subspecies, many of them formerly considered individual species of Homo. None of these subspecies have universal consensus among paleontologists.

• Homo erectus erectus (Java Man) (1970s)
• Homo erectus yuanmouensis (Yuanmou Man) (Li et al., 1977)
• Homo erectus lantianensis (Lantian Man) (Woo Ju-Kang, 1964)
• Homo erectus nankinensis (Nanjing Man) (1993)
• Homo erectus pekinensis (Peking Man) (1970s)
• Homo erectus palaeojavanicus (Meganthropus) (Tyler, 2001)
• Homo erectus soloensis (Solo Man) (Oppenoorth, 1932)
• Homo erectus tautavelensis (Tautavel Man) (de Lumley and de Lumley, 1971)
• Homo erectus georgicus (1991)
• Homo erectus bilzingslebenensis (Vlček, 2002)

Human evolutionary genetics

From Wikipedia, the free encyclopedia

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

Origin of apes

Hominin timeline

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Hominini

Nakalipithecus

Ouranopithecus

Sahelanthropus

Orrorin

Ardipithecus

Australopithecus

Homo habilis

Homo erectus

H. heidelbergensis

Homo sapiens

Neanderthals

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Earlier apes

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Gorilla split

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Possibly bipedal

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Chimpanzee split

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Earliest bipedal

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Stone tools

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Exit from Africa

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Earliest fire use

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Earliest cooking

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Earliest clothes

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Modern speech

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Modern humans

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Axis scale: million years

The taxonomic relationships of hominoids.

Biologists classify humans, along with only a few other species, as great apes (species in the family Hominidae). The living Hominidae include two distinct species of chimpanzee (the bonobo, Pan paniscus, and the common chimpanzee, Pan troglodytes), two species of gorilla (the western gorilla, Gorilla gorilla, and the eastern gorilla, Gorilla graueri), and two species of orangutan (the Bornean orangutan, Pongo pygmaeus, and the Sumatran orangutan, Pongo abelii). The great apes with the family Hylobatidae of gibbons form the superfamily Hominoidea of apes.

Apes, in turn, belong to the primate order (>400 species), along with the Old World monkeys, the New World monkeys, and others. Data from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) indicate that primates belong to the group of Euarchontoglires, together with Rodentia, Lagomorpha, Dermoptera, and Scandentia.^[1] This is further supported by Alu-like short interspersed nuclear elements (SINEs) which have been found only in members of the Euarchontoglires.^[2]

Cladistics

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 chimps is less than 2%, or twenty 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 lived roughly 200,000 years ago, latest common ancestors of humans and chimps between four and seven million years ago.

Speciation of humans and the African apes

The separation of humans from their closest relatives, the non-human apes (chimpanzees and gorillas), has been studied extensively for more than a century. Five major questions have been addressed:

1. Which apes are our closest ancestors?
2. When did the separations occur?
3. What was the effective population size of the common ancestor before the split?
4. Are there traces of population structure (subpopulations) preceding the speciation or partial admixture succeeding it?
5. What were the specific events (including fusion of chromosomes 2a and 2b) 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 (hg38) that had one-to-one exact matches in the chimpanzee genome (pantro6) 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 (IDs) between different primates. Basically the study measured the strength of immunological response that an antigen from one species (human albumin) induces in the immune system of another species (human, chimpanzee, gorilla and Old World monkeys). 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 (e.g. human to human) 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 (MYA), 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 (>15 MYA).

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 (using much more sophisticated methods in molecular genetics) 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

The sequences of the DNA segments diverge earlier than the species. A large effective population size in the ancestral population (left) preserves different variants of the DNA segments (=alleles) for a longer period of time. Therefore, on average, the gene divergence times (t_A for DNA segment A; t_B for DNA segment B) will deviate more from the time the species diverge (t_S) compared to a small ancestral effective population size (right).

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 (including humans) 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 can't tell absolute divergence times exactly, we can be pretty sure that the divergence time between chimpanzees and humans is about sixfold shorter than between chimpanzees (or humans) and monkeys.

One study (Takahata et al., 1995) 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 (and chimps) 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 (and thus genetic diversity) in its evolution.

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 (Chen & Li, 2001) sequenced 53 non-repetitive, intergenic DNA segments from a human, a chimpanzee, a 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 (that is that humans and chimpanzees are the closest related species of the four). When three species are fairly closely related to each other (like human, chimpanzee and gorilla), the trees obtained from DNA sequence data may not be congruent with the tree that represents the speciation (species tree).

The shorter internodal time span (T_IN) the more common are incongruent gene trees. The effective population size (N_e) 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 (internodal time span) 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 (33 intergenic, 19 protein coding) 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 (Takahata), but still much higher than present day effective population size of humans.

A third study (Yang, 2002) 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.

Genetic differences between humans and other great apes

The alignable sequences within genomes of humans and chimpanzees differ by about 35 million single-nucleotide substitutions. Additionally about 3% of the complete genomes differ by deletions, insertions and duplications.

Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage. Only a very tiny fraction of those fixed differences gave rise to the different phenotypes of humans and chimpanzees and finding those is a great challenge. The vast majority of the differences are neutral and do not affect the phenotype.

Molecular evolution may act in different ways, through protein evolution, gene loss, differential gene regulation and RNA evolution. All are thought to have played some part in human evolution.

Gene loss

Many different mutations can inactivate a gene, but few will change its function in a specific way. Inactivation mutations will therefore be readily available for selection to act on. Gene loss could thus be a common mechanism of evolutionary adaptation (the "less-is-more" hypothesis).

80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for olfactory receptors. Genes involved in chemoreception and immune response are overrepresented. Another study estimated that 86 genes had been lost.

Hair keratin gene KRTHAP1

A gene for type I hair keratin was lost in the human lineage. Keratins are a major component of hairs. Humans still have nine functional type I hair keratin genes, but the loss of that particular gene may have caused the thinning of human body hair. The study predicts the gene loss occurred relatively recently in human evolution—less than 240,000 years ago, but both the Vindija Neandertal and the high-sequence Denisovan sequence contain the same premature stop codons as modern humans.

Myosin gene MYH16

Stedman et al. (2004) stated that the loss of the sarcomeric myosin gene MYH16 in the human lineage led to smaller masticatory muscles. They estimated that the mutation that led to the inactivation (a two base pair deletion) occurred 2.4 million years ago, predating the appearance of Homo ergaster/erectus in Africa. The period that followed was marked by a strong increase in cranial capacity, promoting speculation that the loss of the gene may have removed an evolutionary constraint on brain size in the genus Homo.

Another estimate for the loss of the MYH16 gene is 5.3 million years ago, long before Homo appeared.

Other

CASPASE12, a cysteinyl aspartate proteinase. The loss of this gene is speculated to have reduced the lethality of bacterial infection in humans.

Gene addition

Segmental duplications (SDs or LCRs) have had roles in creating new primate genes and shaping human genetic variation.

Human-specific DNA insertions

When the human genome was compared to the genomes of five comparison primate species, including the chimpanzee, gorilla, orangutan, gibbon, and macaque, it was found that there are approximately 20,000 human-specific insertions believed to be regulatory. While most insertions appear to be fitness neutral, a small amount have been identified in positively selected genes showing associations to neural phenotypes and some relating to dental and sensory perception-related phenotypes. These findings hint at the seemingly important role of human-specific insertions in the recent evolution of humans.

Selection pressures

Human accelerated regions are areas of the genome that differ between humans and chimpanzees to a greater extent than can be explained by genetic drift over the time since the two species shared a common ancestor. These regions show signs of being subject to natural selection, leading to the evolution of distinctly human traits. Two examples are HAR1F, which is believed to be related to brain development and HAR2 (a.k.a. HACNS1) that may have played a role in the development of the opposable thumb.

It has also been hypothesized that much of the difference between humans and chimpanzees is attributable to the regulation of gene expression rather than differences in the genes themselves. Analyses of conserved non-coding sequences, which often contain functional and thus positively selected regulatory regions, address this possibility.

Sequence divergence between humans and apes

When the draft sequence of the common chimpanzee (Pan troglodytes) genome was published in the summer 2005, 2400 million bases (of ~3160 million bases) were sequenced and assembled well enough to be compared to the human genome. 1.23% of this sequenced differed by single-base substitutions. Of this, 1.06% or less was thought to represent fixed differences between the species, with the rest being variant sites in humans or chimpanzees. Another type of difference, called indels (insertions/deletions) accounted for many fewer differences (15% as many), but contributed ~1.5% of unique sequence to each genome, since each insertion or deletion can involve anywhere from one base to millions of bases.

A companion paper examined segmental duplications in the two genomes, whose insertion and deletion into the genome account for much of the indel sequence. They found that a total of 2.7% of euchromatic sequence had been differentially duplicated in one or the other lineage.

Percentage sequence divergence between humans and other hominids

Locus	Human-Chimp	Human-Gorilla	Human-Orangutan
Alu elements	2	-	-
Non-coding (Chr. Y)	1.68 ± 0.19	2.33 ± 0.2	5.63 ± 0.35
Pseudogenes (autosomal)	1.64 ± 0.10	1.87 ± 0.11	-
Pseudogenes (Chr. X)	1.47 ± 0.17	-	-
Noncoding (autosomal)	1.24 ± 0.07	1.62 ± 0.08	3.08 ± 0.11
Genes (Ks)	1.11	1.48	2.98
Introns	0.93 ± 0.08	1.23 ± 0.09	-
Xq13.3	0.92 ± 0.10	1.42 ± 0.12	3.00 ± 0.18
Subtotal for X chromosome	1.16 ± 0.07	1.47 ± 0.08	-
Genes (Ka)	0.8	0.93	1.96

The sequence divergence has generally the following pattern: Human-Chimp < Human-Gorilla << Human-Orangutan, highlighting the close kinship between humans and the African apes. Alu elements diverge quickly due to their high frequency of CpG dinucleotides which mutate roughly 10 times more often than the average nucleotide in the genome. The mutation rate is higher in the male germ line, therefore the divergence in the Y chromosome—which is inherited solely from the father—is higher than in autosomes. The X chromosome is inherited twice as often through the female germ line as through the male germ line and therefore shows slightly lower sequence divergence. The sequence divergence of the Xq13.3 region is surprisingly low between humans and chimpanzees.

Mutations altering the amino acid sequence of proteins (K_a) are the least common. In fact ~29% of all orthologous proteins are identical between human and chimpanzee. The typical protein differs by only two amino acids. The measures of sequence divergence shown in the table only take the substitutional differences, for example from an A (adenine) to a G (guanine), into account. DNA sequences may however also differ by insertions and deletions (indels) of bases. These are usually stripped from the alignments before the calculation of sequence divergence is performed.

Genetic differences between modern humans and Neanderthals

An international group of scientists completed a draft sequence of the Neanderthal genome in May 2010. The results indicate some breeding between modern humans (Homo sapiens) and Neanderthals (Homo neanderthalensis), as the genomes of non-African humans have 1-4% more in common with Neanderthals than do the genomes of subsaharan Africans. Neanderthals and most modern humans share a lactose-intolerant variant of the lactase gene that encodes an enzyme that is unable to break down lactose in milk after weaning. Modern humans and Neanderthals also share the FOXP2 gene variant associated with brain development and with speech in modern humans, indicating that Neanderthals may have been able to speak. Chimps have two amino acid differences in FOXP2 compared with human and Neanderthal FOXP2.

Genetic differences among modern humans

H. sapiens is thought to have emerged about 300,000 years ago. It dispersed throughout Africa, and after 70,000 years ago throughout Eurasia and Oceania. A 2009 study identified 14 "ancestral population clusters", the most remote being the San people of Southern Africa.

With their rapid expansion throughout different climate zones, and especially with the availability of new food sources with the domestication of cattle and the development of agriculture, human populations have been exposed to significant selective pressures since their dispersal. For example, East Asians have been found to be separated from Europids by a number of concentrated alleles suggestive of selection pressures, including variants of the EDAR, ADH1B, ABCC1, and ALDH2genes. The East Asian types of ADH1B in particular are associated with rice domestication and would thus have arisen after the development of rice cultivation roughly 10,000 years ago. Several phenotypical traits of characteristic of East Asians are due to a single mutation of the EDAR gene, dated to c. 35,000 years ago.

As of 2017, the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed a total of 324 million variants found in sequenced human genomes. Nucleotide diversity, the average proportion of nucleotides that differ between two individuals, is estimated at between 0.1% and 0.4% for contemporary humans (compared to 2% between humans and chimpanzees). This corresponds to genome differences at a few million sites; the 1000 Genomes Project similarly found that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence."