Paleogenetics

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Paleogenetics is the study of the past through the examination of preserved genetic material from the remains of ancient organisms. [1] [2] Emile Zuckerkandl and Linus Pauling introduced the term in 1963, long before the sequencing of DNA, in reference to the possible reconstruction of the corresponding polypeptide sequences of past organisms. [3] The first sequence of ancient DNA, isolated from a museum specimen of the extinct quagga, was published in 1984 by a team led by Allan Wilson. [4]

Contents

Paleogeneticists do not recreate actual organisms, but piece together ancient DNA sequences using various analytical methods. [5] Fossils are "the only direct witnesses of extinct species and of evolutionary events" [6] and finding DNA within those fossils exposes tremendously more information about these species, potentially their entire physiology and anatomy.

The most ancient DNA sequence to date was reported in February 2021, from the tooth of a Siberian mammoth frozen for over a million years. [7] [8]

Applications

Evolution

Similar sequences are often found along DNA (and the derived protein polypeptide chains) in different species. This similarity is directly linked to the sequence of the DNA (the genetic material of the organism). Due to the improbability of this being random chance, and its consistency too long to be attributed to convergence by natural selection, these similarities can be plausibly linked to the existence of a common ancestor with common genes. This allows DNA sequences to be compared between species. Comparing an ancient genetic sequence to later or modern ones can be used to determine ancestral relations, while comparing two modern genetic sequences can determine, within error, the time since their last common ancestor. [3]

Human evolution

Using the thigh bone of a Neanderthal female, 63% of the Neanderthal genome was recovered and 3.7 billion bases of DNA were decoded. [9] [10] It showed that Homo neanderthalensis was the closest living relative of Homo sapiens, until the former lineage died out 30,000 years ago. The Neanderthal genome was shown to be within the range of variation of those of anatomically modern humans, although at the far periphery of that range of variation. Paleogenetic analysis also suggests that Neanderthals shared slightly more DNA with chimpanzees than homo sapiens. [10] It was also found that Neanderthals were less genetically diverse than modern humans, which indicates that Homo neanderthalensis grew from a group composed of relatively few individuals. [10] DNA sequences suggest that Homo sapiens first appeared between about 130,000 and 250,000 years ago in Africa. [10]

Paleogenetics opens up many new possibilities for the study of hominid evolution and dispersion. By analyzing the genomes of hominid remains, their lineage can be traced back to from where they came, or from where they share a common ancestor. The Denisova hominid, a species of hominid found in Siberia from which DNA was able to be extracted, may show signs of having genes that are not found in any Neanderthal nor Homo sapiens genome, possibly representing a new lineage or species of hominid. [11]

Evolution of culture

Looking at DNA can give insight into lifestyles of people of the past. Neandertal DNA shows that they lived in small temporary communities. [10] DNA analysis can also show dietary restrictions and mutations, such as the fact that Homo neanderthalensis was lactose-intolerant. [10]

Archaeology

Ancient disease

Studying DNA of the deceased also allows us to look at the medical history of the human species. By looking back we can discover when certain diseases first appeared and began to afflict humans.

Ötzi

The oldest case of Lyme disease was discovered in the genome[ clarification needed ] on Ötzi the Iceman. [12] Ötzi died around 3,300 B.C., and his remains were discovered frozen in the Eastern Alps in the early 1990s, and his genetic material was analyzed in the 2010s. [12] Genetic remains of the bacterium that causes Lyme disease, Borrelia burgdorferi, were discovered in the body. [12]

Domestication of animals

Not only can past humans be investigated through paleogenetics, but the organisms they had an effect on can also be examined. Through examination of the divergence found in domesticated species such as cattle and the archaeological record from their wild counterparts; the effect of domestication can be studied, which could tell us a lot about the behaviors of the cultures that domesticated them. The genetics of these animals also reveals traits not shown in the paleontological remains, such as certain clues as to the behavior, development, and maturation of these animals. The diversity in genes can also tell where the species were domesticated, and how these domesticates migrated from these locations elsewhere. [6]

Challenges

Ancient remains usually contain only a small fraction of the original DNA of an organism. [3] [13] This is due to the degradation of DNA in dead tissue by biotic and abiotic decay. DNA preservation depends on a number of environmental characteristics, including temperature, humidity, oxygen and sunlight. Remains from regions with high heat and humidity typically contain less intact DNA than those from permafrost or caves, where remains may persist in cold, low oxygen conditions for several hundred thousand years. [14] In addition, DNA degrades much more quickly following excavation of materials, and freshly excavated bone has a much higher chance of containing viable genetic material. [6] After excavation, bone may also become contaminated with modern DNA (i.e. from contact with skin or unsterilized tools), which can create false-positive results. [6]

See also

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Homininae, also called "African hominids" or "African apes", is a subfamily of Hominidae. It includes two tribes, with their extant as well as extinct species: 1) the tribe Hominini ―and 2) the tribe Gorillini (gorillas). Alternatively, the genus Pan is sometimes considered to belong to its own third tribe, Panini. Homininae comprises all hominids that arose after orangutans split from the line of great apes. The Homininae cladogram has three main branches, which lead to gorillas, and to humans and chimpanzees via the tribe Hominini and subtribes Hominina and Panina. There are two living species of Panina and two living species of gorillas, but only one extant human species. Traces of extinct Homo species, including Homo floresiensis have been found with dates as recent as 40,000 years ago. Organisms in this subfamily are described as hominine or hominines.

<span class="mw-page-title-main">Early modern human</span> Old Stone Age Homo sapiens

Early modern human (EMH), or anatomically modern human (AMH), are terms used to distinguish Homo sapiens that are anatomically consistent with the range of phenotypes seen in contemporary humans, from extinct archaic human species. This distinction is useful especially for times and regions where anatomically modern and archaic humans co-existed, for example, in Paleolithic Europe. Among the oldest known remains of Homo sapiens are those found at the Omo-Kibish I archaeological site in south-western Ethiopia, dating to about 233,000 to 196,000 years ago, the Florisbad site in South Africa, dating to about 259,000 years ago, and the Jebel Irhoud site in Morocco, dated about 315,000 years ago.

<span class="mw-page-title-main">Genome project</span>

Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.

Archaeogenetics is the study of ancient DNA using various molecular genetic methods and DNA resources. This form of genetic analysis can be applied to human, animal, and plant specimens. Ancient DNA can be extracted from various fossilized specimens including bones, eggshells, and artificially preserved tissues in human and animal specimens. In plants, ancient DNA can be extracted from seeds and tissue. Archaeogenetics provides us with genetic evidence of ancient population group migrations, domestication events, and plant and animal evolution. The ancient DNA cross referenced with the DNA of relative modern genetic populations allows researchers to run comparison studies that provide a more complete analysis when ancient DNA is compromised.

<i>Homo</i> Genus of hominins that includes humans and their closest extinct relatives

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<span class="mw-page-title-main">Neanderthal extinction</span> Prehistoric event

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<span class="mw-page-title-main">Steinheim skull</span> Hominin fossil

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<span class="mw-page-title-main">Timeline of human evolution</span>

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A number of varieties of Homo are grouped into the broad category of archaic humans in the period that precedes and is contemporary to the emergence of the earliest early modern humans around 300 ka. Among the earliest remains of H. sapiens are those from Jebel Irhoud in Morocco, Florisbad in South Africa (259 ka), and Omo-Kibish I in southern Ethiopia. The term typically includes H. antecessor, H. bodoensis, Denisovans (H. denisova), H. heidelbergensis (600–200 ka), Neanderthals, and H. rhodesiensis (300–125 ka).

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<span class="mw-page-title-main">Early human migrations</span> Spread of humans from Africa through the world

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<span class="mw-page-title-main">Self-domestication</span> Scientific hypothesis in ethnobiology


Self-domestication is a scientific hypothesis that suggests that, similar to domesticated animals, there has been a process of artificial selection among members of the human species conducted by humans themselves. In this way, during the process of hominization, a preference for individuals with collaborative and social behaviors would have been shown to optimize the benefit of the entire group: docility, language, and emotional intelligence would have been enhanced during this process of artificial selection. The hypothesis is raised that this is what differentiated Homo sapiens from Homo neanderthalensis and Homo erectus.

<span class="mw-page-title-main">Hominidae</span> Family of primates

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<span class="mw-page-title-main">Denisova Cave</span> Cave and archaeological site in Russia

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<span class="mw-page-title-main">Scladina</span> Caves and archaeological site in Belgium

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The diet of known human ancestors varies dramatically over time. Strictly speaking, according to evolutionary anthropologists and archaeologists, there is not a single hominin Paleolithic diet. The Paleolithic covers roughly 2.8 million years, concurrent with the Pleistocene, and includes multiple human ancestors with their own evolutionary and technological adaptations living in a wide variety of environments. This fact with the difficulty of finding conclusive evidence often makes broad generalizations of the earlier human diets very difficult. Our pre-hominin primate ancestors were broadly herbivorous, relying on either foliage or fruits and nuts and the shift in dietary breadth during the Paleolithic is often considered a critical point in hominin evolution. A generalization between Paleolithic diets of the various human ancestors that many anthropologists do make is that they are all to one degree or another omnivorous and are inextricably linked with tool use and new technologies. Nonetheless, according to the California Academy of Sciences, "Prior to about 3.5 million years ago, early humans dined almost exclusively on leaves and fruits from trees, shrubs, and herbs—similar to modern-day gorillas and chimpanzees."

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