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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]
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]
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]
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]
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]
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.
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]
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]
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]
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.
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.
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.
Homo is a monotypic genus that emerged from the genus Australopithecus and encompasses the extant species Homo sapiens and several extinct species classified as either ancestral to or closely related to modern humans, including Homo erectus and Homo neanderthalensis. The oldest member of the genus is Homo habilis, with records of just over 2 million years ago. Homo, together with the genus Paranthropus, is probably sister to Australopithecus africanus, which itself had split from the lineage of Pan, the chimpanzees.
Neanderthals became extinct around 40,000 years ago. Hypotheses on the causes of the extinction include violence, transmission of diseases from modern humans which Neanderthals had no immunity to, competitive replacement, extinction by interbreeding with early modern human populations, natural catastrophes, climate change and inbreeding depression. It is likely that multiple factors caused the demise of an already low population.
The Steinheim skull is a fossilized skull of a Homo neanderthalensis or Homo heidelbergensis found on 24 July 1933 near Steinheim an der Murr, Germany.
The timeline of human evolution outlines the major events in the evolutionary lineage of the modern human species, Homo sapiens, throughout the history of life, beginning some 4 billion years ago down to recent evolution within H. sapiens during and since the Last Glacial Period.
Human taxonomy is the classification of the human species within zoological taxonomy. The systematic genus, Homo, is designed to include both anatomically modern humans and extinct varieties of archaic humans. Current humans have been designated as subspecies Homo sapiens sapiens, differentiated, according to some, from the direct ancestor, Homo sapiens idaltu.
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).
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.
The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.
Early human migrations are the earliest migrations and expansions of archaic and modern humans across continents. They are believed to have begun approximately 2 million years ago with the early expansions out of Africa by Homo erectus. This initial migration was followed by other archaic humans including H. heidelbergensis, which lived around 500,000 years ago and was the likely ancestor of Denisovans and Neanderthals as well as modern humans. Early hominids had likely crossed land bridges that have now sunk.
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.
The Hominidae, whose members are known as the great apes or hominids, are a taxonomic family of primates that includes eight extant species in four genera: Pongo ; Gorilla ; Pan ; and Homo, of which only modern humans remain.
In paleoanthropology, the recent African origin of modern humans or the "Out of Africa" theory (OOA) is the most widely accepted model of the geographic origin and early migration of anatomically modern humans. It follows the early expansions of hominins out of Africa, accomplished by Homo erectus and then Homo neanderthalensis.
Denisova Cave is a cave in the Bashelaksky Range of the Altai mountains, Siberian Federal District, Russia. The cave has provided items of great paleoarchaeological and paleontological interest. Bone fragments of the Denisova hominin originate from the cave, including artifacts dated to around 40,000 BP. Remains of a 32,000-year-old prehistoric species of horse has also been found in the cave.
Molecular paleontology refers to the recovery and analysis of DNA, proteins, carbohydrates, or lipids, and their diagenetic products from ancient human, animal, and plant remains. The field of molecular paleontology has yielded important insights into evolutionary events, species' diasporas, the discovery and characterization of extinct species. loo In shallow time, advancements in the field of molecular paleontology have allowed scientists to pursue evolutionary questions on a genetic level rather than relying on phenotypic variation alone. By applying molecular analytical techniques to DNA in Recent animal remains, one can quantify the level of relatedness between any two organisms for which DNA has been recovered. Using various biotechnological techniques such as DNA isolation, amplification, and sequencing scientists have been able to gain expanded new insights into the divergence and evolutionary history of countless recently extinct organisms. In February 2021, scientists reported, for the first time, the sequencing of DNA from animal remains, a mammoth in this instance, over a million years old, the oldest DNA sequenced to date.
Scladina, or Sclayn Cave, is an archaeological site located in Wallonia in the town of Sclayn, in the Andenne hills in Belgium, where excavations since 1978 have provided the material for an exhaustive collection of over thirteen thousand Mousterian stone artifacts and the fossilized remains of an especially ancient Neanderthal, called the Scladina child were discovered in 1993.
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."