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Adna redirects here. For the unincorporated community in Washington, see Adna, Washington
Adna, Washington

Adna is an unincorporated community located in Lewis County, Washington. Due to its rural setting with little settlement concentration, it did not meet qualifications as a Census-designated place, a program used by the U.S....
.
Ancient DNA can be loosely described as any DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
 recovered from biological samples that have not been preserved specifically for later DNA analyses. Examples include the analysis of DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
 recovered from archaeological and historical skeletal material, mummified
Mummy

A mummy is a corpse whose skin and organs have been preserved by either intentional or incidental exposure to chemicals, extreme coldness, very high humidity, or lack of air when bodies are submerged in bogs....
 tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost
Permafrost

In geology, permafrost or permafrost soil is soil at or below the freezing point of water for two or more years. Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material....
 cores, Holocene plankton in marine and lake sediments, and so on.






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Encyclopedia


Adna redirects here. For the unincorporated community in Washington, see Adna, Washington
Adna, Washington

Adna is an unincorporated community located in Lewis County, Washington. Due to its rural setting with little settlement concentration, it did not meet qualifications as a Census-designated place, a program used by the U.S....
.
Ancient DNA can be loosely described as any DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
 recovered from biological samples that have not been preserved specifically for later DNA analyses. Examples include the analysis of DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
 recovered from archaeological and historical skeletal material, mummified
Mummy

A mummy is a corpse whose skin and organs have been preserved by either intentional or incidental exposure to chemicals, extreme coldness, very high humidity, or lack of air when bodies are submerged in bogs....
 tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost
Permafrost

In geology, permafrost or permafrost soil is soil at or below the freezing point of water for two or more years. Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material....
 cores, Holocene plankton in marine and lake sediments, and so on. Unlike modern genetic analyses, ancient DNA studies are characterised by low quality DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
. This places limits on what analyses can achieve. Furthermore, due to degradation of the DNA molecules, a process which correlates loosely with factors such as time, temperature and presence of free water, upper limits exist beyond which no DNA is deemed likely to survive. Current estimates suggest that in optimal environments, i.e environments which are very cold, such as permafrost or ice, an upper limit of max 1 Million years exists. As such, early studies that reported recovery of much older DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
, for example, from Cretaceous
Cretaceous

The Cretaceous , usually abbreviated K for its German translation Kreide, is a geologic period from circa to million years ago . In the geologic timescale, the Cretaceous follows on the Jurassic period and is followed by the Paleogene period....
 dinosaur
Dinosaur

Dinosaurs were the dominant vertebrate animals of Landform ecosystems for over 160 million years, from the late Triassic Period until the end of the Cretaceous Period , when most of them became extinct in the Cretaceous?Tertiary extinction event....
 remains, have been proven to be wrong, with results stemming from sample or extract contamination, as opposed to authentic extracted DNA.

History of Ancient DNA studies

Arguably the first aDNA study was in 1984, with a publication by Russ Higuchi and colleagues at Berkeley that was to revolutionise the scope of molecular biology
Molecular biology

Molecular biology is the study of biology at a molecule level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry....
, traces of DNA from a museum specimen of the Quagga
Quagga

The quagga is an List of extinct animals subspecies of the Plains zebra, which was once found in great numbers in South Africa's Cape Province and the southern part of the Orange Free State....
, not only remained in the specimen over 150 years after the death of the individual, but could be extracted and sequenced (Higuchi et al. 1984). Over the next two years, through investigations into natural and artificially mummified specimens, Svante Pääbo
Svante Pääbo

Svante P??bo is a biologist specializing in evolutionary genetics. He was born in 1955 in Stockholm, Sweden and earned his PhD from Uppsala University in 1986....
 both confirmed that this phenomenon was not limited to relatively recent museum specimens, but could apparently be replicated in a range of mummified
Mummy

A mummy is a corpse whose skin and organs have been preserved by either intentional or incidental exposure to chemicals, extreme coldness, very high humidity, or lack of air when bodies are submerged in bogs....
 human
Human

A human being, also human or man, is a member of a species of bipedalism primates in the family Hominidae . Mitochondrial DNA evidence indicates that modern humans originated in east Africa about 200,000 years ago....
 samples that dated as far back as several thousand years (Pääbo
Svante Pääbo

Svante P??bo is a biologist specializing in evolutionary genetics. He was born in 1955 in Stockholm, Sweden and earned his PhD from Uppsala University in 1986....
 1985a; Pääbo
Svante Pääbo

Svante P??bo is a biologist specializing in evolutionary genetics. He was born in 1955 in Stockholm, Sweden and earned his PhD from Uppsala University in 1986....
 1985b; Pääbo
Svante Pääbo

Svante P??bo is a biologist specializing in evolutionary genetics. He was born in 1955 in Stockholm, Sweden and earned his PhD from Uppsala University in 1986....
1986). Nevertheless, the laborious processes that were required at that time to sequence such DNA (through bacterial cloning) were an effective brake on the development of the field of ancient DNA (aDNA). However, with the development of the Polymerase Chain Reaction
Polymerase chain reaction

The polymerase chain reaction is a technique widely used in molecular biology. It derives its name from one of its key components, a DNA polymerase used to amplify a piece of DNA by in vitro enzyme DNA replication....
 (PCR) (Mullis and Faloona 1987; Saiki et al. 1988) in the late 1980s the field was presented with the ability to rapidly progress.

Double primers PCR amplification of aDNA (jumping-PCR) can produce highly-skewed and non-authentic sequence artifacts. Multiple primer, nested PCR
Nested polymerase chain reaction

Nested polymerase chain reaction is a modification of polymerase chain reaction intended to reduce the contamination in products due to the amplification of unexpected primer binding sites....
 strategy was used to overcome those shortcomings.

Single primer extension (abr. SPEX) amplification was introduced in 2007 to address post mortem DNA modification damage.

Problems and errors

aDNA may contain a large number of post mortem mutations, increasing with time. Some regions of polynucleotide are more susceptible to this degradation so sequence data can bypass statistical filters used to check the validity of data.

Antediluvian DNA studies

The post-PCR era heralded a wave of publications as numerous research groups tried their hands at aDNA. Soon a series of incredible findings had been published, claiming authentic DNA could be extracted from specimens that were millions of years old, into the realms of what Lindahl (1993b) has labelled Antediluvian
Antediluvian

The antediluvian period is that period in Biblical history between the Creation according to Genesis of the earth and the Deluge. The story takes up chapters 1-6 of Genesis....
 DNA. The majority of such claims were based on the retrieval of DNA from organisms preserved in amber
Amber

Amber is fossil tree resin, which is appreciated for its color and beauty. Good quality amber is used for the manufacture of ornamental objects and jewelry....
. Insects such as stingless bees (Cano et al. 1992a; Cano et al. 1992b), termites (De Salle et al. 1992; De Salle et al. 1993) and wood gnats (De Salle and Grimaldi 1994), as well as plant (Poinar
Hendrik Poinar

Hendrik Nicholas Poinar is an evolutionary biologist specializing in ancient DNA. Poinar first became widely known for successfully extracting DNA sequences from ground sloth coprolites....
 et al. 1993) and bacterial (Cano et al. 1994) sequences were extracted from Dominica
Dominica

The Commonwealth of Dominica, commonly known as Dominica, is an island nation in the Caribbean Sea. To the north/northwest lies Guadeloupe, to the southeast Martinique....
n amber dating to the Oligocene
Oligocene

The Oligocene is a geologic epoch of the Paleogene Geologic Timescale and extends from about 33.9 million to 23 million years before the present....
 epoch. Still older sources of Lebanese amber-encased weevil
Weevil

A weevil is any beetle from the Curculionidae superfamily. They are usually small, less than 6 mm , and Herbivore. Due to the shape of their heads, weevils are commonly known as snout beetles....
s, dating to within the Cretaceous epoch, reportedly also yielded authentic DNA (Cano et al. 1993). DNA retrieval was also not limited to amber. Several sediment-preserved plant remains dating to the Miocene
Miocene

The Miocene is a Geologic time scale of the Neogene period and extends from about 23.03 to 5.33 million years before the present. As with other older geologic periods, the rock beds that define the start and end are well identified but the exact dates of the start and end of the period are uncertain....
 were successfully investigated (Golenberg et al. 1990; Golenberg 1991). Then, in 1994 and to international acclaim, Woodward et al. reported the most exciting results to date -mitochondrial cytochrome b sequences that had apparently been extracted from dinosaur bones dating to over 80 million years ago. When in 1995 two further studies reported dinosaur DNA sequences extracted from a Cretaceous egg (An et al. 1995; Li et al. 1995) it seemed that the field would truly revolutionise knowledge of the Earth’s evolutionary past. Unfortunately the golden days of aDNA did not last. A critical review of ancient DNA literature through the development of the field highlights that, with two famous but highly criticised exceptions that claim the retrieval of 250 million years old halobacterial sequences from Halite
Halite

Halite is the mineral form of sodium chloride, sodiumchlorine, commonly known as rock salt. Halite forms Cubic crystals. The mineral is typically colorless to yellow, but may also be light blue, dark blue, and pink depending on the amount and type of impurities....
 (Vreeland et al. 2000; Fish et al. 2002), few recent studies have succeeded in amplifying DNA from remains older than several hundred thousand years (ky) (c.f. Willerslev et al. 2003). The Dinosaur DNA was later revealed to be human Y-Chromosome (Zischler et al. 1996)

Ancient DNA studies

Despite the problems associated with ‘antediluvian’ DNA, a wide, and ever-increasing range of aDNA sequences have now been published from a range of animal and plant taxa
Taxon

A taxon or taxonomic unit is a name designating an organism or a group of organisms. In biological nomenclature according to Carl Linnaeus, a taxon is assigned a taxonomic rank and can be placed at a particular level in a systematic hierarchy reflecting evolutionary relationships....
. Tissues examined include artificially or naturally mummified animal remains (c.f. Higuchi et al. 1984; Thomas et al. 1989), bone (c.f. Hagelberg et al. 1989; Cooper et al. 1992; Hänni et al. 1994b; Hagelberg et al. 1994), paleofaeces (Poinar
Hendrik Poinar

Hendrik Nicholas Poinar is an evolutionary biologist specializing in ancient DNA. Poinar first became widely known for successfully extracting DNA sequences from ground sloth coprolites....
 et al. 1998; Hofreiter et al. 2000), alcohol preserved specimens (Junqueira et al. 2002), rodent middens (Küch et al. 2002), dried plant remains (Goloubinoff et al. 1993; Dumolin-Lapegue et al. 1999) and recently, extractions of animal and plant DNA directly from soil
Soil

Soil is the naturally occurring, unconsolidated or loose covering on the Earth's surface. Soil is composed of particles of broken rock that have been altered by chemical and environmental processes including weathering and erosion....
 samples (Willerslev et al. 2005).

Ancient DNA studies on human remains

Due to the considerable anthropological
Anthropology

Anthropology is the study of humans and humanity in its totality. Anthropology has origins in the natural sciences, and the humanities. In Great Britain it was originally divided into physical anthropology and cultural anthropology, which itself was divided into archaeology, technology, ethnology and sociology ....
, archaeological
Archaeology

Archaeology, archeology, or arch?ology is the science that studies Homo cultures through the recovery, documentation, analysis, and interpretation of material remains and environmental data, including architecture, Artifact , features, Biofact s, and cultural landscape....
, and public interest
Public interest

The public interest refers to the "common well-being" or "general welfare." The public interest is central to policy debates, politics, democracy and the nature of government itself....
 directed towards human remains, it is only natural that they have received a similar amount of attention from the DNA community. Due to their obvious signs of morphological
Comparative anatomy

Comparative anatomy is the study of similarities and differences in the anatomy of organisms. It is closely related to evolutionary biology and phylogeny ....
 preservation, many studies utilised mummified tissue as a source of ancient human DNA. Examples include both naturally preserved specimens, for example those preserved in ice, such as the Ötzi the Iceman
Ötzi the Iceman

?tzi the Iceman , and Similaun Man are modern names of a well-preserved natural mummy of a man from about 34th century BC . The mummy was found in 1991 in the Schnalstal glacier in the ?tztal Alps, near Hauslabjoch on the border between Austria and Italy....
 (Handt et al. 1994), or through rapid desiccation
Desiccation

Desiccation is the state of extreme dryness, or the process of extreme drying. A desiccant is a hygroscopic substance that induces or sustains such a state in its local vicinity in a moderately-well sealed container....
, for example high-altitude mummies from the Andes (c.f. Pääbo 1986; Montiel et al. 2001)), as well as various sources of artificially preserved tissue (such as the chemically treated mummies of ancient Egypt (c.f. Hänni et al. 1994a)). However, mummified remains are a limited resource, and the majority of human aDNA studies have focused on extracting DNA from two sources that are much more common in the archaeological record
Archaeological record

The archaeological record is a term used in archaeology to denote all archaeological evidence, including the physical remains of past human activities which archaeologists seek out and record in an attempt to analyze and reconstruct the past....
 – bone
Bone

Bones are rigid organ that form part of the endoskeleton of vertebrates. They function to move, support, and protect the various organs of the body, produce red blood cell and white blood cells and store minerals....
 and teeth
Tooth

Teeth are small whitish structures found in the jaws of many vertebrates that are used to tear, scrape, and chew food. Some animals, particularly carnivores, also use teeth for hunting or defense....
. Recently, several other sources have also yielded DNA, including paleofaeces
Coprolite

A coprolite is fossilized animal dung. Coprolites are classified as Trace fossil as opposed to body fossils, as they give evidence for the animal's behaviour rather than morphology....
 (Poinar
Hendrik Poinar

Hendrik Nicholas Poinar is an evolutionary biologist specializing in ancient DNA. Poinar first became widely known for successfully extracting DNA sequences from ground sloth coprolites....
 et al. 2001) and hair
Hair

Hair is a protein filament that epidermal growth from hair follicle deep within the dermis. The fine, soft hair found on many nonhuman mammals is typically called fur; wool is the characteristically curly hair found on sheep and goats....
 (Baker et al. 2001, Gilbert et al. 2004). Contamination remains a major problem when working on ancient human material.

Neanderthal
  • mtDNA
Neanderthal
Neanderthal

The Neanderthal , or Neandertal, is an extinct member of the Homo genus that is known from Pleistocene specimens found in Europe and parts of western and central Asia....
 ancient mtDNA was partially sequenced in the HVR region for following specimens: Feldhofer 1
Neanderthal 1

Feldhofer 1, Neanderthal 1 is the common name for the initial 40 ky old Neanderthal specimen found in Kleine Feldhofer Grotte in August 1856....
 ,Feldhofer 2 from Germany , Mezmaiskaya from the Russian Caucasus; Vindija 75 , Vindija 77, Vindija 80 from Croatia; Engis 2 from Belgium; La Chapelle-aux-Saints from France; El Sidrón
Sidrón Cave

The Sidr?n Cave is an ancient cave in Pilo?a municipality, Asturias, northwestern Spain, where Paleolithic rock art and Neanderthal remains have been found....
: 441, 1253, and 1351c from Spain; and Rochers-de-Villeneuve from France and Riparo Mezzena from Itally.

  • Chromosomal DNA


Two distinct Neanderthals from El Sidrón cave (1253 and 1351c) have the same mutations at position A-911, G-977 in exon 7 of FOXP2
FOXP2

FOXP2 is a gene that is implicated in the Language development, including grammatical competence....
 gene as present day people.

Pathogen and microorganism aDNA analyses using human remains

The use of degraded human samples in aDNA analyses has not been limited to the amplification of human DNA. It is reasonable to assume that for a period of time post mortem, DNA may survive from any microorganisms present in the specimen at death. This not only includes pathogens present at the time of death (either the cause of death or long-term infections) but commensals and other associated microbes. Despite several studies that have reported limited preservation of such DNA, for example the lack of preservation of Helicobacter pylori
Helicobacter pylori

Helicobacter pylori is a Gram-negative, microaerophile bacterium that inhabits various areas of the stomach and duodenum. It causes a chronic low-level inflammation of the stomach lining and is strongly linked to the development of duodenal and gastric peptic ulcers and stomach cancer bacteria....
 in ethanol-preserved specimens dating to the 18th century (Barnes et al. 2000), over 45 published studies report the successful retrieval of ancient pathogen
Pathogen

A pathogen , infectious agent, or germ, is a biological agent that causes disease or illness to its Host .There are several substrates and pathways whereby pathogens can invade a host; the principal pathways have different episodic time frames, but soil contamination has the longest or most persistent potential for harboring...
 DNA from samples dating back to over 5,000 years old in humans, and as long as 17,000 years ago in other species. As well as the usual sources of mummified tissue, bones and teeth, such studies have also examined a range of other tissue samples, including calcified pleura
Pleural cavity

In human anatomy, the pleural cavity is the body cavity that surrounds the lungs. The lungs are surrounded by the pleurae, a serous membrane which folds back upon itself to form a two-layered, membrane structure....
 (Donoghue et al. 1998), tissue embedded in paraffin
Paraffin

In chemistry, paraffin is the common name for the alkane hydrocarbons with the general formula CnH2n+2. Paraffin wax refers to the solids with n=20–40....
 (Jackson et al. 1998; Basler et al. 2001), and formalin-fixed tissue (Taubenberger et al. 1997).la

Researchers specializing in ancient DNA



  • Lori Baker
  • Gila Kahila Bar-Gal
  • Ian Barnes
  • Deborah Bolnick
  • Abigail Bouwman
  • Terry A. Brown
  • Joachim Burger
  • Ruth Bollongino
  • Graciela Cabana
  • David Caramelli
  • Marco J.L. Coolen
  • Jason A. Eshleman
  • Marina Faerman
  • E.L. Rodriguez Florez
  • Carles Lalueza Fox
  • Eva-Maria Geigl
  • M. Thomas P. Gilbert
  • Chuck Greenblatt
  • Martin Bay Hebsgaard
    Martin Bay Hebsgaard

    Martin Bay Hebsgaard is an evolutionary biology known for applying evolutionary methods on the geologically ancient DNA. He has also pioneered in the work of applying ancient DNA techniques systematically to anthropogenic sediment layers in order to investigate the methods potential in archaeology....
  • Michael Hofreiter
  • K. Ann Horsburgh
  • Susanne Hummel
  • Frederika Kaestle
  • Brian M. Kemp
  • Diana M. Lawrence
  • Cecil M. Lewis Jr.
  • Odile Loreille
  • Ripan Malhi
  • Carney Matheson
  • Lisa Matisoo-Smith
  • Cara Monroe
  • Connie Mulligan
  • Dennis H. O'Rourke
  • Svante Pääbo
    Svante Pääbo

    Svante P??bo is a biologist specializing in evolutionary genetics. He was born in 1955 in Stockholm, Sweden and earned his PhD from Uppsala University in 1986....
  • Hendrik Poinar
    Hendrik Poinar

    Hendrik Nicholas Poinar is an evolutionary biologist specializing in ancient DNA. Poinar first became widely known for successfully extracting DNA sequences from ground sloth coprolites....
  • Carsten Pusch
  • Beth Shapiro
    Beth Shapiro

    Beth Shapiro is an evolutionary molecular biologist in the department of biology at the Pennsylvania State University. She was formerly a researcher in the department of zoology at Oxford University....
  • Beth Shook
  • David Glenn Smith
  • Meradeth Snow
  • Mark Spiegelman
  • Anne C. Stone
  • Mark G. Thomas
    Mark G. Thomas

    Mark G. Thomas is a human evolutionary geneticist, Senior Lecturer in the Research Department of Genetics, Evolution and Environment at University College London....
  • Eske Willerslev
    Eske Willerslev

    Eske Willerslev is a Denmark evolutionary biologist notable for his pioneering work on Ancient DNA. He is currently a full professor at Copenhagen University and leader of the Ancient DNA and Evolution Group....
  • Dongya Yang
  • Andrew Rambaut
  • Alexei Drummond

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  • Basler CF, Reid AH, Dybing JK, Janczewski T A, Fanning TG, Zheng H, Salvatore M, Perdue ML, Swayne DE, Garcia-Sastre A, Palese P, Taubenberger JK. 2001. Sequence of the 1918 pandemic influenza virus non-structural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes. Proc Natl Acad Sci USA 98:2746-2751
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Conferences

  • - The 9th International Conference on Ancient DNA and Associated Biomolecules will be held in Pompeii (Naples), Italy, from October 19 to October 22, 2008


See also

  • List of DNA tested mummies
    List of DNA tested mummies

    This is a list of Mummy and ancient humans remains that have been genealogical DNA test along with a brief description of when and where they lived....
  • List of genetic results derived from historical figures
    List of genetic results derived from historical figures

    This is a list of haplogroups of historical and famous figures. Haplogroups can be determined from the remains of historical figures, or derived from genealogical DNA tests of people who trace their direct maternal or paternal ancestry to a noted historical figure....
  • Human mitochondrial DNA haplogroups
    Human mitochondrial DNA haplogroups

    In human genetics, a human mitochondrial DNA haplogroup is a haplogroup defined by differences in Human mitochondrial genetics. These haplogroups have led some researchers to trace the matrilineal inheritance of modern humans back to human origins in Africa and the subsequent spread across the globe....
  • Human Y-chromosome DNA haplogroup
  • Phylogenetic tree
    Phylogenetic tree

    A phylogenetic tree or evolutionary tree is a tree showing the evolutionary relationships among various biological species or other entities that are believed to have a common descent....
  • Tyrannosaurus#Soft tissue
    Tyrannosaurus

    Tyrannosaurus is a genus of theropod dinosaur. The famous species Tyrannosaurus rex , commonly abbreviated to T. rex, is a fixture in popular culture around the world....
    , Dinosaur mummy


External links

  • - mtDNA analysis.
  • (PDF) better link http://www.pnas.org/cgi/content/full/98/23/13460 - mtDNA
  • - no data on YDNA only mtDNA
  • - samples from USA no sequence data here.