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Intro to aDNA and bioarchaeology
 

Intro to aDNA and bioarchaeology

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With case study of Cypriot Hippos

With case study of Cypriot Hippos

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  • MutationSelection
  • Integrity of cells is continually maintained in lving organisms-When death occurs, maintenance stops and DNA is rapidly degraded by enzymesFaces an onslaught of bacteria, fungi and insetcts that break down the macro moleculesOnce macro molecules are gone, so is the DNA!Even in best preservation, DNA slowly degrades and eventually loses its integrity and decomposes
  • Many ancient samples have no detectable DNA (with current techniques)Of 24 Neanderthal remains, only 4 had any recoverable DNAPrimers designed to pick up aDNA of Neanderthal and cave bear so similar to modern humans that we may amplify these insteadNeed for some kind of standard criteria
  • Based on rates of DNA damage… survival of millions of years? Not likely… Recent studies that have retrieved a 124bp segment of pygmy elephant from the Mediteranean that dates over 100kya
  • Paisley Caves
  • 1918 flu epidemicone of the deadliest natural disasters in human historykilledbtwn 50-130 million people globallyas much as 27% of global population was infectedmost lethal in healthy adults
  • not the species I will be evaluating, but comparable in sizeI plan to look at the extinction of the pygmy hippo from Cyprus. Attempting to evaluate the cause for its extinction and relate it to the current debate over climate vs. human overkill.
  • I’m starting by evaluating an island species because it conveniently eliminates the need to account for emigration and immigration. Cyprus has been biogeographically isolated for 5.3my, and even before then was only connected to mainland by an impassable salt dessert.So, fauna is likely to be unique in composition, and the island environment should amplify the effects of any outside stressors.
  • this is the site. level 2, level 4debate over where the coastline was at time of depositionbone bed in level 4
  • thumbnail scrapers
  • over 80% of the bones are in level 4, over 90% of the artifacts are in level 2the current literature leans in favor of human overkill, although there has been much debate. Despite the overwhelming number of bones, or perhaps because of it, no one has done a faunal analysis of the entire assemblage… in the archaeological literature, this is often utilized as the determining factor of determining human influence on the deposit.
  • works with GENbank
  • Collagen- mainly flesh and connective tissue of animals, most abundant protein in the body
  • Bone is proteins and minerals. ~60% of weight of bone is mineral (mainly calcium and phosphate). Rest is water and matrix. Matrix, formed before the mineral is deposited. 90% of matrix proteins are collagen.Hydroxyapatite (apatite) makes up majority of the ‘hard part’. Also in teeth (enamel)
  • In people we can tell how they may have migrated from young age to adult hood
  • Carbon and Nitrogen- generally to reconstruct dietOxygen- geographic origin measure of moisture content, varies regionally and globallyStrontium- migration and cultural affinity?Nitrogen and strontium in determining trophic level changesYou can get very nuanced and detailed answers to questions about diet and migration

Intro to aDNA and bioarchaeology Intro to aDNA and bioarchaeology Presentation Transcript

  • Ancient DNA in ArchaeologyArchy 205, Fall 2012
  • Genetics and Inheritance:the “Basics”•DNA is passed from offspring tochild•Nuclear DNA •one copy from each parent •recombination leads to offspring possessing parts of each parent’s genetic material•Mitochondrial DNA •maternally inherited (for the most part) • subject to all evolutionary forces nuclear DNA is except recombination
  • DNA
  • Ancient DNAHaploid Human genome:3.2 billion base pairsLength of aDNA material:100’s of base pairs
  • aDNA – Molecular Damage DNA degradation and preservation  Bacteria, fungi and insects- macro molecules  Natural degradation (no more maintenance) DNA damage in ancient samples  Small average size, 100-500pb  Blocks  Nucleotide misincorporations- “modified” bases
  • aDNA- Contamination Pervasiveness of contaminating DNA  Neanderthal, Human or Bear… oh my! Criteria of Authenticity  e.g. replication in multiple laboratories Human DNA Sequences  May not be able to detect contamination
  • How far can we go…
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • What we can do… Species phylogenies Hominids Diet and Behavior Medical Molecular Archaeology Origins of Domestication Population History and Phylogeography
  • Case Study: Pygmy Hippos of Cyprus Question:  Why did the pygmy hippopotamus Phanourios minutus go extinct on the island of Cyprus 12kya What we know- Extinction occurred in conjunction with:  first evidence of human occupation  during a period of significant climate change (Younger Dryas)  global large mammal extinctions at the end of the Pleistocene
  • Case Study: Pygmy Hippos of Cyprus  traditional zooarchaeological analysis  relative skeletal abundance (RSA)  demography (using teeth)  presence of cut marks  distribution of burnt bone November 26th, Mike Etnier  review of palynology records  pollen diagrams from surrounding mainland Nov. 20th  aDNA  population dynamics  Isotope analysis
  • pygmy hippopotamusimages fromTaronga Zoo
  • CyprusAkrotiri Aetorkremnos
  • Over 220,000 Phanourios minutus bones
  • mtDNAPolymerase Chain Reaction“PCR”
  • Variation of a few…Constant Rates of MutationEffective Population SizeTrack changes in population through time
  • Three scenarios of pop change population already dwindling hunting to below recoverable levels (death> replacement) change in carrying capacity
  • Population DynamicsWhat can this tell us about mechanisms leading to extinctions?
  • Preliminary Results:Out of five samples run (two paleontological and three from Aetokremnos), two contained aDNA.One BLASTed to modern HippoOne BLASTed to “mouse”
  • Population DynamicsAllows us to:  pinpoint the timing of decline in population  decipher differences between proximate causes versus ultimate cause  in non-island environments, allows us to track species response(s) to various stressors
  • deciphering diets- stable isotopes bone collagen apatite  bone carbonate  tooth enamel carbonate
  • deciphering diets- stable isotopes bone collagen Continually reabsorbed Reflects diet over the past few apatite years  bone carbonate Reflects diet at time of  tooth enamel carbonate formation
  • Different Isotopes  Carbon  Nitrogen  Oxygen  Strontium
  • Pygmy HipposDid their diet change? Climate Change Introduced Competitor Modification of the Landscape
  • Questions