2. Genetics and Inheritance:
the “Basics”
•DNA is passed from offspring to
child
•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
4. Ancient DNA
Haploid Human genome:
3.2 billion base pairs
Length of aDNA material:
100’s of base pairs
5. 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
6. 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
8. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
9. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
10.
11. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
12.
13. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
14.
15. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
16.
17. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
18.
19. What we can do…
Species phylogenies
Hominids
Diet and Behavior
Medical Molecular Archaeology
Origins of Domestication
Population History and Phylogeography
20. 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
21. 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
28. Variation of a few…
Constant Rates of Mutation
Effective Population Size
Track changes in population through time
29. Three scenarios of pop change
population already dwindling
hunting to below recoverable levels
(death> replacement)
change in carrying capacity
31. Preliminary Results:
Out of five samples run (two paleontological and three from
Aetokremnos), two contained aDNA.
One BLASTed to modern Hippo
One BLASTed to “mouse”
32.
33. Population Dynamics
Allows 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
34. deciphering diets- stable isotopes
bone collagen
apatite
bone carbonate
tooth enamel carbonate
35.
36. 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
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
