Intro to aDNA and paleoecology Flashcards
(45 cards)
What is aDNA?
Ancient DNA (aDNA) is DNA isolated from ancient specimens. Also, aDNA can also be referred to as DNA samples recovered from biological samples not intended for DNA use, including historical and archeological samples.
The Arrhenius equation describes the parameters that affect DNA breakdown/preservation. Which are the two main factors in the equation that affects DNA decay?
The main takeaways from the Arrhenius equation is that DNA decay is dependent on temperature and time (humidity and light are also factors in the case of DNA but not implied in the Arr. Eq.)
So:
- The hotter things are, the faster the reaction
- The colder things are, the slower the reaction
–> Therefore, cold storage is good for DNA
- Also the longer the time, the more decay –> younger samples = better for DNA preservation.
Think of DNA as an ice cream - Keep it cold or use it quick, heating it up or leaving it out for a long time will make a mess.
What is the optimal conditions for aDNA preservation?
Cold, dry, dark environment and dense specimens are the most optimal for aDNA preservation.
What are the main characteristics of aDNA?
- Its heavily fragmented (between 50-100 bp length)
- post mortem damage (e.g. C -> T modifications)
- usually very little endogenous DNA can be recovered (<1%) - a lot of contaminants.
What is the difference between endogenous and exogenous DNA?
Endogenous DNA is DNA that was present in the living organism at the time of death. Exogenous DNA is everything else, can be ancient contaminants or modern.
How can you tell the difference between modern and ancient contaminants?
Ancient contaminants have degraded and have similar patterns of post mortem damage ad the endogenous aDNA.
Name at least three different sources of aDNA.
Some sources of aDNA includes:
- Bone/teeth found through excavations
- Ancient sediments
- Museum collections
- Permafrost findings: e.g. bones, soft tissue etc.
What was the first aDNA to be sequenced?
The first aDNA sequence was from the Quagga (an extinct member of the horse family, study published in Nature 1984).
At the beginning of the whole field, the process was very complicated. For example, first one needed to use bacterial cloning of the fragments to get a lot and then PCR extremely time consuming before NGS.
Pretty early on in the field, there were extraordinary claims of aDNA sequences from VERY far back being sequenced, what and what happened to these claims?
During the early 90s there were several publications regarding aDNA sequences from dinosaurs, these papers were under a lot of scrutiny and later it was found to be modern contaminants that had been sequenced. This did however not stop Jurassic park hehe.
A lot of careers were flushed down the toiloets from this, “extraordinary claims require extraordinary evidence“ but from this stricted regulations and better practices came so that was good at least.
What are the two key aspects when working with aDNA?
Precautions and authentications are key for aDNA work. The precautions are there to minimize modern contamination and authentication is needed to show that the DNA is indeed ancient, for example showing that the DNA is fragmented, that there is post mortem damage and having blanks for every step to show that there hasn’t been any contamination in the handling process.
Also making phylogenetic sense is a good way to approach data, for example, if you extract DNA from a big bone, it makes little sense that you have extracted DNA from it if it comes back being more closely related to a fungi than a big animal.
Give three examples of measures taken to avoid contamination in an aDNA study.
- Sterile equipment: UV treating everything that is brought into the lab to avoid modern contamination.
- positive air pressure: To make sure nothing from the outside can come in.
- Polishing the area of extraction to avoid surface contaminants.
- Separate extraction from PCR facilities: Since PCR produces huge amounts of DNA, this practice is entirely separate from handling of the samples to avoid contamination.
What is the oldest aDNA ever sequenced?
The currently oldest aDNA that has been sequenced is for animals an about 1.1-1.2 million year old mammoth (krestovska) and for sedaDNA/eDNA an about 2 million year old ecosystem in greenland!
https://pmc.ncbi.nlm.nih.gov/articles/PMC10586222/
What is palaeoecology?
The study of past ecosystem functioning
(the interactions between species and their environment in the past)
What is the goal of palaeoecology?
To use the past to inform the present and predict the future.
Explain the term “shifting baseline syndrome”.
Shifting baseline syndrome is a phenomenon that occurs as ecosystems change over time, and new generations only remember the recent/current state as the baseline, even though an older generation might remember an entirely different situation. So the baseline is shifting, and changes might not appear as severe as they are due to the newer baselines.
Paleoecology offers a solution to this problem, as it allows us to study past ecosystems - which can inform about “true” baselines (assumes uniformitarianism) It also allows for answering different questions, for example “How much diversity have we actually lost” or how population size of different species can be affected by changes in the environment.
What is Uniformitarianism?
Uniformitarianism he belief that ‘the present is the key to the past’.
For example, erosion as a process works the same way today as it did in the past, or the fact that spruce trees today grow in cold climates, so if we find evidence of spruce growing in the past, it was probably cold in the region at the time.
Palaeoecology links two disciplines together, which?
Palaeoecology links palaeoenvironmental research (study of past abiotic systems) with palaeontology (the study of past biotic systems).
There are three types of palaeoecology, which?
The three types of palaeoecology are:
- Classical: single-species interactions which environment
- Evolutionary: The cycle of evolutionary innovation and generation of novel ecological niches, rise and fall of species (palaeontological deep-time palaeoecology)
- Community: Interactions between multiple taxonomic groups and their environment (Quaternary palaeoecology) - Focus on the last 2,6 million years.
How old is the earth?
The earth is approximately 4,5 billion years old.
When did the great oxygenation event occur? What is the evidence of this? What was the consequences of this event?
The great oxygenation event occurred about 2,4 billion years ago. It was a period in which the earth first experiences an increase in free oxygen in the atmosphere due to photosynthesizing microbes, leading to the death of many anaerobic species and paved the way for more complex life (multicellular life).
The evidence of this is that we can see banded iron formation (caused by oxidation) in layers dating back to this time. When atmospheric oxygen was low, iron was soluble but when the oxygen levels rose, the iron was oxidized and precipitated - forming the bands. Before this, there is no evidence of oxidation - Paleosols (fossil soils) older than 2.4 billion years old have low iron concentrations that suggest anoxic weathering (reducing environment).
During which time/period do we find the evidence of the first multicellular organisms?
The first evidence of multicellular life are from the the Ediacaran, ~610–540 million years ago. This “fauna” was soft bodied so we only have trace fossils, e.g. impressions in stone, no physical fossils.
At which time did the Cambrian explosion start? What is so special about it?
The Cambrian explosion started ~540 million years ago and lasted somewhere between 13-25 million years. This was a time of weirdness, also called “the time where life tried to figure out what life was supposed to look like”. During this time, there was a major increase in taxonomic diversity and all practically all major animal phyla started appearing in the fossil record. A lot of new behaviors seem to have evolved (e.g. burrowing), leading to new niches available and thus high speciation.
This period was followed by the Ordovician and Silurian periods, which a lot of geographic changes and further increase in diversity of life. The first plants are from about 470 million years ago during mid-Ordovician and the first terrestrial fungi appear in early Silurian records.
When was the Devonian? What is the Devonian fauna known for?
Devonian ~420–360 million years ago was a time of terror, with the first appearance of jaws - large predators which led to armored fish for protection. During this time we also find terrestrial vascular plants and arthropods. Two major mass extinctions during this period.
When was the Carboniferous period and what is it known for?
The Carboniferous period, ~350–290 million years ago, is known as being “the time of giant bugs”. During this time, oxygen levels were very high and could thus support large bugs. There were very limited fungi and other detritus/lignin consumers, so we have a lot of coal deposited from this period from falling into vast swamps and stagnant water.
