Biology 3594A Lecture Notes - Lecture 17: Woolly Mammoth, Tasmanian Devil, Hypervariable Region
13 May 2018
School
Department
Course
Professor
Major events contributing to extinction
Humans arrive –killing animals and moving them out of natural environments
Tasmania became an island, restricted population size. Animals like to be in demes, smaller pop = less migration between them = diversity smaller = pop smaller.
Contributed to their decline and extinction, and things we see with the Tasmanian devil
Putting major landmarks on the skull, full morphology analysis
Diff nasal and orbital bones and cranium –how tall, how broad
Differs between herbivores and carnivores
Diet affects the skull
Why does Tasmanian wolf have a dog-like skull?
Marsupial looks like a mammal skull –diet is the same but it’s also striking that it would come to such similarity when their ancient ancestor probably did not look like
that
Tasmanian wolf relatives don’t have dog skulls
Based on morphometry and metrics, phenotypic convergence
What genes have been altered/proteins did these two species end up with?
At a genomic and molecular level, how are they similar to one another?
But we’re not going to find evidence of genomic convergence
Can’t find a strong story, purifying selection to that kind of skull
Homoplasy –didn’t inherit from ancestor, but from environments and pop genetics, they end up having a similar skull
Similar DNA sequences and proteins but not because of common ancestry
No evidence of genomic convergence
Thylacine is grouped with other mammals and other vertebrates too –clustered in same area, can’t distinguish amino acids that are more associated with specific
mammals vs other vertebrates. Everyone occupies same space in data –if there was some genomic contributor you would expect some separation
As we get more distance between species, end up with decrease in homoplasious amino acids
Because organisms are phenotypically similar, maybe they have similar genes and pathways
Somehow share diversity in their pathways?
Didn’t work out either, can’t identify what is underlying this convergence of the skull shape (and the rest of their body but using the skull as the most definitive similarity
between the two of them)
People start by looking at exons and PCGs but there is so much more of the genome to look at
End of paper: don’t know what has led to convergent evolution for the wolf to look like dogs, marsupial to look like mammal, but there is a lot more of the genome that
hasn’t been looked at
Make sure you have high quality sequence info for regulatory elements
Next steps: how much protein we have, regulation of proteins. About time and space and development –when a gene is expressed and which tissue it is expressed in
Resurrection experiments –take an ancient gene and resurrect it by putting it into cells or even mouse model
But gene is from extinct animal
In paleogenomics –also people that study individual genes of the genome and resurrect them into cell and mouse systems –figure out why that protein allows for
adaptations (not just people raising up woolly mammoths)
Expect a question on the exam with mitochondrial DNA, we shouldn’t just talk about nuclear genomes
Mitochondrial DNA is easy to study, small (16k base pairs, remember for exam)
Population genetics –find DNA from many organisms!
D loop region –popular piece of DNA to look at, human populations, ancient human populations, woolly mammoth too
Only need this small part of the mitochondrial genome to have survived
Do the D loop or hypervariable region (in slides coming up) –most of the variability between animals, the rest of the genes are highly conserved
But now our tech is good so we can look at the whole thing
Matrilineal –mother to all offspring
When we want to study pop genetics from maternal and matrilineal side of things, we study mitochondrial DNA
When we want to study paternal and patrilineal we study the Y chromosome
When interested in whole population dynamics look at nuclear DNA, plus the other two
Challenges in studying ancient DNA
pg. 8 of the paper
Expensive lab required: positive pressure, cleaned daily for microbes, need separate dedicated hoods for reactions, UV radiated agents, full clean room suits, hairnets,
masks, double gloves
Controls: cave bear bone, negative controls like water
Can’t sequence the wrong DNA – avoid contamination. When studying humans don’t’accidentally sequence the technician
Problems: microbes, people, putting the same thing back into the reaction
Studying pops of extinct species
- Need a lot of individuals, more than 1
Essay questions for exam
Lec 17 Woolly Mammoth
May 13, 2018
2:53 PM
3594 Page 1
Document Summary
Humans arrive killing animals and moving them out of natural environments. Animals like to be in demes, smaller pop = less migration between them = diversity smaller = pop smaller. Contributed to their decline and extinction, and things we see with the tasmanian devil. Putting major landmarks on the skull, full morphology analysis. Diff nasal and orbital bones and cranium how tall, how broad. Marsupial looks like a mammal skull diet is the same but it(cid:859)s also striking that it would come to such similarity when their ancient ancestor probably did not look like that. But (cid:449)e(cid:859)(cid:396)e (cid:374)ot goi(cid:374)g to fi(cid:374)d e(cid:448)ide(cid:374)(cid:272)e of ge(cid:374)o(cid:373)i(cid:272) (cid:272)o(cid:374)(cid:448)e(cid:396)ge(cid:374)(cid:272)e. Ca(cid:374)(cid:859)t fi(cid:374)d a st(cid:396)o(cid:374)g sto(cid:396)(cid:455), pu(cid:396)if(cid:455)i(cid:374)g sele(cid:272)tio(cid:374) to that ki(cid:374)d of skull. Homoplasy didn(cid:859)t inherit from ancestor, but from environments and pop genetics, they end up having a similar skull. Similar dna sequences and proteins but not because of common ancestry.
