Keynote: Webb Miller - Bioinformatics Methods to Study Species Extinctions
10 Steps to Success in Bioinformatics - sebi
has been 40 yrs in computers, 20 yrs in bioinformatics: but doesn't have enough money to retire (tongue-in-cheek) - Michael Kuhn
Step 1: Become a biologist. - sebi
extinction - Venkata P. Satagopam
Extinction: How to save endangered species - Peter Menzel
which species are in trouble? - Venkata P. Satagopam
Here's the article "10 steps to success..." - Michael Kuhn
3 stories - Venkata P. Satagopam
(out of batteries, not sure the iPhone is adequate for this. So far a great intro :) ) - Oliver Hofmann from iPhone
3 studies: Tasmanian tiger, Mammoth, ... - Peter Menzel
explains how DNA can be found in hairs. - Peter Menzel
For extinct species, mitochondrial genome is easier to sequence, as it is up to 1,000 times more abundant than genomic DNA - sebi
aDNA = ancient DNA - Peter Menzel
background of ancient DNA ... - Venkata P. Satagopam
what can be learned from aDNA? - Venkata P. Satagopam
1. phylogenetics - Peter Menzel
2. population genetics - Peter Menzel
This has some parallels to the last talk in today's session in T1 by RE Green: Neandertal mitochondrial DNA to place them (and us) in the phylogenetic tree - sebi
3. directly observe evolutionary rates - Peter Menzel
4. observe evolution of function - Peter Menzel
short reads are good enough for aDNA junks - Peter Menzel
next-generation seq of aDNA - Venkata P. Satagopam
aDNA from hairs can easily be decontaminated - Peter Menzel
aDNA from hair shafts enclosed in a plastic bag like .... - Venkata P. Satagopam
Tasmanian tiger: extinction date 7/9/1936 - Peter Menzel
over 700 know specimens - Venkata P. Satagopam
thylacine = tasmanian tiger - Peter Menzel
attempts to study thylacine DNA - Venkata P. Satagopam
observations - Venkata P. Satagopam
2 mitochindrial genomes in GenBank - Peter Menzel
in GenBank two genes 12S, cytb both were wrong - Venkata P. Satagopam
both wrong at 10% of nucleotides - Peter Menzel
tasmanian devil closest relative to tiger - Peter Menzel
split at ~40m years ago - Peter Menzel
30% of new sequence data are from nuclear genome - Peter Menzel
-> maybe sequence whole genome? - Peter Menzel
one imp question ... did an epidemic contribute to extinction? - Venkata P. Satagopam
Epidemic probable cause of extinction - Peter Menzel
(the quiet comments are hillarious. 'we sequenced one from Stockholm swimming in alcohol. Long way from home, extinct, drowning his sorrows...') - Oliver Hofmann from iPhone
story 2 wooly mammoth - Venkata P. Satagopam
Mammoth: - Peter Menzel
hair sample from eBay - Peter Menzel
we found sample on ebay - Venkata P. Satagopam
for 90$ :-) - Peter Menzel
most samples are from Sibiria - Peter Menzel
have now 18 different complete mtDNA sequences - Peter Menzel
what we draw from this analysis ....mammoth separated from living elephants 6m years ago - Venkata P. Satagopam
like chimp and human - Peter Menzel
want to sequence the full nuclear genome - Peter Menzel
already got 0.7-fold coverage - Peter Menzel
= 3.3 billion bp - Peter Menzel
assuming real size of genome is 4.7Gb - Venkata P. Satagopam
aa identitiy is nearly 99.8% between mammoth and elephant - Peter Menzel
99.4% overall nucleotide identity - Peter Menzel
This equals 1 mutation per protein - sebi
(all this excluding indels) - Peter Menzel
90% seq from the sample from the wooly mammoth - Venkata P. Satagopam
Mammoths differ from all other vertebrates in some highly conversed genes, such as MRTO - Venkata P. Satagopam
maybe due to living in cold places - Peter Menzel
extinction scenario ...human killed them all - Venkata P. Satagopam
certainly not - Venkata P. Satagopam
extinction szenario: killed by humans.. become to warm... -> but thats' not true - Peter Menzel
humans arrives to late in Siberia - Peter Menzel
3rd story Tasmanian devil - Venkata P. Satagopam
tasmanian devil now - Peter Menzel
threatened by extinction due to cancer - Peter Menzel
cancer cells passed around by biting each other - Peter Menzel
cancer is passed through infection (biting other individuals, spreading cancer cells) - sebi
some resistant individuals - sebi
Trying to preserve the species, keeping the gene pool large enough - sebi
compared two individuals: one who is resistant, one who died - Peter Menzel
Finding out about the resistance: considering an ortholog of a human tumor supressor gene - sebi
the guy who died, has a mutation at an extremely conserved position - Peter Menzel
but not much is known what it means.. - Peter Menzel
want to look at non-coding nuclear SNPs - Peter Menzel
closest sequenced relative is oppossum - Peter Menzel
90m years of separation - Peter Menzel
-> computational problem: SNPs without a reference genome - Peter Menzel
produce sequences from many individuals instead - Peter Menzel
and compare SNPs there - Peter Menzel
-> extract population structure - Peter Menzel
seems to work.. but no final data... - Peter Menzel
Quick summary: Bioinformatics very helpful, but much more data needed - Peter Menzel
Role of genetic diversity in extinction still not really known.. no simple story - Peter Menzel
but genetic diversity not necessary a good indicator for risk of extinction.. - Peter Menzel
e.g. panda has high diversity, but endangered - Peter Menzel
TV documentary from Australia: - Peter Menzel
(only to get the blog on top of the ISCB portal site; the figures messed up our layout) - Reinhard Schneider
Related: 11 Extinct Animals That Have Been Photographed Alive: - Peter Menzel