Transcript Conservation Genomics: An Introduction

By Jack Francis
May 2nd 2016
What does this mean?
 Conservation
 The act of preserving, protecting, or restoring natural
systems.
 Is at the forefront of biological sciences
 How does genomics play a part?
 Applying genomic technology to the preservation of the
viability of populations in nature

Genetic diversity, allele frequency, hybridization, identity,
forensics.
Introduction
 Using genomic technology, scientists will be able to
understand the current status of threatened and
endangered species.
 Assembly of the genome of endangered species can
keep their information with us even if they are lost
Purpose
 Step 1:
 To introduce the issues facing global biodiversity and
emphasis the cause and effects of these problems
 Step 2:
 To show how genomic techniques are being used to
understand threatened species and to highlight a few
efforts being done by scientists
Why is this Important?
 Conservation has become one of the most pressing
issues of our time.
 ~20,000 described species listed as Endangered or
Vulnerable by the IUCN.
 Important to maintain diversity of life:
 For Human Existence
 For the Sake of our Species
 Human caused extinctions
unprecedented in history of life.
The
th
6
Extinction
 Scientists believe that we have entered the 6th mass
extinction in the history of earth.
 Defined by a loss of >70% biodiversity of multicellular
organisms in a geologically short period of time (~10 my)
 The Holocene Extinction:
 Extinction rates in the last few centuries are over 600
times the background extinction rate.
 Background extinction rate: In million years (MSY)
formula = one estimated extinction per million species
years.
 This formula means that if there are a million species on
the planet earth, one would go extinct every year, while
if there was only one species it would go extinct in one
million year
 The current estimation for extinction is now ~400 years.
Who we’ve lost
Thylacine ex. 1936
Passenger Pigeon, ex. 1914
Great Auk, ex. 1844
Steller’s Sea Cow, ex. 1768
Rabb’s Fringed Limbed
Tree Frog, ex. 2011
Dodo , ex 1662
Caspian Tiger, ex. 1970
Cosmos atrosanginues
ex. 2012
What is Happening?
 Mass Hunting
 Deforestation
 Pollution
 Climate Change
 Overfishing
 Overpopulation
 Introduced Species
 Pet Trade
 Pesticide Use
 Just to name a few….
Human Change
 So pressing that geologists see the layer of carbon and
other gases built up so much on the layers of the
planet that we could be entering a new epoch called
the “Anthropocene*”.
 The effects of
climate change on
the planet can be
seen in a variety of
ways.
 Weather, extinctions, drought
Disease, hibernation issues.
Science of Conservation
 Geologists, Ecologists, Paleontologists, Climatologists,
Systematists, Physicists, Chemists, and a wide host of
other scientific disciplines are studying this crisis.
 How Do Genome Biologists Play a Part?
 Study the genetic relationship of endangered taxa.

Combined use of fusing population genetics with ecological
issues via genomic technologies.
Population Genetics
 This is the study of
genetic variation
within populations.
 Monitor frequency
of genetic changes
 Study Allele
Frequencies to
determine
evolutionary
changes
 Peppered Moth
•Used in Conservation genomics to
determine allele frequencies and other
genetic issues between endangered
populations to test a variety of issues.
Conservation Genetics
 Sequencing technology
can determine allelic or
the “genetic stock”.
 Will help biologist,
governments, clearly
define threatened
populations.
 Captive Breeding
 Knowing the genetic
history of an individual
will provide information
for best potential mate.
Methods
 This field utilizes the latest genetic
technology. The ability to sequence 1,000s
of sequences.
 Illumina technology is used most
frequently now
 RADseq has started to be used to
understand population genetics.
 EX: SNPs of Atlantic Salmon used to track
migration routes and monitor ancestral
spawning sites (Boulding et. al.).
More Uses
 Monitor Hybridization
 Adams et. al. Sequences fecal samples to gauge
hybridization between coyotes and the critically rare red
wolf.
 Forensic Science
 The USFW has a state of the art forensic laboratory that
only sequences DNA related to wildlife crimes (other
countries have also begun to get these facilities).

Ivory Trade, Illegal Meat, Origin of pet trade, skin trade, age.
Sequence Library
 Having a Database of genome sequences can:
 Have information about what may or may not have
made a species vulnerable to the cause of decline.
 Can have to genetic data even if an organism is extinct.
 Get sequences from well preserved extinct species



Tasmanian Tiger Mitochondrial Genome Published
Steller’s Sea Cow Genes successfully recovered
Passenger Pigeon, Great Auk, Golden Toad, Ghouzhou Soft
Shell Turtle are suggested future candidates.
Cloning
 With a sequenced genome, cloning extinct taxa would
be much easier.
 Has many hurdles:
 Filling in missing gaps
 Successful implementation into a extant species
 Keeping the animal alive
 Having the animal grow
 Diplomatic Issues
 Explaining to it that it is all alone
Genome 10K Project
 Founded in 2009 by Stephen O’ Brien, David Haussler,




Oliver Ryder.
Assembling a “Noah’s Ark” of genomic data to save
dying species
A joint effort between Universities, Zoos, Museums,
and Government research stations.
227 species selected from public done so far, and an
additional 102 are on the way from G10K
https://www.youtube.com/watch?v=B57xDIGtCT0
Other Efforts
 First World Countries have signed International treaties to
assist in global conservation.
 In the US, the Endangered Species Act (ESA, 1973), and 56 species
have recovered. Crimes against these listed species are viewed by
the FBI, Department of defense, the forensics lab.
 Non profit Organizations raise around ~1B dollars annually
 WWF
 National Wildlife Federation
 Disney
 Often times these organizations and
governments provide grants and aid to
scientist working on conservation.
Optimism
 Funding for conservation as lead to a increase in
genomic activities for endangered species.
 Coupled with the work being done by other fields in
Biology and the other sciences, these efforts provide
hope for the future of life on earth.
 But these efforts need more support and human
attention to continue to be successful.
Success Stories
 Mapping the Tasmanian Devil genome has provide
insight to DFT disease.
 Genome technology as assisted
in the shut down of the largest
illegal black market whale meat
trade in 2015.
 Similar event shut down Asia’s 2nd largest ivory trade.
 After the gorilla genome was sequenced, researcher
focused on similarities between humans and gorilla
immune genes that aided in disease ecology.
Literature Cited
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DRAFT REPORT OF THE NINETEENTH SESSION OF THE INTERGOVERNMENTAL PANEL ON CLIMATE CHANGE (IPCC)
2012
Thomas, C. D.; et al. (2004-01-08). "Extinction risk from climate change". Nature 427 (6970): 145–148.
Bibcode:2004Natur.427..145T. doi:10.1038/nature02121. PMID 14712274. Retrieved 2010-05-28. minimal climate-warming
scenarios produce lower projections of species committed to extinction (approx18%) (Letter to Nature received 10 September
2003.)
Mora, C.; Tittensor, D.P.; Adl, S.; Simpson, A.G.; Worm, B. (23 August 2011). "How many species are there on Earth and in the
ocean?". PLOS Biology 9: e1001127.doi:10.1371/journal.pbio.1001127. PMC 3160336. PMID 21886479. Retrieved26 May 2015.
Avise, J. 15-Nov-2009: Perspective: conservation genetics enters the genomics era. Conservation Genetics 11 2: pp 665-669
Boulding, E. G., M. Culling, B. Glebe, P. R. Berg, S. Lien, T. Moen. Conservation genomics of Atlantic salmon: SNPs associated
with QTLs for adaptive traits in parr from four trans-Atlantic backcrosses. 2008. Heredity 101, pp 381-391
Adams, J. R., B. T. Kelly, L. P. Waits, Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis
rufus) and coyotes (Canis latrans). 2003 Molecular Ecology 12: 8 pp: 2175-2186
Narum, S. R., C. A. Buerkle, J. W. Davey, M. R. Miller, P. A. Hohenlohe Genotyping –by- sequencing in ecological and
conservation genomics. June 2013 Molecular Ecology 22: 11 pp 2841-2847
Miller et.al. The mitochondrial genome of the Tasmanian tiger (Thylacinus cynocephalus) Genome Research 2009 19: 213-220
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Further Questions?