Transcript Lessons 1-3 Presentation

Pieris Project
Using evolution and genetics
to understand nature
Lesson 1
Evolution: Understanding the processes that drive
species diversity
Photo: University of Southampton/PA Wire
What is evolution?
Descent with modification from a
common ancestor
It’s simply the change in allele frequency of a population through time
- Each color is a different “allele” for a gene
4
3
6
Reproduce
(produce offspring)
2
Amoeba population
at generation 2
Amoeba population at
generation 1
Time
What causes evolution?
Natural Selection
3 conditions are required
Variation in trait (phenotype)
Differential fitness
Inheritence of trait
Bird photo credit: Dûrzan cîrano
Butterfly photo credit: Andy Emcee
How can a trait not be inherited (“heritable”)?
Phenotypic plasticity - variation in a trait due to the environment
Some variation in the
traits of a species are not
due to genetic
differences, but differ
because the environment
they inhabit is different
Photo credit: Scott Wylie
Evolution without natural selection?
Mutation
Migration
Genetic Drift
Mutations: create genetic and sometimes
phenotypic diversity (it also provides the raw
material for natural selection to act upon)
C
A
G
T
Replicating strands
Mutation (supposed to be
)
Migration / Gene flow
Population 1
Population 2
Photo credit: Evan Twomey
Genetic Drift
Change in the genetic
composition of a population
that is due to random
chance. Fitness differences
have nothing to do with
phenotypes (traits). The
difference between the
“winners and losers” is just
due to chance.
Remember
Evolution is simply a change in the genetic composition of a
population over time
Evolution can be
Adaptive – result from natural selection where different
traits lead to differences in fitness
AND
Non-adaptive - have nothing to do with fitness (mutation,
migration/gene flow, and genetic drift)
Lesson 1 Activity: Small Group Discussion on
Misconceptions of Evolution
Lesson 2 Phylogenetics
A tool for estimating the evolutionary relationship
among species
Phylogentics: understanding the evolutionary
relationship between different species
Illustration credit: James McInerney
Which animals are most closely related?
Which animals are most closely related?
OK, that was easy, how about these?
So how do we go about
determining the evolutionary
relationship between species?
Evolutionary Tree - Phylogeny
Similar to a family tree, scientists use evolutionary trees, or phylogenies, to show
the evolutionary relationship among species
clade
More recent
Common ancestor
Past
Building a phylogeny
To build a phylogeny, biologists must identify a set of characters and then
conmpare these characters among the different species
Requirements of characters:
- Present in some, but not all species
- Have a shared ancestry (“homologous” characters)
These can be phenotypic characters or genetic characters
What might be a shared character for this
phylogeny?
What might be a shared character for this
phylogeny?
evolution of limbs
evolution of lungs
Which two species are most closely related?
Photo by: Oliver Bain
Photo by: Oryan Espanto
Photo by: Angell Williams
Which two species are most closely related?
Photo by: Oliver Bain
Photo by: Oryan Espanto
Photo by: Angell Williams
There’s a problem….
Convergent evolution –
traits can look similar
between species (especially if
they are used for similar
functions, such as flying), but
have evolved independently
(that is, they do not share a
common ancestor); they are
not homologous, they are
analogous.
Let’s build a phylogeny
Character
Taxa
Activity: Construct a phylogeny
Character
Taxa
Eyes
Vertebrae
Four limbs
Hair
Virus
Insect
Fish
Lizard
Wolf
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1
1
1
1
0
0
1
1
1
0
0
0
1
1
0
0
0
0
1
Does our phylogeny match the fossil record?
Lesson 3 Pieris Project (Part 1)
Using genetic information and citizen science to
track the spread of a butterfly across the globe
Let’s use our understanding of
phylogenetics to do some “forensics”
Have you seen me?
150 yrs ago
2,000 yrs ago
100 yrs ago
Photo credit: NASA
Why were these butterflies so successful in
spreading across the world?
• What they eat is what we eat ☺
• They eat plants in the Brassicaceae (mustard) family
Photo credit: Alan Buckingham
Photo credit: Chrissine Rios
Photo credit: Linda
How can we use genetics to “reconstruct”
the invasion of this butterfly?
Not only can traits (phenotypes)
be used as characters to
construct a phylogeny, but DNA
contains characters too
Native population 1
Native population 2
Non-native
(introduced)
population
SNP: Single Nucleotide Polymorphism
So far we have been focusing on “deep”
divergence between species
But we can also look at the very “tips” of the tree
France
Your City
(USA)
Spain
Germany
Finland
Turkey
China
Russia
Mitochondrial DNA
• Why is this type of DNA useful to looking at an organism’s lineage?
Maternally inherited
No recombination (haploid)
Participate in the Pieris Project as a citizen scientist
We sequence a portion of a mitochondrial gene from each of the butterflies sent in
from citizen scientists – people just like you – from around the world. We can then
use that genetic data to infer where the butterflies invaded from.
Individually and/or as a class, collect a few cabbage white butterflies from around
your neighborhood.
Visit the Pieris Project website for a break down on the proper protocol for this
study
Send in your butterflies and we’ll put your samples on our map and send you back
the genetic data so we can identify the country from which the butterflies you
collected originated.
A walk through of the Pieris Project
Photo by: Woodleywonderworks
Photo by: John Taylor
Step 1. Find a cabbage white butterfly. They’re pretty much everywhere, but most common
in urban environments (e.g., side of the road, near farms, in gardens, and meadows)
Male
Female
Mike, Nick and Dasco
Photos by Dennis Walker
Step 2. Catch a cabbage white butterfly. It will help to have a net. It’s also easiest if you wait
until they land, but they are one of the easier butterflies to catch – they are not too fast. Check
out our video on how to properly swing a butterfly; yes, there is a technique =)
Step 3. Place each butterfly in their own individual envelope. You can make these
envelopes very easily. Check out our video on how to make an envelope. Record the date
(month/day/year) and the location – watch a video on how to use your iPhone to get GPS
coordinates.
Step 4. Place the butterflies in the freezer overnight. This is a humane way to euthanize the
butterflies, which is something we have to do in order to collect DNA from them. AVOID
FREEZE-THAW CYCLES (ONLY PUT SPECIMENS IN THE FREEZER ONCE). IF YOU
ARE NOT READY TO SEND THEM YOU CAN LEAVE THEM IN THE FREEZER UNTIL
YOU ARE READY TO SHIP. GOING FROM FROZEN TO THAWED MULTIPLE TIMES
WILL SHEAR THE DNA INTO VERY SMALL FRAGMENTS, WHICH IS VERY BAD.
Step 5. After taking them out of the freezer, let them dry in their envelopes somewhere
where they won't be in direct sunlight or near moisture. The key is to let them dry
quickly, so mold doesn't grow on them while they dry out. If left in their envelopes and
placed on some paper towels for 3-4 days at room temperature (~20°C or 70°F)
should be good enough to dry them out. (No need to heat them, this is bad for DNA as
well.)
Mail to:
Pieris Project (attn: Sean Ryan)
USDA-ARS
1600/1700 SW 23rd Dr
Gainesville FL, 32608
Step 6. Send in your butterflies. Be sure to use a crush-proof container (e.g., old Altoids or CD
case, Tupperware, candy box, … feel free to be creative) – for shipping the butterflies without
them getting squished
What will we do with the butterflies you send in?
First, Dr. Ryan will extract the DNA from some of
your butterflies and sequence a mitochondrial
gene that can you will be able to use to construct
a phylogenetic tree and determine where in
Eurasia the butterfly you collected originated.
Which of these butterflies is most closely related to yours?
Next, we can also use the DNA inside the butterfly to look
for the presence of other organisms. Yes, seriously!
There is a bacteria called Wolbachia that infects many
different species of insects. What is really interesting is
that the infection of this bacteria can actually prevent
some insects from carrying diseases (like malaria), turn
males into females, and even prevent infected individuals
from producing offspring with uninfected individuals.
Wolbachia
Surprisingly, no one knows whether this bacteria infects cabbage white
butterflies in the USA or whether some regions of the USA have different
“species” of this bacteria living inside these butterflies. Help us find out!
Next, Anne Espeset will photograph your
butterflies so that we (and you!) can
measure their phenotypic variation – their
size and shape. Many butterflies are known
to change in size and color throughout the
summer and with these photographs we can
measure we these changes.
Last, we will look at how the diet of these butterflies affects their color.
Researchers have shown that cabbage white butterflies that eat a lot of nitrogen
as caterpillars, tend to have more white pigment in their wings. Agricultural fields
usually have lots of extra nitrogen that has been added by famers to help their
crops grow. Given that cabbage white butterflies like to eat many agricultural
plants (cabbage, broccoli, kale, etc.), what would be expect?
photo: Dennis Walker
photo: Richard Hurd
To determine this, Anne will measure a pigment on the wings called pterin, which
gives the wings its white color. Using a machine called a wand
spectrophotometer she will measure how much light the wings reflect (the more
they reflect, the more pterin present).