evolutionary biology fall 2014 when:mwf 11:30 – 12:20 where: 283 galvin life sciences instructor:...
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EVOLUTIONARY BIOLOGYFALL 2014
WHEN: MWF 11:30 – 12:20WHERE: 283 Galvin Life Sciences
INSTRUCTOR: Mike Pfrender
Course webpage:
http://www3.nd.edu/~mpfrende/Evolutionary_Biology/Homepage.htm
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“Nothing in biology makes sense except in light of evolution”
Theodosius Dobzhansky 1973
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Managing Evolving Fish Stocks
Evolutionary impact assessment is a framework for quantifying the effects of harvest-induced evolution on the utility generated by fish stocks.
Conover, Nature 2007 450:179-180Jorgensen et al. Science 318:1247- 8
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How do complex organisms evolve?
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What explains these exaggerated phenotypes???
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What happened to these organisms?
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How does social behavior evolve?
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Human HIV Protein Structure
How do host – pathogen relationships change through time?
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What are the evolutionary consequences of small population size?
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MAJOR GOALS IN THIS COURSE:
Describe major evolutionary events and patterns in the history biological diversity on Earth
Develop an analytical frame work to describe the process of evolutionary change in natural populations
Apply this framework to understand evolutionary dynamics – especially with regard to human populations
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COURSE REQUIREMENTS:
1) Problem Sets, Writing Assignments, etc.
Total 100 pts.
2) Exams
1st Midterm 100 pts.2nd Midterm 100 pts.Final 100 pts.Total 300 pts.
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ACHIEVING HIGH FITNESS IN EVOLUTIONARY BIOLOGY:
Attend lectures regularly.
Take detailed notes.
Read over material before lecture.
Ask lots of questions and discuss the material with instructor and classmates.
Take advantage of review sessions & office hours!!!!
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Recommended Text for Evolutionary Biology
On reserve at the Library
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#1 Question in Evolutionary Biology
What material is going to be on the exams?
Answer:
Any material in Assigned Readings, PowerPoints or discussed in lecture is fair game.
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Pharmaceutical Industry:
Drug design by in vitro or in vivo evolution.
Targeted searches for natural products; bio-prospecting.
Agriculture:
Crop & Livestock improvement by selective breeding.
Evolution of pesticide resistance.
Transgenic organisms – evaluating the advantages and risks.
Some Practical Applications of Evolutionary Biology:
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Fisheries Biology:
Genetic consequences of selective harvesting.
How does selective harvesting affect the future of fisheries?
Genetic consequences of hatcheries.
How do hatchery raised fish affect wild stocks?
Some Practical Applications of Evolutionary Biology:
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Conservation Biology:
Identification of evolutionary significant units (ESUs).
Avoidance of inbreeding depression in captivity.
Avoiding the loss of adaptive variation.
Identification of minimal population size for viability.
Predicting the response to global change.
Some Practical Applications of Evolutionary Biology:
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Pfrender Lab
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How do natural populations and communities cope with
environmental change?
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Response to Environmental Challenges
NATURAL POPULATIONS FACED WITH A CHANGING ENVIRONMENT CAN:
Physically move to track a beneficial habitat
Accommodate the altered environment with phenotypic plasticity (direct response to the environment)
Adapt to the altered environment through genetic changes
Go extinct!
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FROM: Gomulkiewicz & Holt. 1995. When does evolution by natural selection prevent extinction. Evolution 49:201-207
Even populations capable of rapid evolution may face a high risk of extinction due to reductions in population size during the initial period of adaptation.
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Model Systems For Evolutionary & Ecological Genomics?
?WELL
CHARACTERIZED ECOLOGY
KNOCKOUT - RNAi -
TRANSGENIC LINES
QTL PANELS
GENOME SEQUENCE
GENETIC MAP
GENE EXPRESSION
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In the Sierra Nevada ecosystem, the recent introduction of salmonids is a dramatic and rapid change in the environment.
Rapid Ecosystem Changes
UNIVERSITY OF
NOTRE DAME
Mt. Mendel
Darwin Lakes
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Dark pigmentation is due to the elevated levels of incident UV-B radiation at these extreme elevations
No vertebrate predators leads to large body size
High elevation populations of Daphnia melanica are typically highly pigmented and have large body size.
Undisturbed Daphnia Populations in the Sierra Nevada
4 mm
Lower Skelton LakeElevation ~3,000 meters.
Yosemite Natl. Park
UNIVERSITY OF
NOTRE DAME
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Rates of Adaptation
From these data we can estimate the rate of adaptation
Do Sierra Nevada Daphnia show high rates of evolutionary change in response to introduced predators?
Fisk et al. 2007
r2=0.33p<0.0001
r2=0.08p<0.01
UNIVERSITY OF
NOTRE DAME
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Changes in Pigmentation
Daphnia exposed to predation from introduced fish have reduced pigmentation
Scoville & Pfrender 2009
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(Melanin pathway modified from True 2003)
Tyrosine
DOPA
Dopamine
DOPAmelanin
Dopaminemelanin
NADA
NADASclerotin
NBADSclerotin
NBAD
THpale
DDCDdc
DATaaNAT
NBADHYDROLASE
tan
NBADSYNTHASE
ebony
PO PO
yellow
PO
-alanine-alanine
Insect Melanin Biosynthesis Pathways
Genetic Basis of Changes in Pigmentation
Data from other arthropod systems provides a set of candidate genes involved in pigmentation
We are examining these gene for structural and functional changes as well as examining the patterns of gene expression
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Transcriptional response of Daphnia to thermal stress- Up-regulated (28°C)
- Down-regulated (28°C)
The complexity of organismal responses to their environment requires an understanding of regulatory networks.
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Our Current Understanding of the Genetic Basis of Adaptation
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1. To document evolutionary history.
2. To understand the mechanisms that drive biological change through time.
3. To apply this knowledge to understand the genetic underpinnings of biological diversity, and to solve practical problems in the life sciences.
Primary Goals of Evolutionary Biology:
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WHAT IS EVOLUTION?
Darwin: descent with modification
Futuyma: changes in the properties of populations that transcend the lifetime of a single individual.
F & H: changes in allele frequencies over time.
Key Ingredients:
1. Change that is heritable across generations.2. A property of populations, not individuals.3. Includes the possibility of cultural evolution (not in our
genes).
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All evolving systems have the following properties:
POPULATIONS: Groups of entities.
VARIATION: Members of the population differ from one another with respect to some characteristic.
HEREDITARY SIMILARITY: Offspring resemble parents.
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Historical Background
Plato (427-347 BC) – Believed in 2 worlds: the real world (ideal and eternal), and an illusionary world (imperfect and perceived through the senses). Typological view of nature – individual variation as the imperfect manifestation of ethos.
Aristotle (384-322 BC) – Believed that all living organisms could be arranged in a “scale of nature” or Great Chain of Being. The ladder of life consists of graduation from inanimate material through plants, through lower animals and humans to other spiritual beings.
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Carolus Linnaeus (1707-1778) – Established the modern system of taxonomy in an attempt to discover order in the diversity of life “for the greater glory of God”.
Groupings based on similarity Hierarchal relationships of organisms
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Jean-Baptiste Pierre Antoine de Monet, Chevalier de
Lamarck
1809 Philosophie Zoologique
First articulated theory of evolution:
Organisms continually arise by spontaneous generation.
“Nervous fluid” acts to move each species up the “great chain of being”.
Organisms develop adaptations to changing environment through the use and disuse of organs. (Heavy use attracts more “nervous fluid”.)
Acquired characteristics are inherited.
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SC
AL
E O
F O
RG
AN
IZA
TIO
N
TIME
“Chain of Being”
LAMARCKIAN EVOLUTION
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Problems with Lamarck’s ideas:
1) There is no evidence of spontaneous generation.
2) There is no evidence of an innate drive toward complexity.
- E. coli - Parasites - Cave dwelling
organisms
3) There is no evidence of inheritance of acquired characteristics. (BUT…..epigenetics???)