FISH BIOL 340

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Welcome !!!

• FISH / BIOL 340
• Introduction to
• Genetics and Molecular Ecology
• Spring 2003

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Instructors

• Dr Lorenz Hauser
• School of Aquatic and Fishery Sciences
• Marine Studies, room 207
• Tel [phone], lhauser_at_u.washington.edu
• Todd Seamons
• School of Aquatic and Fishery Sciences
• Marine Studies, room 185
• seamonst_at_u.washington.edu

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MMBL Marine Molecular Biotechnology Lab

• 4 faculty
• 2 fisheries (Naish, Hauser)
• 2 oceanography (Armbrust, Rocap)
• Main research areas
• Genomics
• Phytoplankton Ecology
• Conservation Genetics
• Molecular Ecology
• Come and visit us!

Labs Th / Fr
We are here
MMBL
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Aim of the course

• Introduction to Genetics and Molecular Ecology
• Application of molecular markers
• Fundamentals of genetics
• Specific Objectives
• Interpretation of genetic data in an applied
  context
• Potential and limitations of various genetic
  markers
• Appropriate genetic method for a specific
  question
• Conceptual misunderstandings between genetic
  experts and end-users of research
• Assumed knowledge
• Biology 102 or 200
• Links from website

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Some General Info

• Class homepage
• http//fish.washington.edu/classes/fish340/
• Check frequently subject to change
• Lecture slides and reading material will be
  uploaded
• Password protected
• Username mb_340
• Password tS043F
• Textbook
• No specific textbook
• Will place readings on website
• Some books placed on reserve
• Avise JC (1994) Molecular Markers, Natural
  History and Evolution
• Very good reading book, slightly outdated ( 91
  for paperback)
• Freeman S Herron JC (2001) Evolutionary
  Analysis. Prentice Hall
• Excellent textbook, used by other courses ( 92,
  used 65)
• Futuyma DJ (1998) Evolutionary Biology. Sinauer
  Associates.
• Excellent general book on macroevolution, ( 93,
  used 66)

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Assessment

• Laboratory participation 15
• Computer labs problems and write ups.
• Practical labs short report (1 or 2 pages)
• Term Paper 15
• Scientific paper of lab results
• Other Assignments 20
• Two essays on scientific papers we will provide
• Mid term exam 20
• Final exam 30

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Lab SectionComputer Labs and Practical Labs

• Computer labs
• Aims
• Consolidation of lecture material by computer
  simulation
• Hands-on experience with data analysis and
  software
• Training in independent thinking
• Assignments
• Problems given after each computer lab

• Practical labs
• Project
• Species identification of rockfish fillets
• Aims
• Hands-on experience in the lab
• Experience in interpretation of molecular gels
• Exercise in scientific writing
• Assignments
• Lab write-ups
• Final report on findings in all labs

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Lab Sections

• Unbalanced
• 20 on Thursday, 10 on Friday
• Additional people on Th
• If possible, please move to Friday
• Advantage for you
• Easier access to equipment
• More interaction with instructors
• Smaller groups
• Advantage for us
• More interaction with you
• Easier demonstration

Th
Fr
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FirstPlease tell me where you are

• Crossword
• Hand out clues
• Read and mark the ones you know
• Idea is that you start where you feel most
  comfortable
• 5 min
• Hand out crosswords
• Fill in
• 10 min
• Not graded
• Dont put you name on
• Its purposefully difficult dont expect to
  know everything
• Lets me know where to start

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What is Molecular Ecology?Why are we all here?

• The application of molecular genetic markers to
  ecology and evolution
• Molecular genetic markers Genes or proteins that
  can be used to identify individuals, populations
  or species
• Human Forensics
• Molecular Ecology in the courtroom

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Why use molecular markers ?Key Concepts

• What are the features of molecular markers that
  make them particularly useful?
• Molecular markers
• Are universal
• Are heritable
• Are stable
• Have almost unlimited variability
• Can distinguish between homologies and analogies
• Provide tools for genome analysis
• Can assess microbial communities
• Are there reasons not to use molecular markers?

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Why use molecular markers ?

• Molecular markers are universal

• All life contains DNA
• Common yardstick throughout life
• Compare life-forms which are different
  morphologically, physiologically, ecologically
• For example

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Why use molecular markers ?

• Molecular markers are universal

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Why use molecular markers ?
Molecular markers are heritable

• Markers are passed on to next generation
• Tagging only possible for (adult) individuals
• Molecular markers inherited
• Detectable in offspring
• E.g. hatchery salmon
• E.g. you!!

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Why use molecular markers ?
Molecular markers are heritable

• Can be used to reconstruct pedigrees
• E.g. captive breeding in zoos

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Why use molecular markers ?
Molecular markers are heritable

• Can be used to reconstruct pedigrees
• E.g. captive breeding in zoos
• Or to investigate relatedness in wild populations
• E.g. extra pair mating in birds

piping plover
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Why use molecular markers ?
Molecular markers are stable

• Stable throughout the lifetime of an individual
• Can compare different life-history stages
• Not dependent on environment
• Unlike morphometrics, physiology etc.

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Why use molecular markers ?
Molecular markers are stable

• DNA is a very stable molecule
• Extracted from Egyptian mummies
• Not from dinosaur blood in mosquitoes!
• Can be used to reconstruct the past
• Scale samples
• Non-destructive sampling
• Fecal samples
• Hair
• Feathers

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Why use molecular markers ?
Molecular markers have almost unlimited
variability

• Human genome
• About 30,000 genes
• If only 300 are variable (1)
• 2 alleles (A, B)
• 3 genotypes (AA, AB, BB)
• 3300 genotypes
• 10143 genotypes!
• Human population
• Present 6 x 109
• Ever alive 13 x 109
• 10133 possible genotypes / human
• number of electrons in visible universe 1075
• No two humans are the same
• Except identical twins
• Used in forensics

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Why use molecular markers ?
Molecular markers can distinguish homologies from
analogies

• Major problem in systematics and evolution
• Analogy
• Identity by state (convergent evolution)
• E.g. bird wing and butterfly wing
• Homology
• Identity by descent
• E.g. bird wing and dolphin flipper

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Why use molecular markers ?
Molecular markers can assess microbial communities

• Microorganisms
• Play an important role in ecology
• Element recycling
• Important bioindicators
• Only 1 culturable
• Molecular markers can separate species
• For example
• River Changjiang (China)
• Samples taken from a gradient along the river
• Shows change in bacterial community
• Bands can be sequenced and bacteria identified

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Why use molecular markers ?
Molecular markers provide tools for genome
analysis

• Genomics
• Will hear more about that later
• Human genome project
• Completely sequenced
• Postgenomics
• What does it all mean?

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Publicationsusing molecular markers
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Why NOT (only) use molecular markers ?
(New) molecular markers are not the Holy Grail

• Explosion in the development of new methods
• (and acronyms)
• Techniques in search of a problem
• Do not always deliver

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Why use molecular markers ?

• Molecular markers
• Are universal
• Are heritable
• Are stable
• Have almost unlimited variability
• Can distinguish between homologies and analogies
• Provide tools for genome analysis
• Can assess microbial communities
• Molecular markers are not
• 42 (the answer to the great question of life,
  the Universe and everything Douglas N. Adams,
  1981)

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But

• Molecular markers have revolutionized our
  understanding of
• Mating systems
• Population ecology
• Conservation biology
• Taxonomy and species ID
• Species ID
• Especially micro-organisms
• Like most good approaches in science, molecular
  markers have provided more good questions than
  good answers
• And thats why we are here!