Whale of a Tale: Solving Mysteries of Declining Whale Populations

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Whale of a TaleSolving Mysteries of Declining
Whale Populations
Name this whale. Hint Globicephala melas
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Whats the problem?

• International moratorium on whaling 1986
• Certain species did not rebound.
• Develop your own hypothesis.

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A Few Whales and Their Statuses
Data from International Union for Conservation
of Nature, 2004
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Scott Bakers Hypothesis

• Baker feels the protected whales are still being
  hunted by Japanese Fishermen.
• How would you collect data to back up this
  hypothesis?

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What is Bioinformatics??

• Biological Data
• Computers
• Statistics
• Information Science
• Internet

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Biological Data

• Lots of data!
• DNA Sequences
• RNA
• Protein Sequences
• Protein Structures

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Computers and Bioinformatics to

• Store Data
• Retrieve Data
• Analyze Data
• Many Tools on Internet, for free
• Solve biological problems

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What does a Bioinformatics tool look like and how
can it be used?
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Bioinformatics to Examine Catches from Japanese
Fish Markets

• Scott Baker-Sampled 655 Whale Products in
  Japanese Fish Markets, 1997-2002
• Sequenced DNAs of Samples
• Witness for the Whales
• Whale, dolphin, and porpoise DNA sequences
  submitted into database

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Lab Analysis Sequence of __.
Unknown1 GAAAATATATATTGTACAATAACCACAAGGCCACAGTATTA
TGTCCGTATTAAAAATAACTTATTTTATTGCATACTGTTATGTAACTTGT
GCATGTATGTACTCCCACATAACCCATAGTAGTTAGTATTCCCCTGTGAA
TATGTATATGTACACATACTATGTATAATTGTGCATTCAATTATCTTCAC
TACGGAAGTTAAAGCCCGTATTAAATTTTATTAATTTTACATATTACATA
ATATTTATTAATAGTACAATAGTACATGTTCTTATGCATCCTCAGGTCAT
TCTAGACGGAATGACTCTTATGGCCGCTCCATTAGATCACGAGCTTAATC
AGCATGCCGCGTGAAACCAGCAACCCGCTCGGCAGGGATCCCTCTTCTCG
CACCGGGCCCATCAATCGTGGGGGTAGCTATTTAATGATCTTTATAAGAC
ATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTC
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BLAST Basic Local Alignment Search Tool

• http//www.ncbi.nlm.nih.gov/BLAST/
• Compares nucleotide or protein sequences against
  others submitted into database
• Useful in identifying an unknown sequence or
  finding closely related sequences

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BLAST Applications

• With a DNA sequence, you could
• find out the species.
• determine the gene location (if known).
• find the corresponding amino acids.
• determine protein shape function.
• diagnose possible mutations.
• compare to other species for molecular
  relatedness.
• do much, much, more!

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Most of Whale Meat Legal But

• Grey Whale--illegal
• 10 of Samples Illegal
• 10 of Samples Sheep and Horse!
• Bioinformatic Tools for Tracking Species,
  Conservation, Ecology, and Environment

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Results (cont.)

• These results confirmed the power of molecular
  methods for monitoring retail markets and pointed
  to the inadequacy of the current moratorium for
  insuring the recovery of protected species. More
  importantly, the integration of genetic evidence
  with a model of population dynamics identified an
  urgent need for actions to limit undocumented
  exploitation of a 'protected' stock of whales .

Predicted Decline of protected whales based on
molecular genetic monitoring of Japanese and
Korean markets PROC. ROY. SOC. LOND. B, VOL 267,
NO. 1149, 22 JUNE 2000.C.S. Baker, G.M. Lento,
F. Cipriano and S.R. Palumbi
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Meet Scott Baker
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