Evolution of Animal Body Plans
Holland 2003 Nature Reviews Neuroscience Vol 4.
Ctenophores?
Modified from
Pang et al 2010
Combination of markersEST Sequences
Phylogenomic Data
Morphological Data 18S rDNA
Phylogenom...
Placozoa – creeping detritivore/algavore,
diploblastic, continually change shape
Cnidaria – planktonic or sessile predator...
Andrea Kohn Leonid Moroz
Billie Swalla
Mat Citrella
2010 and 2012
Genomics
Apprenticeships
At FHL
The Early Evolution of Nervous System
Development:
Genomics of Pleurobrachiabachia
Undergraduate Research
Apprenticeship
Genome Biology
• Undergraduate students engaged in field activities
• Enhance comput...
Friday Harbor Labs - San Juan Island
Beautiful setting, amazing biological diversity, all students doing research in the c...
New Computer Lab for teaching Computational Methods
Bioinformatics/Modelling/Phylogenetics/Genomics
Specific genes inform us about animals
Cell-Cell adhesion (Collagens) Nathan
Germ Line
(Piwi) - Caleb
(Nanos)-Gabby
Epigen...
Ctenophores are small marine
organisms
Ctenophores are basal
metazoans
Figure 1. Basal metazoan phylogenetic relationship.
From Dunn et al. 2008.
Placozoa
Cnidar...
Ctenophore anatomy
Mouth
Stomach
Tentacle bulb
Combs
Apical organ
Tentacle
Figure 2. Pleurobrachiabacheianatomy.
The Apical Organ - one of the
first centralized nervous
systems
Comb Rows
BalancersStatolith
Dome
Polar Fields(PF)
The PleurobrachiabacheiGenome
• First ever genome from an
FHL animal to be sequenced.
– Being the first ctenophore
genome ...
The Pleurobrachia Genome
• Five separate libraries (3 fragmented, 2 paired-end) were
constructed, but satisfactory annotat...
Genomic
organization
of P2X
Kohn, AB. (2010) Phylogenomics of P2X receptors. Unpublished
1
Importance of The Wnt Signaling
Pathway
• gastrulation
• germ layer specification
• axial polarity
• Patterning of limbs
•...
Cell Membrane
LRP
Frizzled
Dishevelled
Β-catenin
NucleusAxin
APC
Gsk-3
Β-catenin
Cytoplasm
p
Degraded
Secreted Frizzled
An...
Pleurobrachia Wnt genes contain
conserved Wnt domain characteristics
Pb Wnt X
WNTMl Wnt X
100aa
Domain organization:
SMART...
Wnt conservation between ctenophores
M. leidyi
P. bachei
Wnt Frizzled Dickkopf WIF Ceberus
Homo 19 Yes Yes Yes Yes
Saccoglossus
Branchiostoma 10+? Yes Yes No No
Drosophila 7 Yes N...
Common Wnt Pathway Components present and
missing in basal metazoans
Gene P. bachei M. leidyi A. queenslandica
Wnt 3 4 3
F...
Scientific Conclusions
• Pleurobrachiacan show us the minimum
members ofsignaling pathways needed for
function
• Wnt, TGFß...
Education Conclusions
• Students learn computational skills easily when
they are immersed in a research experience
• Stude...
Acknowledgements
• Wonderful Professors:
Dr. Andrea Kohn,Dr. LenoidMoroz, Dr. Billie
Swalla
• Amazing TAs: Gabrielle Winte...
Upcoming SlideShare
Loading in …5
×

Getting undergrads excited about evolution and science

717 views

Published on

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
717
On SlideShare
0
From Embeds
0
Number of Embeds
25
Actions
Shares
0
Downloads
6
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • Ctenophores- also called comb jellies (Greek- ctene= comb, phore= carry)A phylum of small jelly-filled animals that live all throughout the world in marine habitats.Size- Pleurobrachiabachei – pea sized to large grapeMain feature are their combs or ctenes which are rows of cilia used for swimming. Predators which eat small marine animals.
  • Ctenophores are one of the most basally branched organisms. Relationship between all the basal metazoans has been an issue of debate. Placozoa- one species in this phyla “trichoplaxadhaerens”Cnidarians – jelliesPorifera – SpongesOur ctenophoresChoanozoa – choanoflagellates - outgroup- single celled organisms that aren’t considered animals, but are the closest relative of animals. Highly debated whether porifera or ctenophora branched off first.This tree supported from ***
  • Ctenophore anatomy-Highly coordinated ciliary movement and predation skills suggests complex nervous systemApical organ- nervous system structure
  • Apical organ- early brain?Their basal position in the Metazoa, along with the presence of a nervous system containing a nerve net and an apical organ make ctenophores the ideal candidate for studies concerning the early evolution of the nervous system
  • WHAT IS A SIGNALING PATHWAY EXPLAIN-Signaling pathway transduces a signal from the outside of the cell to the inside of the cell and interacts in a cascade of events to induce a specific response WHY ARE PLEUROBRACHIA a good system to look at this in??-Because they are a basal metazoan so we can gain key insight onto the early evolution of this pathway.
  • Things missing in PB-FOUND by doing genome wide search why having a sequenced genome is so nice
  • EXPLAIN THAT THIS IS ONE OF 3 WNT Genes found in PBWnt domain contains common charactorists of a secretory peptideContains signal peptide N- glycosylation sites22 conserved cysteines used for disulfide bonds
  • EXPLAIN THAT PB is missing a homolog to WNT A
  • Explain expansion occurs in common ancestor to cnidarians and bilitarians
  • -
  • Getting undergrads excited about evolution and science

    1. 1. Evolution of Animal Body Plans
    2. 2. Holland 2003 Nature Reviews Neuroscience Vol 4. Ctenophores?
    3. 3. Modified from Pang et al 2010 Combination of markersEST Sequences Phylogenomic Data Morphological Data 18S rDNA Phylogenomic Data + More ESTs The position of Ctenophora on the Metazoan tree is unresolved
    4. 4. Placozoa – creeping detritivore/algavore, diploblastic, continually change shape Cnidaria – planktonic or sessile predators, diploblastic, radial symmetry Basal Metazoans exhibit a wide variety of body plans and life history strategies Porifera (Sponges) – sessile filter feeders, no true tissues, asymmetry Ctenophora (Comb Jellies) – active predators in the plankton, triploblastic, bi-radial symmetry Joint Genome Institute
    5. 5. Andrea Kohn Leonid Moroz Billie Swalla Mat Citrella 2010 and 2012 Genomics Apprenticeships At FHL
    6. 6. The Early Evolution of Nervous System Development: Genomics of Pleurobrachiabachia
    7. 7. Undergraduate Research Apprenticeship Genome Biology • Undergraduate students engaged in field activities • Enhance computational skills • Clone genes and examine gene expression to study evolution of nerve networks with marine invertebrates as a collaborative research experience. • Instructors and/or themes vary from year to year • FHL has housing, dining facilities & a computer classroom • Students are recruited from UW and other universities
    8. 8. Friday Harbor Labs - San Juan Island Beautiful setting, amazing biological diversity, all students doing research in the course, few distractions for them.
    9. 9. New Computer Lab for teaching Computational Methods Bioinformatics/Modelling/Phylogenetics/Genomics
    10. 10. Specific genes inform us about animals Cell-Cell adhesion (Collagens) Nathan Germ Line (Piwi) - Caleb (Nanos)-Gabby Epigenomics (DNMT) - Emily Cell-Cell signaling (WNTs) - Rebecca Mesoderm ? (Brachyury, BarX) - Isaac (Tropomyosin, Calponin, ß catenin) - Zander Neuronal Development (LIMs) - Rachel Neuronal Signaling (Glutamatergic pathway) - Josh Neuropeptides - David Evolution of Animal Body Plans Insights from Marine Genomics FHL Apprenticeship 2012
    11. 11. Ctenophores are small marine organisms
    12. 12. Ctenophores are basal metazoans Figure 1. Basal metazoan phylogenetic relationship. From Dunn et al. 2008. Placozoa Cnidaria Porifera Ctenophora Choanozoa (non-animal) Bilateria
    13. 13. Ctenophore anatomy Mouth Stomach Tentacle bulb Combs Apical organ Tentacle Figure 2. Pleurobrachiabacheianatomy.
    14. 14. The Apical Organ - one of the first centralized nervous systems Comb Rows BalancersStatolith Dome Polar Fields(PF)
    15. 15. The PleurobrachiabacheiGenome • First ever genome from an FHL animal to be sequenced. – Being the first ctenophore genome is both exciting and challenging because without the genomes of related organisms assembly must be done de novo. – Having the genome allows for comparison of homologies between phyla – other attempts to place them are “speculative”. • Size of genome = ~100-160 megabases Photo Credit: Mat Citarella
    16. 16. The Pleurobrachia Genome • Five separate libraries (3 fragmented, 2 paired-end) were constructed, but satisfactory annotation and assembly of the genome has not yet been accomplished. –This is due to short fragments from sequencing technology and highly repetitive regions of the genome that cause problems in assembly. • Currently: –Sequences: 5,431,390 reads –Bases: 1,924,202,519 bases –Coverage: 10X –Number of Contigs: 211,869 –Average Contig Size: 1,086 base pairs –Scaffold
    17. 17. Genomic organization of P2X Kohn, AB. (2010) Phylogenomics of P2X receptors. Unpublished 1
    18. 18. Importance of The Wnt Signaling Pathway • gastrulation • germ layer specification • axial polarity • Patterning of limbs • Central Nervous System Development • Wntpathway is oncogenic when mutated • Evolved in the metazoan common ancestor
    19. 19. Cell Membrane LRP Frizzled Dishevelled Β-catenin NucleusAxin APC Gsk-3 Β-catenin Cytoplasm p Degraded Secreted Frizzled Antagonists Dickkopf WIF Ceberus Conservation of Wnt Pathway in Pleurobrachia(OFF) ? ? DNA
    20. 20. Pleurobrachia Wnt genes contain conserved Wnt domain characteristics Pb Wnt X WNTMl Wnt X 100aa Domain organization: SMART database WNTAq Wnt 2 WNT =Exon In Situ Probe =Signal peptide
    21. 21. Wnt conservation between ctenophores M. leidyi P. bachei
    22. 22. Wnt Frizzled Dickkopf WIF Ceberus Homo 19 Yes Yes Yes Yes Saccoglossus Branchiostoma 10+? Yes Yes No No Drosophila 7 Yes No Yes No Caenorhabditis 5 4 No No No Capitella 12 Yes No? Yes No? Lottiagigantea 11 Yes No? Yes No? Nematostella 11 Yes Yes Yes No Trichoplax 3 Yes No No No Amphimedon 3 Yes No No No Pleurobrachia 3 Yes No No No Mnemiopsis 4 Yes No No No Monosiga 0 No No No No Choanoflagellates Ctenophores Sponges Placozoans Cnidarians Deuterostomes Evolution of Wnt in the Animal Kingdom Bilaterians Ecdysozoa Lophotrochozoa
    23. 23. Common Wnt Pathway Components present and missing in basal metazoans Gene P. bachei M. leidyi A. queenslandica Wnt 3 4 3 Frizzled (Fzd) 2 2 2 Secreted-frizzled related protein (Srfp) Present Present Present LRP Present Present Present APC No? Partial Present Missing domains Axin Dix-domain like protein Dix-domain like protein Axin domain with no B-Catenin binding domain GSK3 Present Present Present Dishevelled Present Present Present B-catenin Present Present Present TCF/LEF Present Present Present CK1 Present Present Present groucho Present Present Present WIF Absent Absent Absent Dickkopf Absent Absent Absent Cerberus Absent Absent Absent CREB-biding Protein (CBP) Present Present Present
    24. 24. Scientific Conclusions • Pleurobrachiacan show us the minimum members ofsignaling pathways needed for function • Wnt, TGFßand other developmental signals areexpressed in adult Pleurobrachia • There may beinvolved as neurotransmitters in Pleurobrachia
    25. 25. Education Conclusions • Students learn computational skills easily when they are immersed in a research experience • Students become more engaged when they have their own specific project • Speaking and writing skills are best taught over a period of time, with repetition. • Some students work better in a team, others individually, but computational analyses allow flexibility in projects.
    26. 26. Acknowledgements • Wonderful Professors: Dr. Andrea Kohn,Dr. LenoidMoroz, Dr. Billie Swalla • Amazing TAs: Gabrielle Winters, Caleb Bostwick, Emily Dabe, and Kevin Kocot. • The Best Bioinformaticians: Mat Citarella and David Girardo. • Funding: FHL, NIH, and NSF.

    ×