4. Sources for the Origin of Novelty
• New biochemical functions
– Evolution of new genes
– Old genes with new functions
– Mixing and matching existing genes
• Changes in uses of existing genes
– Targeting
– Regulation
• Acquisition of new functions
– Recombination
– Lateral gene transfer
– Symbioses
7. “Nothing in biology makes sense
except in the light of evolution.”
T. H. Dobzhansky (1973)
8. Phylogenomic Analysis
• Evolutionary reconstructions greatly
improve genome analyses
• Genome analysis greatly improves
evolutionary reconstructions
• There is a feedback loop such that these
should be integrated
9. Wolbachia pipientis wMel
• Wolbachia are obligate, maternally transmitted
intracellular symbionts
• Wolbachia infect many invertebrate species
– Many cause male specific deleterious effects
– Model system for studying sex ratio changes in hosts
– Some are mutualistic (e.g., in filarial nematodes)
• wMel selected as model system because it infects
Drosophila melanogaster
19. Endosymbiont Trends
• Compared to free-living relatives
– Smaller genomes
– Lower GC content
– Higher pIs
– Higher rates of sequence evolution
• Wolbachia shows ALL of these
20. Explanations for Endosymbiont
Differences with Free-Living Relatives
• Repair hypothesis
– Loss of DNA repair genes leads to increased mutation rate
– Trends are the direct and indirect result of this increased mutation rate
• Population genetics hypothesis
– Smaller effective population size leads to more genetic drift
– Trends are mostly the result of accumulation of slightly deleterious
mutations
• PopGen explanations favored
– Wolbachia has full suite of repair genes
21. Endosymbiont Trends
• Compared to free-living relatives
– Smaller genomes
– Lower GC content
– Higher pIs
– Higher rates of sequence evolution
• Wolbachia shows ALL of these
• However ….
26. Glassy Winged Sharpshooter
• Feeds on xylem sap
• Can transmit Pierce’s
Disease agent from
infected plants to
uninfected plants like
mosquitoes with malaria
• Potential bioterror agent
• Needs to get amino-
acids and other nutrients
from symbionts like
aphids
36. Endosymbiont Trends
• Compared to free-living relatives
– Smaller genomes
– Lower GC content
– Higher pIs
– Higher rates of sequence evolution
• Baumannia shows ALL of these
40. Polymorphisms in Metapopulation
• Data from ~200 hosts
– 104 SNPs
– 2 indels
• PCR surveys show that this
is between host variation
• Much lower ratio of
transitions:transversions than
in Blochmannia
• Consistent with absence of
MMR from Blochmannia
45. Suggested Methods for Binning Did
Not Work Well
• Assembly
– Only Baumannia generated good contigs
• Depth of coverage
– Everything else 0-1X coverage
• Nucleotide composition
– No detectible peaks in any vector we looked at
46. Binning by Phylogeny?
• Identified putative genes
• Built phylogenetic trees
• Examined and classified trees
57. What is Next?
• More endosymbioses
– Diversity of host species
– Diversity of symbionts
– Diversity of biology
• Epibionts and other obligate symbioses
• Commensals
– Human gut
– Hotspring mats
58. TIGRTIGR
Other peopleOther people
Mom and DadMom and Dad
H. OchmanH. OchmanF. RobbF. Robb
J. BattistaJ. Battista
E. OriasE. Orias
D. BryantD. Bryant
S. O’NeillS. O’Neill
M. EisenM. Eisen
N. MoranN. Moran
R. MyersR. Myers
C. M. CavanaughC. M. Cavanaugh
P. HanawaltP. Hanawalt
J. HeidelbergJ. Heidelberg
N. WardN. Ward
J. VenterJ. Venter
C. FraseC. Fraser
S. SalzbergS. Salzberg
I. PaulsenI. Paulsen
$$$$$$
NSFNSF
DOEDOE
NIHNIH
M. WuM. Wu
D. WuD. Wu
S. ChatterjiS. Chatterji
H. HuseH. Huse
A. HartmanA. Hartman
MooreMoore
VIVI
D. RuschD. Rusch
A. HalpernA. Halpern
EisenEisen
GroupGroup
J. MorganJ. Morgan
JGIJGI
E. EisenstadtE. Eisenstadt
M. FrazierM. Frazier
T. WoykeT. Woyke
E. RubinE. Rubin
61. C. magnifica symbiont sequencing
• Collaboration between Cavanaugh Lab at
Harvard (Irene Newton led analysis), Eisen
lab, and JGI (Woyke and others).
• Funded by DOE through CSP program and
sequencing and closure done at JGI
• Annotation and analysis involved DOE
(JGI, ORNL), Harvard, TIGR, Davis, et al.
66. Correlation of Endosymbiont Features
• Correlation makes
it difficult to tease
apart cause and
effect
• Need examples
where properties
are decoupled
• May be the case in
Baumannia with
genome size
67. Long Term Effects of Repair Loss
• Endosymbionts are model systems for understanding the
consequences of loss of repair activities
• RecA lost in Buchnera and Blochmannia but kept in
Baumannia and Wigglesworthia
• MutSL loss mentioned previously
• RecBCD present even in species without RecA
• Mfd present in many species without UvrABCD
68. Endosymbionts and Extremophiles
Origin of New Functions
Species
Evolution
Genome
Dynamics
Phylogeny,
Processes,
Biogeography,
Convergence
Mutation,
Selection,
Repair,
Replication
Multiple Origins,
Simple Communities
New genes,
Changes in old genes,
AcquisitionEisen
Lab
69. Comparative vs. Evolutionary
Approaches
• Comparative approaches involve
documenting similarities and differences
• Evolutionary approaches involve
documenting how and why the similarities
and differences arose
70. Comparative vs. Evolutionary
Topic Comparative Evolutionary
Structure
prediction for
rRNA
Conserved regions Correlated
changes along
tree
Gene presence vs.
phenotpye
Presence and
absence of genes
Gain and loss,
lateral transfer
Selection Degree and pattern
of conservation
HKA, Ds/Dn
Functional
prediction
Ranking by level
of similarity
Predicting
function from
trees
71. Phylogenomic Analysis
• Evolutionary reconstructions greatly
improve genome analyses
• Genome analysis greatly improves
evolutionary reconstructions
• There is a feedback loop such that these
should be integrated
Editor's Notes
The Wolbachia genome revealed an unexpectedly high amount of repetitive DNA and mobile genetic elements (which were never seen before in a small-genomed intracellular species)