paul hebert - saturday closing plenary
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Barcodes, Organelles, Genomes
Paul Hebert Justin Schonfeld
Sujeevan Ratnasingham
Sequence Data for Arthropod Species
Genomes - 46
Mitochondrial Genomes - 214
Barcodes - 121,000
Probing Arthropod Mitochondrial Genomes With DNA Barcodes
1. Nucleotide Composition
2. Amino Acid Evolution
3. Structural Change
55%
60%
65%
70%
75%
80%
85%
90%
50% 55% 60% 65% 70% 75% 80%
Gen
ome
Sequ
ence
COI
A/T % inArthropod Mitochondrial Genomes vs COI
Nucleotide Composition of COI in Arthropods
1
10
100
1000
10000
100000
42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90
# of
Spe
cies
AT Composition (%)
Crustaceans Scale Insects
Nucleotide Composition of COI in 17 Insect Orders
% AT
% o
f Spe
cies
Nucleotide Composition of COI in Two Insect Orders
% AT
Spec
ies
0.60 0.65 0.800.70 0.75
2,000
0
4,000
6,000
8,000
10,000
Hymenoptera
Lepidoptera
Barcode Region as a Sentinel for Mitochondrial Evolution
Amino Acid SubstitutionsInsertions & Deletions
0.0
0.2
0.4
0.6
0.8
1.0
atp6 atp8 nd1 nd2 nd3 nd4 nd4l nd5 nd6 co2 co3 cytb
Cor
rela
tion
with
CO
I
Amino Acid Divergence in COI Versus Other Mitochondrial Proteins
Amino Acid Divergences in the Barcode Region forDifferent Families of Hymenoptera
Amino Acid Divergences in the Barcode Region for Two Insect Orders
Lepidoptera Hymenoptera
atp6 nd1 nd2 nd3 nd4 nd41 nd5 co1 co2 co3 cytb
Lepidoptera
Hymenoptera
>30
25
20
15
10
5
0
# of Indels in Mitochondrial Genes of Two Insect Orders
Indels in the barcode region for Lepidoptera and Hymenoptera
3 bp
6 bp
9 bp
Varied Rates of Protein Evolution & Indels in Barcode Region
Haplodiploid
Diploid
Insect Phylogeny and Haplodiploidy
Haplodiploid
Some Haplodiploid
DiploidHaplodiploid
Amino Acid Divergences at COI for Diploid Hemiptera
Amino Acid Divergences at COI for All Hemiptera
DiploidHaplodiploid
WHY?It aids co-evolution of nuclear and mitochondrial genomes
BASIS FOR CO-EVOLUTION10% of nuclear gene products are exported to the mitochondrion.Nuclear and mitochondrial gene products interact stronglyMale haploidy provides perfect screening system for nuclear variants
improving mitochondrial performance
EVIDENCE FOR CO-EVOLUTIONMolecular analysis shows residue by residue substitutions Studies on cybrids
Haplodiploidy Greatly Accelerates Mt Evolution
80 %Chimpanzee mt
0 %Orangutan mt
80 %Gorilla mt
0 %Lower Primate mt
Evidence for Co-evolutionATP generation in Cybrids
Human Nucleus +
Does the accelerated rate of mtDNA evolution in haplodiploids provide insight into general patterns
of mtDNA evolution?
CONSIDER:1. Land Plants2. Cnidarians3. Fungi4. Protists
Consider Land Plants
Consider Land PlantsA ThreeParticle Problem
Consider Land Plants
A ThreeParticle Problem
A ThreeParticle Problem
Consider Corals
Consider Other Cnidaria A TwoParticle Problem
Consider Fungi A TwoParticle Problem
A TwoParticle Problem
Consider Non-Photosynthetic Protists
A ThreeParticle Problem
Consider Photosynthetic Protists
Consider SeaweedsA ThreeParticle Problem
But someHaplodiploids
Fast Runners
Why Does Haplodiploidy Evolve?Might rapid mitochondrial evolution convey an advantage in Red Queen situations?
Now, here, you see, it takes all the running you can do to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!
ChurchillCecidomyiidae
Cecidomyiidae
Tenthredinidae
Tenthredinidae
Eriophyidae
San Diego
Cynipidae
Tenthredinidae
Cecidomyiidae
Cynipidae
Adelaide
Eriococcidae
Eriococcidae
Thysanoptera
Eulophidae
Eriococcidae
Consider Parasitoids
Mitochondrial genomes are fractals
Interactions among genomic compartments impact molecular evolution
These interactions can explain the lack of a universal barcode marker
The Red Queen may drive genomic structure
Horizontal Genomics – We have only begun!
Consider Mosses and Ferns
A ThreeParticle Problem
ButHaplodiploids
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