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