This document discusses mitochondrial genomes and DNA barcodes in arthropods. It presents data on the number of genomes, barcodes, and mitochondrial genomes that have been sequenced for arthropod species. It also shows graphs and data on the nucleotide composition of mitochondrial genomes and barcodes across different arthropod groups. A key point discussed is that haplodiploidy in arthropods is associated with faster evolutionary rates of mitochondrial proteins and more insertions/deletions compared to diploid groups. This is hypothesized to be due to co-evolution between mitochondrial and nuclear genomes enabled by the haploid stage in males.

1. Barcodes, Organelles, Genomes
Paul Hebert
Justin Schonfeld
Sujeevan Ratnasingham

2. Sequence Data for Arthropod Species
Genomes - 46
Mitochondrial Genomes - 214
Barcodes - 121,000

3. Probing Arthropod Mitochondrial
Genomes With DNA Barcodes
1. Nucleotide Composition
2. Amino Acid Evolution
3. Structural Change

4. A/T % in
Arthropod Mitochondrial Genomes vs COI
90%
85%
80%
Genome Sequence
75%
70%
65%
60%
55%
50% 55% 60% 65% 70% 75% 80%
COI

5. Nucleotide Composition of COI in Arthropods
Crustaceans Scale Insects
100000
10000
1000
# of Species
100
10
1
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
AT Composition (%)

6. Nucleotide Composition of COI in 17 Insect Orders
% of Species
% AT

7. Nucleotide Composition of COI in Two Insect Orders
10,000
8,000 Hymenoptera
Lepidoptera
Species
6,000
4,000
2,000
0
0.60 0.65 0.70 0.75 0.80
% AT

8. Barcode Region as a Sentinel for Mitochondrial Evolution
Amino Acid Substitutions
Insertions & Deletions

9. Amino Acid Divergence in COI
Versus Other Mitochondrial Proteins
1.0
0.8
Correlation with COI
0.6
0.4
0.2
0.0
atp6 atp8 nd1 nd2 nd3 nd4 nd4l nd5 nd6 co2 co3 cytb

10. Amino Acid Divergences in the Barcode Region for
Different Families of Hymenoptera

11. Amino Acid Divergences in the Barcode Region
for Two Insect Orders
Lepidoptera Hymenoptera

12. # of Indels in Mitochondrial Genes of Two Insect Orders
>30
Lepidoptera
25
Hymenoptera
20
15
10
5
0
atp6 nd1 nd2 nd3 nd4 nd41 nd5 co1 co2 co3 cytb

13. Indels in the barcode region for
Lepidoptera and Hymenoptera
3 bp
6 bp
9 bp

14. Varied Rates of Protein Evolution & Indels in Barcode Region

16. Haplodiploid
Diploid

17. Insect Phylogeny and Haplodiploidy
Haplodiploid
Some Haplodiploid

18. Diploid
Haplodiploid

19. Amino Acid Divergences at COI
for Diploid Hemiptera

20. Amino Acid Divergences at COI
for All Hemiptera
Diploid
Haplodiploid

21. Haplodiploidy Greatly Accelerates Mt Evolution
WHY?
It aids co-evolution of nuclear and mitochondrial genomes
BASIS FOR CO-EVOLUTION
10% of nuclear gene products are exported to the mitochondrion.
Nuclear and mitochondrial gene products interact strongly
Male haploidy provides perfect screening system for nuclear variants
improving mitochondrial performance
EVIDENCE FOR CO-EVOLUTION
Molecular analysis shows residue by residue substitutions
Studies on cybrids

22. Evidence for Co-evolution
ATP generation in Cybrids
0% 0% 80 % 80 %
Lower Primate mt Orangutan mt Chimpanzee mt Gorilla mt
Human Nucleus +

23. Does the accelerated rate of mtDNA evolution in
haplodiploids provide insight into general patterns
of mtDNA evolution?
CONSIDER:
1. Land Plants
2. Cnidarians
3. Fungi
4. Protists

24. Consider Land Plants

25. Consider Land Plants A Three
Particle
Problem

26. Consider Land Plants
A Three
Particle
Problem

27. Consider Corals A Three
Particle
Problem

28. Consider Other Cnidaria A Two
Particle
Problem

29. Consider Fungi A Two
Particle
Problem

30. Consider Non-Photosynthetic Protists A Two
Particle
Problem

31. Consider Photosynthetic Protists A Three
Particle
Problem

32. Consider Seaweeds
A Three
Particle
Problem
But some
Haplodiploids

33. Fast Runners

34. 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!

35. Churchill
Cecidomyiidae
Tenthredinidae
Cecidomyiidae
Tenthredinidae
Eriophyidae

36. San Diego
Cynipidae Cynipidae
Cecidomyiidae
Tenthredinidae

37. Adelaide
Eriococcidae
Thysanoptera Eriococcidae
Eulophidae
Eriococcidae

38. Consider Parasitoids

39. Mitochondrial genomes are fractals

40. Interactions among genomic compartments
impact molecular evolution

41. These interactions can explain the lack
of a universal barcode marker

42. The Red Queen may drive genomic structure

43. Horizontal Genomics – We have only begun!

45. Consider Mosses and Ferns
A Three
Particle
Problem
But
Haplodiploids