Synthesizing Neutral Theories of Ecology and Molecular Evolution

1. Synthesizing Neutral Theories of Ecology and Molecular Evolution Ken Locey

2. Neutrality • "Variations neither useful nor injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphicspecies, or would ultimately become fixed, owing to the nature of the organism and the nature of the conditions." (Darwin, 1859)

3. Neutral Theory of Molecular Evolution (MNT) • Motoo Kimura (1968) • 1. Vast majority of molecular differences are selectively neutral • 2. Most evolutionary change is the result of genetic drift acting on neutral alleles

4. Ecological Neutral Theory(ENT) • Hubbell (2001) • 1. Majority of ecological differences within a community are competitively neutral • 2. Most demographic change among species is the result of ecological drift.

5. ENT • Species • Species abundance • θ = 2JMV • Speciation/Dispersal • Distribution of species abundance • Ecological drift MNT • Allele • Allele frequency • θ = 4NeV • Mutation/Migration • Distribution of allele frequencies • Genetic drift

6. Brand X • Alleles and Species • Allele frequency and species abundance • θ1 = 4NeV , θ2 = 2JMV • Mutation, Speciation, Migration • Distribution of allele frequencies and species abundances • Genetic drift and Ecological drift

7. MENT, EMNT? • Some unit • Abundances of some unit • θ = 42 • Mutation, Speciation, Evaporation, Condensation • Distribution of unit abundances • drift

8. MENT, EMNT? • Some unit • Abundances of some unit • θ = 42 • Mutation, Speciation, Evaporation, Condensation • Distribution of unit abundances • drift

9. SyMENT Synthesized Molecular Ecological Neutral Theory • Goal: to account for how genetic diversity is generated and distributed via random drift among ecologically equivalent individuals that interact genetically, ecologically, or both. SyMENT

10. Synthesized Molecular Ecological Neutral Theory (SyMENT) • Question: What unit will the stochastic process act on to affect both molecular and ecological diversity? • Answer: Genomes Genomes?

11. Foundational statements for SyMENT • Molecular changes involve changes within and among genomes of individuals and ecological changes involve the replacement of an individual of one genome with that of another. • All changes within and among genomes involves genomic sequences. • All genomic sequences have a size.

12. Size matters • Sequence size is a general attribute that captures changes within and among genomes of individuals of a community

13. Relating sequences size to genome changes • Some events are more frequent, and hence, more likely than others • Replacing one genome with another (i.e. reproduction) is more likely than adding a copy of a gene (i.e. gene duplication) • Replacing a base with a base (i.e. point mutation) is more likely than adding a copy of a gene (i.e. horizontal gene transfer)

14. First obvious source of systematic error (i.e. rule #1): • Allow randomly chosen sequences of similar relative size (0-100%), from randomly chosen individuals, to replace one another • A base can replace a base • A genome can replace a genome • An allele can replace an allele

15. Replace .01% of B with .01% of A A B B+

16. Replace .01% of B with .01% of A A B B+ Replace 99.99% of B with 99.99% of A A B A+

17. Probability of a genomic change involving a sequence of a particular size Point mutation Point mutation + Individual replacement P (being involved in a replacement) 50/50 combination 50% % Length of Genome

18. Probability of a genomic change involving a sequence of a particular size MNT ENT& MNT P (being involved in a replacement) 50% % Length of Genome

19. Deriving the shape of the distribution Individual replacement (w/ point mutation) point mutation P (being involved in a replacement) 50/50 combination 50% % Length of Genome

20. Deriving the shape of the distribution Individual replacement (w/ point mutation) point mutation Individual replacement w/Gene changes P (being involved in a replacement) Gene changes 50/50 combination 50% % Length of Genome

21. Deriving the shape of the distribution Individual replacement (w/ point mutation) point mutation Individual replacement w/Gene changes P (being involved in a replacement) Gene changes 50/50 combination 50% % Length of Genome

22. Beta distribution: β < 1, α < 1 including β = α < 1 Hand drawn, not drawn to scale, & enlarged to show texture P DF 0.0 1.0

23. Beta distribution: β < 1, α < 1 MNT ENT& MNT P DF 0.0 1.0

24. Beta distribution: β < 1, α = 1or β ≤ 1, α > 1 ENT& MNT P DF 0.0 1.0

25. MNT ENT& MNT 0.0 1.0 P DF ENT& MNT 0.0 1.0

26. MNT ENT & MNT Microbes 0.0 1.0 P DF Log abundance Macrobes ENT & MNT 0.0 1.0 Rank

27. A genome sequence 1000 copies 10,000 bases each

28. SyMENT simulation model 1000 copies 10,000 bases each

29. SyMENT simulation model replacements MUMmer 1 vs 1: 100% 1 vs 2: 79% 1 vs 3: 99% Align and compare against

30. Ecological drift RAD’s distributions will go to ‘equilibrium’ between the rise of new groups and extinction of others. U-shaped/ Microbes J-shaped/ Macrobes Rank

31. OTU-RADs

32. Genetic Drift…community style • How similarity within groups varies with abundance • Prediction: Similarity varies negatively with abundance ? %Similarity w/in a Group ? ? Rank in abundance

33. Similarity decreases with rank in abundance T = 500K, α = 1, β = 0.001

34. SyMENT ENT & MNT ENT & MNT MNT Community Population Individual