The role of genomic islands of divergence during speciation. Connor Morgan-Lang November 18th

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1 The role of genomic islands of divergence during speciation Connor Morgan-Lang November 18th

2 Outline 1) Review of speciation 2) Genomic architectures 3) Genomic islands of divergence 4) Methods for identification

3 (Basic) mechanics of speciation Pre- and/or post-zygotic reproductive barriers Reproductive isolation between populations

4 (Basic) mechanics of speciation Genome is differentiating between populations The threshold is the upper limit of expected neutral divergence with no gene flow Above sea level genetic divergence indicates locus is under divergent selection Genetic divergence Sea level Genomic position

5 (Basic) mechanics of speciation Speciation (isolation) genes Genes that contribute to reproductive isolation Genetic divergence Selected locus Genomic position

6 Genomic architectures of diverging populations Genome architecture between populations with no gene flow (allopatry) Roughly uniform, extensive divergence Genetic divergence Genomic position

7 Model with gene flow (sympatry) Heterogeneous genomic divergence Nosil, P., Funk, D. J., & Ortiz-Barrientos, D. (2009). Divergent selection and heterogeneous genomic divergence. Molecular Ecology, 18(3),

8 Why do these exist? There is a distinct advantage in reducing the recombination between locally adapted loci Certain combinations of alleles will have the highest fitness in a specific environment

9 Why do these exist? Arise from regions with reduced recombination rate Strength of the barrier (θ) is the ratio of selective pressure on barrier loci to recombination rate (Barton & Bengtsson, 1986): θ=s/r Where: S is the total strength of selection on the barrier Number of loci (n) multiplied by the selection coefficient (s) R is the total map length (in cm) Number of loci multiplied by the map distance (r)

10 Why do these exist? Arise from regions with reduced recombination rate Renaut, S., Grassa, C. J., Yeaman, S., Moyers, B. T., Lai, Z., Kane, N. C., Rieseberg, L. H. (2013). Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nature Communications, 4.

11 Why do these exist? Arise from regions with reduced recombination rate Rearrangements, such as inversions, are frequently involved in local adaptation Loci being actively selected have decreased recombination rates Gives hitchhiker loci the opportunity to develop advantageous mutations divergence hitchhiking Reduces gene flow between populations!

12 Creation: Chromosomal region with low recombination rate (e.g., inversion site) creating a static rearrangement Figure from: Minkoff E.C Evolutionary Biology. Addison-Wesley, Reading, Mass. May encapsulate beneficial alleles and immediately rise in frequency (Nosil and Feder, 2012) Or mutations are eventually introduced to these regions via mutation

13 Creation: Divergence hitchhiking Genetic divergence Divergent selection on one or more loci carries hitchhiker (neighbouring) loci along during local adaptation Advantageous mutation! Genomic position

14 Creation: Divergence hitchhiking Divergent selection on one or more loci carries hitchhiker (neighbouring) loci along during local adaptation Genetic divergence Genomic position

15 Creation: Divergence hitchhiking Divergent selection on one or more loci carries hitchhiker (neighbouring) loci along during local adaptation Heavily dependent on some mechanism to reduce recombination rate

16 Islands may grow if: Hitchhiker loci accumulate mutations that are advantageous for local adaptation Loci responsible for local adaptation (thus conferring a fitness advantage) are clustered Genomic rearrangement model (Yeaman, 2013)

17 Φ = strength of selection m = migration rate N = population size τ = rearrangements/ locus/ generation Yeaman, S. (2013). Genomic rearrangements and the evolution of clusters of locally adaptive loci. Proceedings of the National Academy of Sciences of the United States of America, 110(19).

18 Dynamics in the face of gene flow Gene flow restricted near the selected loci and increases with distance from selected loci Effective migration rate indicates level of gene flow me = δp / Δp (Barton and Bengtsson, 1986) Where: - δp is the change in allele frequency due to migration - Δp is the difference between allele frequencies between two populations

19 Identification of Genomic Islands Genome scans: Looking for outlier loci loci that have become significantly more diverged than expected FST is used to measure the fixation of alleles (e.g. SNPs, indels, etc.) FST of populations are compared at all sites If there exists a fixed difference above some threshold, the locus is considered an outlier

20 Identification of Genomic Islands Renaut, S., Grassa, C. J., Yeaman, S., Moyers, B. T., Lai, Z., Kane, N. C., Rieseberg, L. H. (2013). Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nature Communications, 4.

21 Take-home message Genomic islands of divergence are an analogy to describe a possible genomic architecture found during the speciation process They act as a formidable barrier to gene flow, reinforcing the initial gene flow barrier Formed by divergent selection and reinforced by reduced recombination A possible driver of speciation

22 References Barton, N., & Bengtsson, B. (1986). The barrier to genetic exchange between hybridising populations. Heredity, 56, Nosil, P., Funk, D. J., & Ortiz-Barrientos, D. (2009). Divergent selection and heterogeneous genomic divergence. Molecular Ecology, 18(3), Nosil, P., & Feder, J. L. (2012). Genomic divergence during speciation: causes and consequences. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 367(1587), Rieseberg, L. H. (2001). Chromosomal rearrangements and speciation. Trends in Ecology & Evolution, 16(7), Renaut, S., Grassa, C. J., Yeaman, S., Moyers, B. T., Lai, Z., Kane, N. C., Rieseberg, L. H. (2013). Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nature Communications. Yeaman, S. (2013). Genomic rearrangements and the evolution of clusters of locally adaptive loci. PNAS, 110(19).