Fundamentals of Evoluon Fundamentals of Evoluon EEEB G6110 EEEB - - PowerPoint PPT Presentation
Fundamentals of Evoluon Fundamentals of Evoluon EEEB G6110 EEEB G6110 Session 11: The Coalescent Session 11: The Coalescent 1 Today's topics Today's topics 1. Recap (Fst, Wright-Fisher) 2. The coalescent 3. Coalescent simulaons
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Measure an inbreeding coefficient (deviaon of H from expected). Applied at different hierarchical grouping of alleles (e.g., individuals, subpopulaons) these stascs can measure populaon structure. The prob. two randomly sampled alleles are the same in an individual (compared to in a subpop or total), or that they are the same in one subpop (compared to the combinaon of two subpops).
hps:/ /en.wikipedia.org/wiki/F-stascs
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can be interpreted as a measure of populaon differenaon. If between two populaons is 1 then they are fixed for different alleles (no variaon is segregang in both populaons).
hps:/ /en.wikipedia.org/wiki/F-stascs
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Although is formally describe as paroning variance relave to the total populaon, in pracce we are oen interested in pairwise as a measure of differenaon between two populaons. This is simply done by re-defining what we mean by the total populaon.
source
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can be defined and measured in several ways. The measure itself is informave, and it also can set a benchmark against which to test hypotheses about selecon or introgressive gene flow.
“Genecs in Geographically Structured Populaons: Defining, Esmang and Interpreng FST.”
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“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.” "Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags"
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What is so interesng about the Heliconius buerfly radiaon? Do Heliconius populaons form good taxa (idenfiable by geography + morphology)? What types of paerns do the authors observe? And what do they conclude from these?
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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There are many examples of phenotypic convergence in Heliconius between closely related and distantly related species and populaons. Here the authors focus on H. cyndo and H. melpomene which co-occur broadly, rarely hybridize, but may have experienced adapve introgression. To what extent do color paerns reflect independent evoluon versus retenon of ancestral alleles, versus introgressed exchange of alleles? Genome-wide can shed some light.
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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Genome-wide pairwise . Populaons showed increasing divergence with increasing geographic distance, as well as increases with taxonomic distance (Fig. 3). In addion, correlaon between all pop distances with geography (mantel P=0.003).
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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per-locus pairwise . Sympatric species pairs show correlated regions of high FST.
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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Associaon with geography, taxon, and color paern. Analysis of Molecular Variance.
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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Associaon with geography, taxon, and color paern. Analysis of Molecular Variance.
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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"If the loci most strongly associated with 'taxon' are those under divergent selecon, these should also be loci with high FST in sympatric mel v. cydo/m pairs. ... The 21 loci that are FST outliers do appear as outliers in AMOVA." "Convergent wing color paerning may be controlled by loci that are introgressed between taxa. Fourteen loci were found to be more strongly associated with color paern than taxon or geography (Fig. 4B). Two of these are known to be associated with wing color."
“Genome-Wide Paerns of Divergence and Gene Flow across a Buerfly Radiaon.”
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Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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What is so interesng about threespine Scklebacks? What are the relaonships of sampled populaons in this study? What types of paerns do the authors observe? And what do they conclude from these?
Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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There are many examples of phenotypic convergence in scklebacks that have adapted recently to freshwater lakes from marine environment. Genec diversity and differenaon stascs support the repeated colonizaon of small freshwater pops from a large marine populaon. FST scans reveal evidence of balancing and divergent selecon, oen in parallel but not always among freshwater pops.
Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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Marine populaons have lile differenaon even over large geographic distance, while marine/fresh or fresh/fresh FST shows much larger differenaon.
Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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Genec diversity and heterozygosity vary considerably across the genome.
Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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Despite the phenotypic divergence of freshwater pops, a huge amount of genec variaon is sll shared among all populaons (no windows reach FST=1). The regions of highest differenaon are shared among most freshwater-marine comparisons, showing convergence at the genec level. Similar regions responding to direconal selecon. Private alleles are greater in marine than freshwater, supporng that fresh is a subset
maintained by balancing selecon or gene flow.
Populaon Genomics of Parallel Adaptaon in Threespine Sckleback using Sequenced RAD Tags
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Each generaon randomly sample alleles from the parental generaon. By incorporang a finite populaon size (N) into our sampling probabilies we can esmate the expected change in allele frequencies due to dri. A discrete me model in which each generaon is composed of 2N copies of each
previous generaon. The probability of obtaining k copies the next generaon is:
hps:/ /en.wikipedia.org/wiki/Genec_dri#Wright.E2.80.93Fisher_model
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A neutral evoluonary process (no selecon) can be modeled using the WF model in which allele frequencies change over me by genec dri.
Source: Alexei Drummond
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Read both of these: Gene tree discordance, phylogenec inference and the mulspecies coalescent Inferring the Joint Demographic History of Mulple Populaons from Muldimensional SNP Frequency Data
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