Modeling the Evolution of Genes and Genomes in the Presence of ILS and Hybridization

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Presents a likelihood framework that sums over coalescent histories to compute gene tree probabilities under both incomplete lineage sorting and hybridization, converts networks into a multi-labeled (MUL) tree and enumerates allele mappings, and speeds inference with ancestral configurations. Implementation (Java) uses cross-validation to choose model complexity. Applied to ~20,000 independent mouse loci it infers two reticulations, estimates ~6% and ~4% introgressed gene trees, detects VKORC1 introgression and 19 introgressed regions; scalability beyond dozens of taxa remains limited.

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" chapters (12)

1. 0:00Introduction to study
2. 0:48Hybridization vs lineage
3. 3:30Biological significance
4. 6:12Inferring species histories
5. 8:12Computing gene tree odds
6. 10:42Coalescent theory models
7. 13:42Three-species case study
8. 15:41Phylogenetic network theory
9. 20:11Multi-labeled tree methods
10. 24:31Searching network space
11. 30:44Annotating genomes
12. 35:54Conclusion and discussion