Phylogenetics and Coalescent Theory
Trees as hypotheses about history
Phylogenetic inference
Phylogenetics reconstructs evolutionary relationships from molecular and morphological data. At the graduate level, the central issue is not whether a tree can be drawn, but how to distinguish gene histories from species histories, how to model substitution processes realistically, and how uncertainty propagates through downstream inference.
The coalescent
The coalescent models the ancestral relationships of sampled alleles backward in time. Under a standard neutral model, the expected waiting time for two lineages to coalesce is proportional to . This framework links present-day sequence variation to historical demography, selection, and population structure.
Essential concepts
Why gene trees disagree with species trees
Incomplete lineage sorting
- Common in rapid radiations
- Arises from deep ancestral polymorphism
Introgression
- Transfers alleles across species boundaries
- Can mimic shared ancestry
What does the coalescent primarily describe?
The coalescent traces sampled lineages backward to common ancestors.
Correct answer: Backward-time ancestry of sampled lineages
What is incomplete lineage sorting?
This is especially important in rapid radiations and large ancestral populations.
Correct answer: A pattern where gene trees differ from the species tree because ancestral polymorphism persists across speciation events.
Common phylogenetic methods
| Method | Strength |
|---|---|
| Maximum likelihood | Model-based estimation with strong statistical foundation |
| Bayesian inference | Integrates over uncertainty and priors |
| Species-tree methods | Accounts for gene tree discordance across loci |
| Network methods | Can represent reticulate evolution and hybridization |
How to think about phylogenetic uncertainty
-
1
Check alignment quality and orthology assumptions.
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2
Choose an explicit substitution or trait-evolution model.
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3
Quantify support with bootstrap, posterior probabilities, or local measures.
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4
Assess whether discordance may reflect ILS, introgression, or model misspecification.
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5
Report uncertainty in topology, branch lengths, and ancestral state estimates.
Which phenomenon is best captured by phylogenetic networks rather than strictly bifurcating trees?
Networks can represent reticulate histories such as hybridization and introgression.
Correct answer: Recombination or hybridization
Why can rapid radiations be difficult to resolve phylogenetically?
Closely spaced speciation events leave little time for lineages to sort.
Correct answer: Because short internal branches increase incomplete lineage sorting and reduce phylogenetic signal.