Molecular Phylogenetics, Gene Trees, and Tree-Building Methods

Vocabulary flashcards covering concepts in molecular phylogenetics, gene tree discordance, DNA mutation types, maximum parsimony versus maximum likelihood, and phylogenetic support metrics.

Gene genealogy

The evolutionary history traced using a single gene or a small set of genes, serving as the best estimate of phylogenetic relationships in the absence of other data.

Incomplete lineage sorting

A condition occurring during rapid speciation where ancestral polymorphism fails to sort prior to divergence, causing gene trees to conflict with the true species tree.

Introgression

The transfer of genetic material from one species into the gene pool of another through hybridization while reproductive isolation is incomplete.

Peter and Rosemary Grant

Researchers who spent decades tracking Darwin's finch genealogies on the island of Daphne Major, documenting rare hybridizations between the large ground finch and the medium ground finch.

Birdsong imprinting

A behavioral process where young female finches learn and imprint on their father's song in the nest, directing their mate choice and acting as a barrier to persistent introgression.

Selective sweep

The rapid spread and fixation of a beneficial gene (such as one conferring resistance to drought or disease) across a population following an introgression event.

Back mutation

A homoplasious event where a mutated nucleotide subsequently mutates back to its ancestral nucleotide state (for example, from $C$ to $T$ and then back to $C$).

Maximum parsimony

A phylogenetic optimality criterion grounded in Occam's razor that gives equal weight to all characters and selects the tree requiring the fewest evolutionary changes.

Maximum likelihood

A phylogenetic approach that identifies the tree most probable under an explicit statistical model of molecular evolution, weighting character changes based on their empirical mutation rates.

DNA polymerase III

The primary DNA replicating holoenzyme possessing a proofreading function that detects structural mispairings and repairs replication errors.

Transition

A point mutation exchanging a purine for another purine or a pyrimidine for another pyrimidine, occurring approximately $10$ times more frequently than a transversion because it more readily avoids proofreading detection.

Transversion

A rare point mutation substituting a purine for a pyrimidine or vice versa, causing significant structural distortions in the double helix that are easily recognized by proofreading enzymes.

Purines

Two-carbon-ring nitrogenous bases ($A$ and $G$) that pair with single-ring pyrimidines ($T$ and $C$) to create a standard three-ring wide rung in the DNA double helix.

Pyrimidines

Single-carbon-ring nitrogenous bases ($C$ and $T$ in DNA) that pair with two-ring purines.

Bootstrapping

A statistical sensitivity technique that repeatedly resamples subsets of the character data to evaluate how consistently a particular node or clade is supported across resampled datasets.

Bayesian phylogenetic methods

Statistical methods that explore tree probability space over iterative computational runs, preventing individual data points from overwhelming the analysis while assessing node support.

TreeRot

A phylogenetic support program that determines clade stability by measuring how many supporting characters must be intentionally removed before a specific node collapses.