Molecular Phylogenetics

Flashcards covering the vocabulary and key concepts of molecular phylogenetics as presented in the lecture.

Phylogenetic Tree

The way we depict the evolutionary process as a branching process where one lineage splits into two daughter lineages.

Reticulate Evolution

Exchange of genetic material between branches.

Homologous Character

Similarity of a characteristic due to shared ancestry.

Convergent Character

Similarity of a characteristic due to independent evolution, not shared ancestry.

Parsimony/Occam's Razor

The principle that, given multiple explanations, the simplest one with the fewest assumptions should be chosen.

Outgroup

A species closely related to, but not part of, the in-group, used as a reference point in phylogenetic analysis.

Homoplasy

When a character must have evolved more than once given a particular phylogenetic branching arrangement.

Heuristic Search

A search strategy for finding the most parsimonious tree by making small changes to an initial tree and keeping the changes that improve the parsimony score.

Multiple Sequence Alignment

A tool used to align DNA sequences of multiple species to identify homologous sites and infer evolutionary relationships.

Transitions

Changes from one purine to another (A to G or vice versa).

Transversions

Changes from a purine to a pyrimidine or vice versa.

Maximum Likelihood

A method of inferring phylogeny that calculates the probability of observing the data (DNA sequences) given a particular tree topology, branch lengths, and substitution model parameters.

Bayesian Phylogenetics

A phylogenetic inference approach similar to maximum likelihood but incorporating prior information to update beliefs and estimate posterior probabilities.

Prosimians

The lemurs, lorises, and tarsiers grouped together based on traditional classification.

Higher Primates/Cemiiforms

New and old world monkeys and the apes.

Strepsirrhinae

Lemurs and lorises.

Haplorrhinae

Monkeys and apes.

Monophyletic Clade

A group of species that includes a common ancestor and all of its descendants.

Paraphyletic Group

A group that includes a common ancestor but not all of its descendants.

Phylogram

A phylogeny where branch lengths represent the amount of evolutionary change.

Chronogram/Time Tree

A phylogeny where all the tips line up and branch lengths are proportional to a meaningful timescale.

Molecular Clock

The concept that DNA substitutions occur at a regular, constant rate, allowing for timescale inference.