Phylogeny Study Guide Flashcards

A set of vocabulary flashcards covering the key terms and concepts of phylogeny, tree components, types of phylogenies, evolutionary groups, and parsimony assumptions.

Tree of Life

The big phylogeny that describes how all organisms are related to one another through shared common ancestry.

Common Ancestral Species Age

All species currently living on Earth—and all species that have ever lived on Earth—are descendants of one single common ancestral species that lived ~$4.5$ billion years ago.

Terminal nodes

Species or groups of species (sometimes called taxa) at the tips of the tree.

Internal nodes

Represent speciation events within a phylogeny.

Root node

The most inclusive internal node that represents the first speciation event in the phylogeny; it is the MRCA of all of the species in the tree.

Terminal branches

Branches that subtend (lead to) the tips of the tree.

Internal branches

Branches that connect two speciation events.

Cladogram

A phylogeny where branch lengths are arbitrary; these trees only convey topological information.

Phylogram

A phylogeny where branch lengths are proportional to the amount of character change.

Chronogram

A phylogeny where branch lengths are proportional to absolute or relative time.

Monophyletic groups (clades)

Natural evolutionary groups that include all of the descendants of a given common ancestor.

Paraphyletic groups

Unnatural evolutionary groups that exclude some of the descendants of a given common ancestor (e.g., the original definition of “Reptilia”).

Polyphyletic groups

Unnatural evolutionary groups that exclude the most recent common ancestor of the included species (e.g., “Homeothermia” based on homoplasious traits).

Diagnostic traits

Inferred traits that refer to the MRCA of a group, rather than statements observed in all members of the group.

Homology

Similarity in a trait among different species that is due to inheritance from the MRCA of those species (e.g., forelimbs of bats, whales, and dogs).

Homoplasy

Similarity in a trait among different species that is due to independent evolution of those traits (e.g., wings of birds, insects, and maples).

Unrooted trees

Trees that constrain but do not completely specify evolutionary relationships and do not specify a temporal direction.

Outgroup

One or more species used to root trees by specifying the location of the root node based on independent evidence.

Parsimony

A phylogeny estimation goal to identify the ‘optimal’ unrooted tree requiring the minimum number of changes to explain the observed data.

Parsimony assumption: Evolutionary cost

Parsimony assumes the probability of character change is the same for every branch, regardless of varying rates of change or branch durations.

Parsimony assumption: Character state change

Parsimony assumes the cost of changing from $0 \rightarrow 1$ is the same as a change from $1 \rightarrow 0$, though character change is often biased in one direction.