ZOOL40040-Molecular Phylogenetics-2026/27 Autumn

Flashcard time on phylogenetic terms!!

Darwin and Homolgy

‘‘The natural system is based upon descent with modification..the ccharacters that naturalist consider as showing true affinity (e.g homologies) are those which have been inherited from a common parent, and in so far as all true classification is genealogical; that community of descent is the common bond that naturalists have been seeking’’

Charles Darwin, Origin of species 1859 p.413

Homolgy

• The similarity of traits between different species that is inherited from a common ancestor.

• Similarity that is the result of inheritance from a common ancestor -derived from the same structure or gene in the ancestor.

• The identification and analysis of homolgies is key to phylogenetic systematics.

Character states

• When organisms (taxa) differ with respect to a feature (e.g. its presence or absence or different nucleotide bases at specific sites in a sequence) the different conditions are called character states.

• Many character staes can describe a character (e.g. nucleotide at a site, maybe A, T, G or C)

Character evolution

• Heritable changes (in morphology, gene sequences etc.) produce different character states.

• This shows differences and similarities in character states that provides the basis for inferring phylogeny (e.g. provide evidence of relationships)

• This evidence depends on how often evolutionary changes that produce the different character states occur independently-ie characters evolve at different rates.

• Example: Darwin’s finches

Most carnivores have shearing carnassial teeth that act as a homologous character

Deletions that support Yangochiroptera

Either the bats have echolocation or not. Hard to decipher apart in gene sequences..

Apomorphy

A derived ‘‘advanced’’ unique character state differing to the ancestral state

Plesiomorphy

An ancestral character state

Autapomorphy

A phylogenetically non-informative character state, unique to taxa in question

Synapomorphies

• A derived character state shared by two or more taxa due to inheritance which diagnoses a clade.

• These are phylogenetically informative and can be used to infer a tree.

Homoplasy

• The similarity of traits that evolve independently in separate lineages and is not due to inheritance from a recent common ancestor

• Similar due to independent evolutionary change -convergence, or reversal

• Must be aware of ‘Homoplastic characters’ will mislead your tree