bio cycle 9 - phylogeny

what does a phylogeny (evolutionary tree) represent?

a hypothesis of evolutionary relationships showing branching patterns of descent from common ancestors, time flows from the root (most ancient) to the tips (most recent)

what is the most important feature when reading a phylogeny?

the sequence of branching events, not the left-right or top-bottom orientation

what is a node?

a branching point where a lineage splits; represents a speciation event and the MRCA of descendant taxa

what is the root of a phylogenetic tree?

the oldest common ancestor of all taxa in the tree; the point from which time flows toward the tips

what is a clade (monophyletic group)?

a group consisting of a common ancestor and all of its descendants; removable with a single “snip”

what is a non-monophyletic group?

any group that excludes some descents of its common ancestor or groups species that don’t share a recent common ancestor (paraphyletic)

what is a sister clade/sister taxa?

two lineages that share an immediate common ancestor; each other’s closest relatives

how can two different phylogenies represent the same information?

if the branching order is identical, rotating subtrees around nodes does not change evolutionary relationships

what is the taxonomic hierarchy (mnemonic: “Diligent Kindly Professors Cannot Often Fail Good Students”)?

domain → kingdom → phylum → class → order → family → genus → species

why do some traditional groups fail to reflect evolutionary relationships?

because many were defined by superficial similarity before evolution was understood; many (ex: fish, dicots, prokaryotes) are non-monophyletic

what is anagenesis?

evolutionary change within a lineage without branching 

what is cladogenesis?

evolutionary branching that creates two or more descendant lineages

what is an ancestral character trait?

a trait evolved before the MRCA of the entire group

what is a derived character state?

a trait that evolved after the MRCA of the entire group; new in particular lineages

how do we determine ancestral vs derived states?

by comparing to an outgroup (a lineage that branched off before the ingroup

trait present in outgroup + all ingroup taxa?

ancestral

trait present in outgroup + some ingroup taxa?

ancestral

trait absent in outgroup but present in some ingroup taxa?

derived

trait present in outgroup but absent in all ingroup taxa?

equally likely ancestral or derived (because either the ingroup lost it or the outgroup independently gained it)

trait absent in outgroup but present in all ingroup taxa?

equally likely ancestral or derived (ingroup could have gained it or outgroup could have lost it)

what is a synapomorphy?

a shared, derived trait that evolved in the MRCA of only the taxa that have it, only type of characteristic useful for building phylogenies

what is a symplesiomorphy?

a shared, ancestral trait; present in the MRCA of the entire group, not useful for phylogenies because it does not indicate close relationships

what is an autapomorphy?

a unique, derived trait found in a single taxon; not useful for determining relatedness

why are synapomorphies preferred for inferring relationships?

because they indicate recent shared ancestry, taxa sharing more synapomorphies are more closely related

what is the principle of parsimony?

the simplest explanation requiring the fewest evolutionary changes is most likely correct

how is parsimony used in phylogenetics?

• compare candidate trees; the one requiring the fewest gains/losses is the most parsimonious

• ex: imagine four species, three of which can hover, and one that can’t

  • a parsimonious tree would suggest the hovering trait evolved once in the common ancestor of those three species, then was passed down, rather than evolving independently three separate times

the chicken-bat-chipmunk example (outgroup = frog): which traits do each animal have?

• outgroup: frog - no lactation, no wings, no fur, no beak

• ingroup:

  • chicken - no lactation, wings, no fur, beak

  • bat - lactation, wings, fur, no beak

  • chipmunk - lactation, no wings, fur, no beak

are those traits ancestral or derived?

• lactation - shared, derived 

• fur: shared and derived

• beak - unique to chicken (autapomorphy/derived)

• wings - shared, derived 

• no fur - shared, ancestral (outgroup and some of the ingroup lack fur)

which taxa share more synapomorphies?

bat and chipmunk share more derived traits (lactation + fur), so they are closer relatives than either is to the chicken

what is homology?

similarity due to shared ancestry; underlying structure is inherited from an ancestor even if function differs

what is convergent evolution?

independent evolution of similar traits in unrelated lineages due to similar ecological pressures; results in analogous structures (body parts in different species with similar functions but evolved independently from different ancestors and have different anatomy)

what is a homoplasy?

a misleading similarity or dissimilarity caused by convergence or reversal; does not reflect shared ancestry

why are homoplasies problematic in phylogenetics?

they mimic synapomorphies and can lead to incorrect trees

what are molecular clocks used for?

to estimate timing of divergence events by comparing approximate mutation rates

what is the comparative method?

using phylogenies to test hypotheses about trait evolution while accounting for shared ancestry

what is the cladistic method of classification?

only monophyletic groups (clades) receive names; classification must reflect evolutionary history

steps for building a phylogenetic tree (parsimony approach)

1. choose an outgroup

2. compare traits across taxa

3. identify ancestral vs derived traits

4. group taxa by shared derived traits (synapomorphies)

5. select the tree with the fewest evolutionary changes