phylogenies pts. 1 + 2 review questions

What is a phylogeny?

a representation of the evolutionary history of a group of chosen species

where does genetic diversity come from?

mutations provide the raw genetic diversity that selections can act upon, all new variants of genes come from mutations—things like genetic drift, gene flow, natural selection can determine how frequent those become in a population

What are the parts of a phylogeny?

the parts of a phylogeny include a root, branches, nodes, and tips

what does reproductive isolation really do (Big Picture)?

reproductive isolation (so pre and post zygotic barriers) keep species separate

How do we read and interpret phylogenies?

we read it root to tip and by tracing the paths of the branch points. also two tips next to each other do not mean more closely related

What happens to the relationships a phylogeny displays when we rotate

sections of the phylogeny at the nodes?

it doesn’t change anything, it would still mean the same thing

What are sister taxa?

2 groups (species, individuals, etc.) that are most closely related to each other because they are the only 2 descendants of a single common ancestor

Do phylogenetic trees reflect relative time or absolute time?

no, but typically time calibrated trees do

What are the three types of phylogenetic groupings?

1. monophyletic group

2. paraphyletic group

3. polyphyletic group

what is a monophyletic group?

a group that includes a common ancestor and all of its descendants

what is a paraphyletic group? *think of para as partial → it partially describes the group

a group that includes a common ancestor and some, but not all, of its descendants

what is a polyphyletic group? *the only group that will only ever include only tips

at most basic: a grouping that does not include the common ancestor. it typically groups species based on similar traits because of convergent evolution
example) bats and birds both fly, and ofc they do share a common ancestor going far back enough, but it couldn’t fly, so their ability to fly evolved independently

How do we build simple phylogenies based on trait data?

step 1: choose an outgroup to use as a reference point

step 2: choose your organisms and traits - phylogenies can be constructed with traits, dna, fossil evidence, or a combination

What is an outgroup?

a less related organism that is useful as a reference point—typically the first branch to diverge and has similar traits to our groups of interest (or ingroup). the ingroup is usually what we care most about learning about and the outgroup acts more of related reference

What is a homologous vs an analogous trait? 

a homologous trait is similar because they have shared ancestry (typically reflect divergent evolution) while analogous traits are similar because of shared selective pressures (results of convergent evolution)

example of analogous trait) a a fish, bird, and a mammal all have similar shapes of wings/flipper because it’s good for moving through water but if looked at internally, the bone structures are different meaning they don’t have a recent common ancestor
example of homologous trait) the same number and order of bones (even with different arrangement) because the bone structure came from the ancestor

what is a synapomorphy?

Synapomorphy is a special case of homologous trait that defines a

monophyletic group (trait evolved once and is in all descendants)

examples)
basic definition: when we have traits that appear and are present in the rest

all mammals have hair and milk glands

all tetrapods have 4 walking legs with snakes as an exception

Which type of trait is the most information and useful in creating

phylogenies?

homologous traits because they actually reflect shared ancestry whereas analogous ones reflect evolved similarities

What is parsimony? How do we apply it to phylogenies? *remember the hedgehog and tenrec phylogeny as a mnemonic device

parsimony is the principle that we use to decide which scenario/explanation of the arrangement of a phylogenetic tree is better or most likely and parsimony’s principle operates on the tree requiring the fewest evolutionary changes → this is usually preferred
*doesn’t always choose the right phylogeny! sort of just operates on “the simplest explanation is the best” so from there we’d choose the tree that has the fewest number of evolutionary changes