Lecture 8 - Phylogenies

included on exam 2

unrooted phylogeny

a phylogenetic tree that shows the relatedness of organisms, without an ancestry relationship

just focuses on genetic relationships between organisms

Newick format

a phylogeny in which taxa are organized with commas and parentheses

does not depict an actual tree

sister taxa are in parentheses, and then next-closely related taxa are added with more parentheses

outgroup is not in parentheses

e.g. the picture would be represented by ((A,B),C),D or (((A,B),C),D)

rooted phylogeny

a phylogenetic tree that describes the ancestry of a group of organisms, as well as the genetic relations of taxa

has a unique node: the most recent common ancestor

most recent common ancestor

aka MRCA

most recent individual from which all organisms in a phylogeny are (supposedly) descended from

the root of a phylogeny, if rooted (the farthest back node)

e.g. in the picture, the lower circle

phylogeny

the history of the evolution of a species or group, especially in reference to lines of descent and relationships among broad groups of organisms

can show genetic or ancestral relationship

typically shown in trees, either rooted or unrooted

nodes

the points at the ends of branches which represent sequences at various points in evolutionary history

typically represented with circles/dots, or just where things branch off

i.e. speciation events

taxa

the tips of a phylogeny

a collection of organisms, representing a species or group

can be sister to one another

outgroup

the group outside the group of interest, or the least related to all the other species

from the root of a phylogeny

e.g. group A in the picture

clade

a grouping that is inclusive of every species in the group

e.g. in the picture, the blue and green highlighted groups are good examples, the red and orange highlighted groups are not

polytomy

a branching of a phylogeny in which it is unsure which groups are more closely related

the simultaneous/unknown ordered speciation of at least three species

looks like a comb

e.g. the highlighted group in the picture

monophyletic

a group including all descendants of a common ancestor

paraphyletic

a group including almost all, but not all, descendants of a common ancestor

polyphyletic

a smaller group of organisms that have converged on a similar characteristic but do not share a common ancestor

e.g. a clade missing some taxa

how to root a phylogeny

choose which group you want to be your outgroup

place the root between the outgroup and the rest of the group

envision pulling a string somewhere between that outgroup and the node, so that there is a bend in the tree branch

adjust the other taxa so they are spaced nicely

(just practice idk how to explain it)

pruning

the “clipping” of taxa (removal)