BIOL 359 Midterm 2

the study of ancestor descendent relationships. the objective is to construct phylogenies

phylogenetics

a hypothesis of ancestor descendent relationships

phylogeny

a graphical summary of a phylogeny

phylogenetic tree

all life forms are related by ______________ and ______________

common ancestry and descent

phylogenies can be based on

morphological data, physiological data, molecular data

phylogenies are usually constructed using

DNA sequence data

phylogenetic trees go from ________ to _________ in amount of ___________

root to tip in amount of time

when a tree is split into 3 or more it is called a

polytomy

length of _______ in phylogenetic trees does not matter

axis

we use __________ to construct phylogenies

characters

any attribute of an organism that can provide us with insights into history (shared ancestry)

character

in molecular phylogenies, characters are typically ____________ each position can possess _____________

nucleotide positions in a gene sequence, each position can possess four character states, A, C, G, T

refers to the ancestral character state

plesiomorphy

a character state different than the ancestral state or derived state

apomorphy

a derived character state (apomorphy) that is shared by two or more taxa due to inheritance from a common ancestor - these character states are phylogenetically informative using the parsimony or cladistic criterion

synapomorphy

a uniquely derived character state

autapomorphy

apomorphy

derived character state different from ancestor

synapomorphy

shared derived characteristic

a group that includes ALL of the descendants of a common ancestor - also known as __________

monophyletic, also known as clades

any case that does not satisfy monophyletic

non monophyletic

examples of non monophyletic groups

paraphyletic, polyphyletic

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

paraphyletic

assemblages of taxa that have been erroneously grouped on the basis of homoplasious characters

polyphyletic

_____________________ identify monophyletic groups

synapomorphies

example of polyphyly

vultures

paraphyletic groups

some but not all of the descendants of a common ancestor

example of paraphyletic group

reptiles, shares common ancestor with birds, but birds are not reptiles

a character state that is shared between two DNA sequences or taxa may be so because they inherited it from a common ancestor or it is __________ a character that is the same because it comes from a common ancestor is ________________

homologous

shared character that occurs because they were evolved independently characteristic that is shared but is uniquely derived

homoplasy

why can homoplasy occur

parallel evolution, convergent evolution, secondary loss

independent evolution of the same feature from same ancestral condition

parallel evolution

independent evolution of the same feature from different ancestral condition

convergent evolution

reversion to ancestral condition

secondary loss

homoplasy results in

erroneous, polyphyletic groupings such as vultures

examples of convergence

peacock and peacock spider crocodile and hippo old world and new world vultures

the fins of a whale and the fins of a shark are an example of ____________ due to a _____________

homoplasy due to a reversal mammals that have reverted back to ancestral state

analogy

non homology

example of parallel evolution

three spine stickle back evolved independently in coastal lakes of BC - positive assortative mating and disruptive selection important divergence into large and small morphs ppl thought large morphs had common ancestor and smalls had common ancestor but - deriving independently in each of these different systems - L1 and S1 closer and L2 and S2 closer

three spine stickle back is an example of ____________ evolution

parallel

mutations can create

synapomorphies

__________ can create synapomorphies

mutations

reversal can remove

synapomorphies

__________ can remove synapomorphies

reversal

we use __________ to construct phylogenetic trees and to identify groups that are monophyletic

homologous characters (synapomorphies)

____________ are phylogenetically informative

synapomorphies

homologous vs homoplasious

homologous same trait same ancestor homoplasious same trait derived independently

principle of __________ says that simple explanations are preferred over more complicated ones

parsimony

least parsimonious tree is the tree with

least number of evolutionary steps

when constructing a phylogeny for a group of organisms, we need to employ an ____________, which is not part of the group of interest but also not too distantly related to it

outgrip

outgroup is used to

infer change - assigns the ancestral characteristic - tells us what the common ancestor is going to be

character state possessed by outgroup is defined as

ancestral (pleisiomorphic)

example of parsimony in antelope

face markings, horns, coloration of tail, coloration of rump horns is ancestral - outgroup has no horns

whale evolution thought to be from a group of hoofed mammals that possess an even number of toes called

artiodactyla camels, pigs, peccaries, deer, hippo

hoofed mammals that possess an odd number of toes

perissodactyla horses, rhinos, tapirs

computational technique for estimating the confidence level of a phylogenetic hypothesis

bootstrap method

bootstrap method

randomly generates new data sets from the original set (1000 replicates is most common) computes number of times that a particular grouping or branch appeared in a tree

taxonomic groups can be

monophyletic paraphyletic

taxonomic group that contains all descendants of a common ancestor

monophyletic

taxonomic group that contains some but not all descendants of a common ancestor, polyphyletic (erroneous homoplasious groupings)

paraphyletic

the goal of cladistic taxonomy

is to only recognize monophyletic groups as valid taxa

the use of parsimony to construct evolutionary relationships

cladistics

cladistic taxonomy =

evolutionary taxonomy

the simplest body of methods for constructing phylogenetic relationships

clustering or distance methods

why are clustering or distance methods the most versatile

they can be used with virtually any type of data, sequence divergences, pairwise Fst values and distances measures like Nei's genetic distance

clustering methods are based on overall similarity hence are referred to as

Phenetic methods

clustering methods utilize a matrix of ______________ distances or similarity values between all possible pairs of taxa, populations, or whatever it is we are studying

pairwise

matrix used in conjunction with clustering algorithm to produce a bifurcating tree called

phonogram

when using DNA sequences to create a matrix of pairwise sequence divergences for clustering, we must first align out sequences such that _____________ are adjacent to each other and then estimate the number of base pair differences between each pair of sequences

homologous positions

nucleotide sequence divergence (d)

proportion of nucleotide differences between 2 haplotypes number of differences/sequence length expressed as a percentage

average pairwise sequence divergence between sequences is called the

p-distance, proportion of differences

basic clustering with equal stem lengths

ultrametric phenogram

basic clustering with non equal stem lengths

additive phonogram

true or false p distance does not account for evolutionary process of sequence divergence (the manner in which sequences change)

true

what is p distance based on

number of observed differences between sequences with no consideration of how that number of differences arose

accounting for multiple substitutions at sequence positions is called

multiple hits used to develop more accurate measures of sequence distance

single substitution

one change, one difference

multiple substitution

2 changes 1 difference

coincidental substitution

2 changes, 1 difference

parallel substitution

2 changes no difference

convergent substitution

3 changes no difference

back substitution

2 changes no difference

multiple hits result in _______________

sequence saturation as time progresses more multiple hits will occur

correcting for multiple hits

if every site and mutation wasn't a multiple hit there would be an infinitely long sequence, every site can only mutate once

simplest model of sequence change

jukes and cantor model corrects for multiple hits

assumptions of jukes and cantor model

nucleotide frequencies are equal (A=G=T=C) probability of substitution between all nucleotides are equal (transitions occur as often as transversions) rates of change at all positions are equal (3rd position codon changes occur as frequently as 1st and 2nd)

when is the jukes and cantor model appropriate

when the numbers of differences between sequences is small (proportion of differences is less than 0.04) because assumptions of the model correspond poorly with reality

substitution of a pyrimidine for a pyrimidine or a purine for a purine

transition

substitution of a purine for a pyrimidine or vice versa

transversion

purines

A G

pyrimidines

C T

would you expect transitions more or transversions? why?

transitions because DNA repair mechanism less likely to recognize that there is an error - more likely to repair transversions

kimuras two parameter model has all the assumptions as jukes and cantor except

assumption of equal rates of transitions and transversions

realistic more complex model with 6 different rate categories

general time reversible model (GTR)

simplest model of sequence evolution

jukes and cantor

most complex model of sequence evolution

general time reversible model

three domains of life

archaea, bacteria, eukaryotes

eukaryotes are hierarchically divided into

super group phylum class order family genus species

example of class

mammalia

example of order

primate

example of family

hominidae