SCILIVSY 12 Study Guide - Midterm Guide: Molecular Phylogenetics, Herman Melville, Igneous Rock
19 Jun 2018
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Lecture Notes for Midterm 3
11/3
Understanding the history of life: Phylogenetic Reconstruction
Phylogenetic Reconstruction
Phylogenetic trees reconstruct the branching order of evolution
oAll equally been a product of 3 and half billion years of evolution
oEqually ancient
SPECIFIC TREE
Humans at the top
Trees come in many forms
oCommon ancestor of all four taxa
Lineages split
Can flip it
Drawn in dif ways
Can be laid out in different ways
Can be useful
oProblem
Dentist believed to be infecting patients with HIV
oPhylogeny
Two hiv sequences (x and y) from each of the detist, his HIV+
patients, and local area aids patients
Find common ancestor
oPatients that fall under common ancestor
Infected
oPhylogenetic remoteness as a conservation priority criterion
Rising extinction
Have to be economical
oPut reserve
If species if very closely related to another
species, pick it k
Tuantara
oIt might look like a lizard
but different
oIt’s the last vestige of an
ancient group
Phenetics reconstructs phylogeny on the basis of distance
oThings that are more similar are more closely related to each other
than things that are different
Phentics
Based on overall similarity (ie distance)
find more resources at oneclass.com
find more resources at oneclass.com
oStarts with two most similar taxa and work
outwards
d(AB)/2
d(AB)C/2
oHow to make a tree?
On the basis of overall similarity (phenetics)
Overall similarity doesn’t always work though
oOnly works if you have uniform rates of
evolution
Rays have accelerated rate of evolution
Doesn’t always proceed at the
same uniform rate
Cladistics(!)
oHomology
Shared by the virtue of common ancestry
Homologies may be in two states (limb)
Ancestral (retained state)
Derived (innovative state -> something new happened)
oWe group organisms based on shared derived
characteristics
When studying a homology , differences can either be
ancestrals (plesiomorphies to cladists) or derived
(apomorphies) shared ancestral characters are
symplesiomorphies shared derived ones synapomorphies
HAS TO BE SHARED
Determine whether character states are derived or ancestral
oOutgroup comparison
Have to be equally distant from ingroups
A character is more likely to stay the same than it is to change
We expect the outgroup to preserve ancestral trait
oNot always true
Same for DNA
Ancestral can be same as out group
Cladistics
oCladistics only recognizes Monophyletic groups
Includes all descendants of a single ancestor
Clade
oParaphyletic group
Includes some but not all of a single ancestor
Ex: fish
Arose once, and diversified
oSpun off out of fish: land vertebrates
oPolyphyletic group
find more resources at oneclass.com
find more resources at oneclass.com
Include descendants of two or more ancestors
Molecular phylogenetics follow same logic
oApplying the shared-derived logic to DNA sequences
ACTG
Analyzing species through DNA
oAnalyzing molecules highlight speciation
Speciation: time leads it to happen
Can use this idea with molecular phylogenetics
oSimply counting number of differences
oThen estimate time of splitting
Linear correlation between the extent of
divergence you see and time of separation
“when did this common ancestor
occur”
oturns out, molecular gene
clocks tick at different
times
this depends on the
intensity of negative
selection acting
against mutation
gene
ex: histogene
so cant be touched
Using molecules can analyze taxa that are beyond the reach of morphological
analyses eg. Microbes
oGet accidental convergence
oAfrotheria
A group of oddball animals that have been united by molecular
analysis
Elephants and ardvarks
oMicrobes
Can catch it and study it
But limited for the most part with studying microbes
Deep ocean growing microbe
oCant let it grow
But can look at it and study it
hOMOPLASY IS CAUSED BY CONTRADICTION
oHerman Melville
“whale is fish”
oConvergence results is noncongruent trees for different characters
Look the same but not
Wolf (placental) vs. thylacine (marsupial)
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Phylogenetic trees reconstruct the branching order of evolution: all equally been a product of 3 and half billion years of evolution, equally ancient. Trees come in many forms: common ancestor of all four taxa. Can be laid out in different ways. Dentist believed to be infecting patients with hiv: phylogeny. Two hiv sequences (x and y) from each of the detist, his hiv+ patients, and local area aids patients. Find common ancestor: patients that fall under common ancestor. Infected: phylogenetic remoteness as a conservation priority criterion. Have to be economical: put reserve. If species if very closely related to another species, pick it k. Tuantara: it might look like a lizard but different, it"s the last vestige of an ancient group. Phenetics reconstructs phylogeny on the basis of distance: things that are more similar are more closely related to each other than things that are different.
