Transcript 3000_2013_1f

GENE 3000
Fall 2013
slides 160-185
More
how old?
• geologists agree
that the age of the
Earth is ~4.5 billion
years old
• geneticists have
independent data
suggesting Last
Universal Common
Ancestor (LUCA)
lived ~3.5-3.8 billion
years ago
• OK, we have a phylogeny
of 5 species
• since (A(BC)) is a clade
nested within the
phylogeny, the common
ancestor to A,B,C was
more recent than
common ancestor to all 5
• but when?
find a fossil (F) that appears to be more
phylogenetically related to A(BC) than D, E
based on sediment isotopic dating, lets say
fossil is 55 million years old (MYA)
ancestor (Y) is thus older than 55 MYA;
more inclusive ancestor (X) also older than
55 MYA
what helps time
estimate?
• uniformitarianism and Poisson
processes - regular expectation of
events allows a ‘clock’ behavior for data
• in particular DNA mutations, rare events
observed over large number of intervals
• multiple fossil ‘calibrations’ of clock
important!
Bromham & Penny, NRG 4:216-224
endangered-ugly.blogspot.com
wikipedia
“modification with
descent”
• modification - mutations or phenotypic
changes of a heritable trait/character
(homology)
• descent - given time/generations,
evolution involves change at heritable
characters
from fins to limbs
from fins to limbs
intermediate fossils
science makes
predictions
• start with phylogeny of teleost fishes,
coelocanths, tetrapods
• fossils are suggesting the transition
happened somewhere 360-390 mya
• hypothesis: find sediments of that age
(mid-Devonian) from appropriate
habitats (wetlands, river deltas)
• stratigraphy - the fossil
layers with similar
organisms can be
mapped
• since isotopic dating,
we know their location
and estimate of age
• paleontologists
predicted a region in
northern Canada might
work
•
•
similar
progression of
fossils and
phylogeny to
describe
evolution of
feathers
“...evolution of
traits of birds
began long
before birds
existed...”
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what more can we do
with phylogenies?
• does one trait lead to another?
• independent contrasts (box 4.4)
independent
contrasts
correlation
one variable
predicts another variable
statistical power requires
many independent
comparisons
body size
independent
contrasts
clade A
clade B
only 2 data points
correlation weak
phylogeny
body size
this change....
independent from
this change....
and this change....
2 clades, only one
change
find the independent
contrasts
how did we get
these numbers?
and, by the way, after independent contrasts, there
IS a significant relationship between body size and
extinction risk
correlation, again
• replicated correlation through evolutionary
time is an observation that evaluates a
hypothesis
• depends on having a robust phylogeny, good
trait measurements
• allows us to predict what will be found in lessstudied system
–mating group size and balance of hermaphroditism
vs. dioecy (separate sexes)
31
phylogeny
• inference of the evolutionary history of organisms,
populations, and genes
• use shared, derived characters and assumptions
about how homologous characters are gained
and lost to reconstruct relationships
• can test our assumptions and test the consistency
of the data in producing a result
• use phylogenies to understand when traits arose,
and how these traits inform other characteristics
LUCA
somewhere in here