GENE 3000Fall 2013

slides 160-185

MoreMore

•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

how old?

•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

wikipedia

endangered-ugly.blogspot.com

“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...”

}

}

what more can we do with

phylogenies?

•does one trait lead to another?

•independent contrasts (box 4.4)

independent contrasts

body size

correlation

one variable predicts another variable

statistical power requiresmany independent

comparisons

independent contrasts

body sizebody size

phylogeny

clade A clade B

only 2 data pointscorrelation weak

this change....this change....

independent independent from this from this change....change....

and this and this change....change.... 2 clades, only one 2 clades, only one

changechange

find the independent

contrasts

how did we get these numbers?

and, by the way, after independent and, by the way, after independent contrasts, there IS a significant relationship contrasts, there IS a significant relationship

between body size and extinction riskbetween 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 less-studied system–mating group size and balance of hermaphroditism vs. dioecy (separate sexes) 3

1

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

LUCALUCAsomewhere in heresomewhere in here