1. GENE 3000 Fall 2013 slides 160-185

2. More

3. 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?

4. 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?

5. 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

6. 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!

7. Bromham & Penny, NRG 4:216-224 wikipedia endangered-ugly.blogspot.com

8. “modification with descent” modification - mutations or phenotypic changes of a heritable trait/character (homology) descent - given time/generations, evolution involves change at heritable characters

9. from fins to limbs

11. intermediate fossils

12. 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)

13. 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 paleontologists predicted a region in northern Canada might work

16. similar progression of fossils and phylogeny to describe evolution of feathers “...evolution of traits of birds began long before birds existed...”

17. } }

18. what more can we do with phylogenies? does one trait lead to another? independent contrasts (box 4.4)

19. independent contrasts body size correlation one variable predicts another variable statistical power requires many independent comparisons

20. comparative method this doesn’t mean we are just comparing species - explicit contrast using relatedness specifically we are asking about the association between two or more traits –did one evolve before the other (causal)? –is one trait predictive of the other? correlation similar to regression, but not the same: what is covariance of variables relative to their standard deviations from mean? (and is it significantly different from 0, a random assocation?) 20

21. independent contrasts body size phylogeny clade Aclade B only 2 data points correlation weak

22. this change.... independent from this change.... and this change.... 2 clades, only one change

23. 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

25. Phylogeny as Pattern of shared Ancestors

26. phylogeny will get into methods in a few weeks; take them as given for now the presence/absence of homologous traits, whether noses or nucleotides, can be used to infer phylogeny can infer how divergent species are, or simply the order/pattern of divergence (topology, or shape, of the tree) 26

29. Brownian Motion 29 simple model of trait evolution over time

31. 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) 31

32. 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

33. LUCA somewhere in here