Lecture 12: Molecular Clock & Origin of Life PDF

Methods for finding the best cladograms Parsimony – picks the tree(s) with the fewest evolutionary steps Parametric (statistical) methods we want to build a tree for these three bird species. We can test our hypotheses using molecular data. What is ancestral? An outgroup...

Methods for finding the best cladograms Parsimony – picks the tree(s) with the fewest evolutionary steps Parametric (statistical) methods we want to build a tree for these three bird species. We can test our hypotheses using molecular data. What is ancestral? An outgroup tells us about the ancestral lineage that we compare to our ingroup taxa -If we are studying the relationships of A-F, then G is an outgroup ingroup ? outgroup  Outgroup comparison indicates that the ancestral state is A  Maximum Parsimony: the best tree requires the fewest changes I I III II III II III II I The tree suggesting a relationship between species I and II has fewer evolutionary steps = more parsimonious  steps steps steps In a parsimony analysis, we enter all the molecular or morphological data, and the computer (ideally) builds all possible trees and counts the number of steps. The fewest steps indicate the best phylogenetic hypothesis  Methods for finding the best cladograms Parsimony – picks the tree(s) with the fewest evolutionary steps Parametric (statistical) methods  Methods for finding the best cladograms Parametric (statistical) methods give clade support values: Maximum likelihood Bayesian inference –Insert model on likelihood for e.g. base substitutions -calculates how well each tree, and each branch, fits the data (ideally checking all possible trees) –computationally demanding (Bayesian inference even more so that Maximum Likelihood, but some say more theoretically sound)  Major Models of Macroevolution Gradualism (e.g. Darwin, Mayr) VS Punctuated equilibria (Gould, Eldredge) -Stasis “punctuated” by rapid change Stephen Jay Gould Ernst Mayr  Not everything in nature is adaptive Some features might be the byproduct of selection for other features Also, some features are Stephen Jay Gould vestigial E.g. human chin? Iridescence of golden mole fur?  Not everything in nature is adaptive Some features might be the byproduct of selection for other features Also, some features are Stephen Jay Gould vestigial E.g. human chin? Iridescence of golden mole fur?  Evidence used in study of Macroevolution Biogeography plus molecular data (e.g. chimpanzees & bonobos) Fossils - morphological change – transitional fossils Fossils - adaptive radiations after extinction events Fossils plus molecular data: molecular clock  Molecular clock How do we estimate the time of divergence of two lineages? Molecular clock studies use both fossil and molecular data  Molecular clock Some parts of the genome will accumulate changes (mutations) at a relatively steady rate The speed of accumulation depends on the part of DNA under study (some fast, some slow) The “clock” is calibrated using the fossil record (e.g. orangutan fossils have been securely dated for apes), or the accumulation of mutations over generations orangutan- like fossils  Molecular clock Orangutan Gorilla Bonobo Chimpanzee Human Pongo pygmaeus Gorilla gorilla Pan paniscus Pan troglodytes Homo sapiens LCA 6-8 mya 14 mya -By using the known age of the orangutan split, plus info on orangutan DNA, we know the rate of mutations in certain parts of the ape genome - Count known differences in DNA between humans and chimps -The data indicates a date of the split between Pan and Homo at about 6-8 mya Studying the origin of life poses some unique problems -Organic molecules do not form fossils -when did it occur? -Earth is 4.5 billion years old -we know prokaryotes were around 3.5 billion years ago or more  Early Earth 4.5 - 4 bill. years ago  Early Earth: Hadean, 4.5 - 4 billion y.a. -A lot of volcanism, meteors -Gradual cooling ca 4 bill. y.a. ; water condenses and forms oceans  - The early atmosphere had little to no oxygen - Water, nitrogen, carbon dioxide, ammonia, hydrogen - Lightning and UV light could have provided energy for the spontaneous production of organic molecules - Early oceans might have been a “primitive soup” of simple organic molecules  “Primitive soup” hypothesis Stanley Miller -Today’s atmosphere is oxidizing -Miller & Urey made an experiment with a hypothetical early atmosphere (reducing) to see if organic molecules could be produced -in this model, a major source of energy is from lightning (and the sun)  - Chromatography showed that very simple compounds had now turned into larger organic monomers (in this case, amino acids) -Amino acids were produced in this “primitive” reducing environment -Others have later shown that other hypothetical atmospheric compositions (neutral) could do the same – and also produce RNA monomers and fatty acids Deep sea vent hypothesis Another idea: -Alkaline deep sea vents could have provided energy in the form of heat and a pH gradient - Organic molecules could have formed in the pores of the vent Volcanic clay hypothesis - Volcanic clays + sun energy can also induce polymerization of macromolecules e.g. RNA  In either case, at some point, protocells with membranes must have formed Packaging of molecules into "protocells" Vesicles could have formed spontaneously – fatty acids (lipids) and other organic molecules added to water Maintain an internal chemical environment  water+clay environment -both vesicle formation and RNA polymerization happen more readily on clay surface -some experiments show replication of RNA within lipid vesicles Origin of self-replication and evolution RNA molecules called ribozymes have been found to catalyze many different reactions Early protocells with self- replicating, catalytic RNA could have absorbed compounds from surroundings (likely on clay surface) Some RNA copies would have been more effective at obtaining resources and would have increased in number through natural selection  Paleontology: Scientific study of Fossils: fossil organisms Preserved mineralized parts of organisms (shells, teeth, bone) Trace fossils left by organisms (indirect evidence) Coprolites and other remains More rarely: soft parts preserved as minerals Paleontology: Dating fossils Dating fossils Stratigraphy Relative dating: -Principle of superposition Absolute dating (chronometric) : -Radiometric dating The history of the Earth is recorded in its strata Principle of Superposition In a sequence of layered sedimentary rocks, any layer is older than the layer above it and younger than layers below it  Paleontology: Dating fossils Absolute dating : -Radiometric dating Using the known half-life of radioactive isotopes in sediments  Paleontology: Dating fossils Radiometric dating Uranium series dating (U- Series) - 238U Turns to lead (Pb) – Series of half-lives (several isotopes) Argon-Argon (40Ar-39Ar) dating is often used on volcanic rock - 1.25 billion y. half-life Carbon 14 (14C) dating (Radiocarbon dating) - Carbon 14 is radioactive, and will slowly disappear (5730 y half-life) Ötzi, 5200y old  Patterns of Extinctions Background Extinctions “Normal” slow rate of extinction 96% of extinctions Mass Extinctions Global Extent Broad Range of Species Often rapid