Evolution and Genetics: Understanding the History of Life on Earth

1. Genesis 1 24 And God said, Let the earth bring forth the living creature after his kind, cattle, and creeping thing, and beast of the earth after his kind: and it was so. 25 And God made the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good.

2. Evolution and Genetics Timothy G. Standish, Ph. D.

3. Historical Science "..Darwin introduced historicity into science. Evolutionary biology, in contrast with physics and chemistry, is a historical science -- the evolutionist attempts to explain events and processes that have already taken place. Laws and experiments are inappropriate techniques for the explication of such events and processes. Instead one constructs a historical narrative, consisting of a tentative reconstruction of the particular scenario that led to the events one is trying to explain." Ernst Mayr 2000 July 2000 issue of Scientific American.

4. Family Trees From the late Renaissance, noble families in Europe had their pedigrees drawn in the form of trees - geneaological trees. By a giant leap of scientific imagination and analogy, these family trees became the prototype for a new theory of humanity's place in the Universe: "I believe this simile largely speaks the truth," wrote Charles Darwin in The Origin of Species (1859), imagining evolution as a tree branching through time. Hestmark, Geir. 2000. Temptations of the tree. Nature 408:911.

5. Imposing Nature on a Tree In 1776, the German-Russian naturalist Peter Simon Pallas proposed in his Elenchus Zoophytorum a systematic arrangement of all organisms in the image of a tree; and in 1861 Heinrich Bronn presented such a tree based on fossil evidence. But it was Ernst Haeckel, in his monumental Generelle Morphologie (1866), who drew the first tree of the common descent of all life on Earth. Haeckel also coined the term 'phylogeny' from the Greek words for tribe or race and origin, and presented phylogenetic trees for all major groups of organisms. Hestmark, Geir. 2000. Temptations of the tree. Nature 408:911.

6. They Look So Real Phylogenetic trees are common in today's scientific journals, but there it is seldom realized how speculative they are because they look so real. This rhetorical power was significant in the popularization and triumph of evolutionary theory. Yet phylogenies are only sketches of historical hypotheses, constructed from imperfect historical evidence: fossils; morphological and anatomical similarity; biogeographic patterns; and, recently, comparison of different molecular sequences. Some phylogenetic trees are certainly more probable than others, but the inherently imperfect nature of the evidence seems to guarantee that we will never be able to reconstruct, except perhaps by accident, the true phylogeny of life on Earth. Hestmark, Geir. 2000. Temptations of the tree. Nature 408:911.

7. What is a Species? Six major concepts: • A - Morphospecies - If it looks different, it is a different species • B - Cohesion - Defined by an integrated complex of genes and set of adaptations • A - Biological - Reproductively isolated groups of organisms • B - Recognition - If two organisms don’t recognize one another as potential mates, they are different species • Ecological - If they do not occupy the same niche, they are not the same species • Evolutionary - If they share the same common ancestor and niche, they are related and may be the same species

8. Evolution • Microevolution - Changes in allele frequency over time (Population genetics) • Macroevolution - Accumulation of changes in a population until it becomes a new species • Macroevolution requires the production of new “information,” microevolution deals with how that information in the form of alleles behaves in populations

9. How Species Evolve • Anagenesis - (an = without, genesis = beginning) Over time the environment in which a species lives changes and the species continually adapts to the new environment. Thus the species changes over time and eventually becomes a new species • Cladogenesis - (clad = branch, genesis = beginning) As new niches become available, members of existing species move into exploit them. As these individuals adapt to their new environment, they become distinctly new species

10. How Species Evolve Time Time D Morphology D Morphology Cladogenesis Anagenesis

11. Where Speciation Occurs • Allopatric Speciation - Speciation that does not occur in the same place. First two populations are separated, then they change and become different species. • Sympatric Speciation - Speciation in the same place. Species arise within the same population due to something other than a physical reproductive barrier.

12. Reproductive Barriers • If a species is to be produced, some sort of reproductive barrier needs to come into play between two populations of the same species • Reproductive barriers fall into two classes: • Prezygotic - Those that occur before a zygote is produced • Post zygotic - Those that prevent the offspring of two species (mule) from reproducing

13. Physical Reproductive Barriers • If a population is separated into two populations by a physical barrier the Hardy-Weinburg assumption of random mating will be violated • If different selective pressures are brought to bare on the separate populations, they will develop different allelic frequencies • Evolutionary theory extrapolates from here to say that they will form new species and if they drift enough new genera and so on • This requires the production of new alleles that improve the fitness of individuals in the population as mere changes in allele frequencies does not make new species

14. Phylogeny Based on Homologous Structures/Fossils Bacteria Archaea Fungi Plantae Animalia Hypothetical common ancestors Last Universal Common Ancestor (LUCA) Spontaneous Generation of Life

15. Phylogeny Based on Homologous Genes/Proteins Archaea Bacteria Fungi Plantae Animalia Hypothetical common ancestors Last Universal Common Ancestor (LUCA) a eukaryote? Spontaneous Generation of Life

16. Problems With Homology Common ancestry • Before Darwin, Richard Owen (1840s) defined homology as structures derived from a common “archetype” • Darwin redefined homologous structures as those derived from a common ancestor • Then turned around and said that homology is evidence of common ancestry • But this is circular reasoning Homology

17. Problems Using Molecular Data • Molecular data runs into the same problems as any other data that assumes homology • Molecular information frequently exhibits dramatically different expression in different organisms. For example genes with similar sequences control production of limbs in: • Echinoderms-Tube feet • Ploycheat worms-Setae • Vertebrates-legs and feet • Insects-jointed legs • Homologous structures can be produced by different genes

18. Prezygotic Barriers • Habitat isolation - If they live in different places, they can’t mate • Behavioral isolation - If species recognition is behavior based, organisms with different behaviors will not mate (i.e. eastern and western meadowlarks are identical in almost all things except song) • Temporal isolation - If they breed at different times, they will not breed with each other • Mechanical isolation - Need any more be said? • Gametic isolation - Gametes have complex recognition mechanisms so that gametes from one species will rarely fuse with those of another species

19. Post Zygotic Barriers • Inviable Hybrids - Hybrids may develop from a zygote formed from the sperm of one species and the egg of another, but they are weak inferior creatures and may not even survive until birth • Infertile Hybrids - Hybrids may be hardy creatures, but they are incapable of reproduction, frequency due to difficulties in producing gametes due to strange chromosome combinations resulting from meiosis • Hybrid Breakdown - At first hybrids are fairly successful, but over the course of several generations problems develop

20. Barriers To Hybrid Formation Inviable hybrids Infertile hybrids + + Hybrid breakdown Happy Hybrid Habitat isolation Behavioral isolation Temporal isolation Prezygotic Barriers Mechanical isolation Gametic isolation Postzygotic Barriers

21. Sympatric Speciation:Autopolyploidy Diploid plant 2n = 4 Somatic nondisjunction Self fertilization results in tetraploid offspring which cannot interbreed with the original diploid species Tetraploid flowers make diploid gametes Tetraploid cells develop into flowers

22. Sympatric Speciation:Allopolyploidy - Scenario 1 Plant species A 2n = 4 Mitotic nondisjunction produces diploid cells capable of producing fertile gametes 1n=2 gamete Gametes combine to make a hybrid 1n=3 gamete 1n=5 hybrid (infertile) 2n=10 hybrid (fertile) Plant species B 2n = 6

23. Sympatric Speciation:Allopolyploidy - Scenario 2 Plant species A 2n = 4 Meiotic nondisjunction produces unreduced gamete Unreduced 2n gamete Unreduced gamete Gametes combine to make a hybrid 1n=3 gamete 1n=7 hybrid (infertile) Plant species B 2n = 6 2n=10 hybrid (fertile) Normal gamete

24. Tempo Of Evolution Time Time D Morphology D Morphology Gradualism Punctuated Equilibrium

25. Edredge on Punctuated Equilibria "At the core of punctuated equilibria lies an empirical observation: once evolved, species tend to remain remarkably stable, recognizable entities for millions of years. The observation is by no means new, nearly every paleontologist who reviewed Darwin's Origin of Species pointed to his evasion of this salient feature of the fossil record. But stasis was conveniently dropped as a feature of life's history to be reckoned with in evolutionary biology. And stasis had continued to be ignored until Gould and I showed that such stability is a real aspect of life's history which must be confronted-and that, in fact, it posed no fundamental threat to the basic notion of evolution itself. For that was Darwin's problem: to establish the plausibility of the very idea of evolution, Darwin felt that he had to undermine the older (and ultimately biblically based) doctrine of species fixity. Stasis, to Darwin, was an ugly inconvenience." Eldredge N., "Time Frames: The Rethinking of Darwinian Evolution and the Theory of Punctuated Equilibria", Simon & Schuster: New York NY, 1985, pp188-189

26. The Rate of Evolution • Sometimes evolution has occurred at an amazingly rapid rate: • Drosophila pseudo-obscura, a native species, has declined since 1978 when the European species Drosophila subobscura was introduced in Chili • In Europe D. subobscura exhibits an increase in wing size as one goes from south to north • A south to north wing size gradient went unobserved when D. subobscura was studied around 1989, but a decade later a difference in wing size distribution mimicking that seen in European flies was evident. • Thus this wing size difference must have evolved in a decade or less, but no new species and no new alleles have been shown to arise in the American population

27. The Rate of Evolution • Galapagos finches are also known to have evolved very rapidly in nature • After a drought in 1978, a dramatic shift in beak size was observed in a local population of finches • However, it is worth noting that when conditions returned back to normal, the finches beaks also reverted back • Thus, selection did produce a morphological change in the finches which appeared to be heritable, but no new species of finch were produced and at the end of it all, the same kinds of finches that were previously there where still present

28. When the Data Speaks "For example, researchers have calculated that 'mitochondrial Eve'--the woman whose mtDNA was ancestral to that in all living people--lived 100,000 to 200,000 years ago in Africa. Using the new clock, she would be a mere 6,000 years old. No one thinks that's the case, but at what point should models switch from one mtDNA time zone to the other?” Gibbons, A. 1998. Calibrating the mitochondrial clock. Science 279:28-29

29. The End

30. Rooted In Eubacteria? "...this rooting [in the eubacteria] was rapidly accepted and advertised in the community of evolutionary biologists and beyond, being now systematically used to draw universal trees in review papers, and even textbooks.” (p. 511) "We have shown in this paper that the rooting of the tree of life in the eubacterial branch has been based on unreliable phylogenies.” (p. 521) Philippe Herve' and Patrick Forterre. 1999. "The Rooting of the Universal Tree of Life Is Not Reliable," Journal of Molecular Evolution 49:509-523.