So…. Evolutionary Stuff

1. So…. Evolutionary Stuff Wooo We’re Almost Done!

2. Some Things that need to be Mentioned a Bit • New alleles usually enter gene pool in a single copy • An Allele that is linked with a beneficial allele is called a Hitchhiker • Drift is intensified as genetic pressures increase because selection lowers population size which lowers the number of alleles in a gene pool

3. Going Over Lamark • His Muscular Baby theory is called orthogenesis. Another example of this are the Giraffes. • Thought that a mechanism for evolution was the inheritance of acquired characteristics and that species never went extinct. • All of this is WRONG

4. At Darwin’s Time There Was BLENDING INHERITANCE • Blending inheritance is the theory of evolution before Darwin did his thing. • This said that all offspring were a middle ground of the parents. So if the parents were tall and short then the offspring would be medium height. • This is also WRONG and proved wrong by……………………………………………………

5. GREGOR MENDEL!!!!!!! • Showed that offspring aren’t the blending of parents through his pea plant experiments. • Interesting fact: Gregor sent Darwin his paper on genetics but Darwin never opened it. • Mendel’s theory was thought to be crazy for a long time and only a few people kind of accepted it. Biometricians thought that Mendel’s theory worked only on certain genes that they considered aberrations.

6. Population Genetics • Biologists wondered how allele frequencies changed in a population. • Hardy and Weinberg independently found that allele frequencies don’t change just because an allele is rare or common. • R.A. Fisher showed that Mendel’s laws could explain continuous traits if these traits were due to many genes. • From this basis Fisher, Wright, and Haldane founded the field of Population Genetics.

7. R.A. Fisher and Natural Selection • Studied the effect of natural selection on large populations • Saw that very small changes in selective alleles could have major changes in their allelic frequencies. • Showed the rate of adaptive change is proportional to the amount of genetic variation present. This is called Fisher’s Fundamental Theorem of Natural Selection even though it doesn’t work all the time. • Weird thing: Sometimes natural selection can cause a decline in the mean of relative fitness of a population

8. Wright and Genetic Drift • Said that large populations subdivided into subpopulations. • Said that drift was more important than Selection. • Because of this there was differentiation between subpopulations and if there was migration among them there would be adaptations amongst the populations. • Came up with the idea of adaptive landscape which is really influential today even though P.A.P. Morgan proved that these didn’t work as Wright thought they did.

9. J.B.S. Haldane Liked Math • So he developed mathematical equations for natural and artificial selection. • With his math he proved that natural selection and mutation combated with each other (deleterious alleles remaining in population) • He also proved that natural selection placed a limit on the amount of adaptive substitutions a population can undergo in a given time frame.

10. Lewontin and Hubby find Genetic Variation in Natural Populations • Protein electrophoresis showed that 30% of the loci in Drosophila pseudoobscura were polymorphic. • This technique is also said to have missed a lot of genetic variants. • This means that there is a lot more genetic variation than anyone thought was possible.

11. The Japanese Always Have a Scientific Explanation • Motoo Kimura said that most genetic variation was neutral and used only Mutation and Drift to explain it. • His theory also said that the majority of genetic variation was transient polymorphisms of neutral alleles. • This Neutral Theory was first thought to be true but then people said nay because: there is less variation than the Neutral Theory predicts, too much variance between species to be explained by mutation and drift alone, Selection was proven to have an impact on nucleotide variation. • Now there is no comprehensive mathematical theory of evolution that works.

12. Macroevolution is hard to Study • Evidence of macroevolution comes through other fields of study which are: comparative biochemical and genetic studies, comparative developmental biology, patterns of biogeography (explaining ecological and historical reasons of species distribution), comparative morphology and anatomy, and the fossil record.

13. DNA Review (Sorry) • 4 types of nucleotides: A, G, C, T • Genes are sequences of DNA that code for proteins • Codons are three letter groupings of nucleotides that code for an amino acid. The sequences that code for each amino acid are the same between all organisms • Genes are transcribed into mRNA for use (What does m stand for and what is the nucleotide that replaces T?) • Ribosomes make proteins • Proteins do everything

14. Pseudogenes are Random Things that do Nothing • Pseudogenes- genes that have been inactivated because of mutation • They can be transcribed and translated but the proteins won’t do anything because it is shaped weirdly. • These also mutate more quickly because mutations don’t change the fitness of the organism

15. Introns and Exons (You would think that their Names would mean the Opposite) • Introns- sequences inside a gene that don’t code for anything. • Exons- sequences of genes that do code for proteins • Introns are spliced out of mRNA before it goes to the ribosome. • Introns are sometimes used in the regulation of a gene and generally mutate more quickly than exons

16. Silent Sites and Replacement Sites • Silent sites- places where nucleotide sequence can change without affecting the protein. • Replacement sites- places where changes result in changes of amino acid sequence. • Silent sites are generally the sites that show the most difference between populations and are usually used for this because replacement sites are constrained from mutation through Natural Selection.

17. Kreitman is the Master of Silent Sites • Demonstrated that Silent sites are more viable than replacement sites by sequencing 11 alleles for alcohol dehydogenase. He found 43 polymorphic nucleotides and only one changed the amino acid sequence. • But silent sites are not always selectively neutral because there are regulatory sites for the gene, so if there is a change here it may be deleterious. • Also several codons code for the same amino acid but an organism may prefer one codon over another, this is a codon bias

18. Li and Graur use Math to find Replacement Rates • They found that silent sites evolve at an average of 4.61 nucleotide substitutions per 1,000,000,000 years • Replacement sites evolve at an average of .85 nucleotide substitutions per 1,000,000,000 years.

19. Organisms that are Related have the Same Types of Things • Take mammals for example: bones of a human hand grow the same way as the wing of a bat or the fin of a whale. They also share the same muscle insertion points. • The only difference is that they are scaled differently; this suggests that all mammals evolved from the same ancestor and thus all mammals have the same type of bones. • We also share the same beginnings of our developmental pathways and all look the same while we’re fetuses.

20. Natural Selection Modifies Stem Cells! • There are differences in early vertebrate embryos • Amphibians form a ball of cells because their eggs aren’t heavily yolked • Birds and Reptiles have heavily yolked eggs, making their embryos form disks by having them stretch out over the yolk. • Humans also form disks because all mammals evolved from reptiles

21. Vestigial Structures help us Delve into Evolutionary Past • Vestigial structures are structures that have not entirely disappeared from our bodies. • Vestigial structures are not always useless; they usually acquire a new function. • Example: the Human appendix is not useless, it houses some immune cells.

22. Organisms that are close Geographically are usually Evolutionary close too. • Australian Marsupials are usually used for this example. • Marsupials fill all the ecological niches on Australia that placentals usually fill. • This means that the physical distance between placentals and marsupials means that the potential niches were filled by marsupial radiation.

23. Selection Chose Lizards that can Reproduce by Themselves • In lizards of the Genus Cnemodophorus, the females can reproduce parthenogenetically (by themselves). • These lizards evolved from sexual lizards whose hormones were aroused by sexual behavior. Now these lizards can’t reproduce sexually but they still need to get aroused to reproduce.

24. Fossils show Similarities between Species and explain Biogeography • Examples: South America was once populated by lots of marsupials but when the Americas collided placentals took the marsupials’ places as they left and most marsupials died. • Then there are transitional fossils that show a stage in between two evolutionary lineages. • Example is a transitional skull between mammals and reptiles. A big difference is that mammal jaws only have one big dentary bone while reptiles have four. Also, mammals have differentiated teeth and nasal passage ways while reptiles don’t. We also have more muscles in our jaw.

25. The Fossils that show the Changes between Mammals and Reptiles • Fossil species that have these differences are: • Procynosuchus has an increase in the size of the dentary bone • Thrinaxodon has fewer incisors and more tooth differentiation • Cynognathus has a gigantic dentary jaw, the other three bones are in the back of the skull, and some teeth are multi cusped and most are differentiated • Diademodon has close fitting teeth • Probelesodon has a double jointed jaw which helped more muscles to come forward, attach, and strengthen • Morgonucudon was the first true mammal that had all of these characteristics

26. Procynosuchus

27. Thrinaxodon

28. Cynognathus

29. Diademodon

30. Strongest Evidence of Macroevolution is… • Taxonomy! All biological entities can be classified into specific categories that are in a pattern. • Example: plants are either non-vascular or vascular, seedless or seeded, gymnosperms or angiosperms. • Each type has its own specific collection of traits that are not mixed with organisms of another type.

31. Speciation is a mechanism of Macroevolution!!! • Speciation is when one species becomes 2 • Paleontologists generally think that certain evolutionary phenomena only occur at speciation and thus macroevolution can’t happen without it • Geneticists, on the other hand, generally believe that major evolutionary change can occur without speciation and that changes between lineages are an extension of changes within each lineage.

32. Two Types of Speciation • Allopatric and Sympatric speciation • Allopatric is the most common and occurs in distinctly separate locations. The resulting species rarely interbreed because of the separate locations. • Sympatric speciation is when subpopulations become reproductively isolated before they are geographically isolated

33. Weird Example of Sympatric Speciation • A type of apple maggot fly (Rhagolettis pomenella) began infesting apples in the 1860s. It was previously infesting hawthorn fruit. Now the flies on both types of fruit will not mate with each other because they are on different fruit. Now the two fly races are diverging in their alleles at six loci. This was shown by Feder, Chilcote, and especially by Bush who is really important and one of the major proponents of sympatric speciation. • Some biologists call sympatric speciation microallopatric speciation to emphasize the fact that the two species are separated geographically at some level.

34. Biologists have no idea how Speciation works so there is a lot of Hypothesizing • Ernst Mayr thinks that the founder effect may set the stage for rapid speciation. • Alan Templeton says a few key genes could change and confer reproductive isolation. This is called genetic transilience. • Lynn Margulis thinks speciation events are caused by internal symbionts. • It is possible that all of these hypotheses are true.

35. Speciation is Happening Even NOW!!!!!! • Under the plant genus Tragopogon two new species (T. mirus and T. miscellus)have emerged in the past 50-60 years!!!!! • They evolved by one diploid plant fertilizing another diploid plant, forming a tetraploid offspring that could not mate with the diploid plants around it, thus it is reproductively isolated and is a new species by definition.

36. Extinction!!!!!!! • Every single organism in a species DIES!!!!!! • This can happen for many reasons: • A species is completely excluded from another close related species • The organism’s habitat disappears • The organisms an organism exploits could rise against the exploiting organism • Some biologists think that species are supposed to go extinct but most believe that if the conditions stay favorable a species can live indefinitely

37. MASS EXTINCTIONS!!!!!! • These shape the over all patterns of macroevolution • When lots of organisms die, the living organisms go through rapid speciation and fill all the niches. • The largest Mass Extinction happened when the world’s continents collided forming Pangaea II • The most well known is when the Dinosaurs died. This most likely occurred because an asteroid hit the earth, forming the K/T Boundary. • Currently Humans are causing a global mass extinction right now!!!

38. Punctuated Equilibrium • Hierarchical Theory of Evolution • Proponents link speciation to mutation and species replacement (species Selection) to Natural Selection • They also say that Evolutionary trends among a group would result of selection among species, not within the individual species. • This last part is really controversial

39. Punctuated Equilibrium is Supported with Transitional Fossils • A transition from one species to another is usually quite abrupt and only happens in a specific place usually. • This led Eldredge and Gould to propose that most morphological changes happen relatively quickly in small, specific places. Thus the transition from one species to another is abrupt.

40. Critics of Punctuated Equilibrium • These people say that species selection isn’t similar to natural selection and thus it doesn’t work. • They back this up with the fact that there are a lot more alleles in a gene pool than there are species in a species pool. So the amount of adaptive evolution produced by species selection would have to be a LOT less than the amount of adaptive evolution within a species through natural selection • Also there can be major polymorphisms within a species. An example is the bluegill sunfish. One morph is big, long living, and protective of its mate. The other is small, short living, and a creep that sneaks matings from unprotected mates.

41. Long Article Thing that is Pretty interesting and talks about Sympatric Speciation • Guy Bush debuted as a major biologist in 1966 talking about sympatric speciation and now he’s spent all these years building an argument that proves he’s right. Did it by proving that the flies use the apples as a stage for their courtship dance and if they don’t dance on an apple the two flies won’t mate. • Others who have talked about or tried to prove this before are: • Darwin • Benjamin Walsh who said this in 1862 when the apple maggot flies first started to go to apples but had no proof

42. People who opposed Sympatric Speciation • Now: Dolph Schutler was against this for multiple years but is now seeing Sympatric Speciation in his stickleback fish which only mate with others that share its diet and are about the same size. EricTaylor confirmed that sticklebacks of the same diet and size were related through DNA comparisons. • 1947-Now: Mayr said that there was no proof so it has been discarded mostly until now. He still believes that this idea should be discarded after seeing all the evidence we will talk about on the next slides

43. Bush Publishes Paper with the help of Colleagues • Bush, Feder (former Grad Student who found that only 6% of the apple and hawthorn flies mated together) and co-workers Stewart Berlocher, Bruce McPheron, and David Courtney Smith published paper that identified the differences in chromosomes of the different populations. • These differences make the different fly populations leave the fruit they are born in to go into the ground at different times and then come out of the ground in the summer at different times too (the apple flies do both things earlier than the hawthorn flies.)

44. Bush Gets Help from Rice and Fish • William R. Rice put Drosophila mekmogaster in a maze and because of their different genes they separated into their slightly different habitats throughout the maze and they only mated in these specific areas so they were all reproductively isolated. • Cichlid species of fish have evolved reproductively isolated from each other in their specific lakes and river areas. This is proven through mitochondrial DNA and this showed that all of the fish in one lake were more closely related to others in the lake than those in the surrounding area and through the diet of all the fish which led them to the specific lake areas and separated the different populations from each other. Ulrich Schliewen discovered this.

45. Last Funny Blurb Thing: Amazon Diversity!!!! I’m Sad. • James L. Patton went to the Amazon to study allopatric speciation caused by Rio Jauruá (tributary of the Amazon) • Gathered lots of gene samples from species, tested their mitochondrial DNA • Found that there were lots of differences and that a couple of these differences occurred because of Rio Jauruá. But others occurred for no apparent reason until he found out that there used to be ancient ridges made by the movement of tectonic plates that are now covered over because the Andes started to erode and fill in the Amazon basin

46. Stupid Bird Names and More Sympatry • Michael Sorenson and Robert Payne study the Blue Indigobird (STUPID NAME). • It lays eggs in two species of finches nests: the African Firefinch and the Black Bellied Firefinch. Then this blue bluebird that hatches gets raised by these finches and acts like them, picking up signature tweets and trills. • Then when they grow up they usually mate with those that share the same types of bird calls.

47. More of the fish, some Trees and Cool Names this time • Axel Meyer (cool name) studied the arrow and the Midas cichlids and found the same stuff as Ulrich found (Yay for repetition!). • Vincent Savolainen and William Baker studied the kentia and the curly palm trees on Lord Howe Island. They found that the curly palm speciated from the kentia palms when they moved to more acidic soils which messed with their timing to flower so the pollens couldn’t mix with the old kentia palms and thus they are two species.

48. MORE FLIES • Thibaut Malausa found that some European corn-borers prefer hop or mugwort or corn. • They types that prefer the different plants have stopped mating because they do the mating on the plants and if the different types don’t go to the plants they don’t like then they will never mate, this is what happens.

49. Arguments against Sympatry • There is still some geographic isolation even on the corn or the apples and the hawthorn trees even if it is small • The kentia and the curly palms may have come about because pollen from far away fertilized the kentia palm making the curly palm. • Richard Glor studied Cuban anoles that speciated because Cuba was flooded 5 million years ago so the anoles were physically separated.

50. THE END!!!!!! GO FORTH AND CREATE A NAME FOR THE BLUE INDIGOBIRDS SO THEY CAN HAVE A BETTER ONE.