But the most obvious feature of life is the staggering DIVERSITY of its many forms

1. So far we have emphasized that life is an interesting form of chemistry. This helps understand its role in transforming the biosphere. But the most obvious feature of life is the staggering DIVERSITY of its many forms We will examine this diversity from the two main perspectives 1. Evolution 2. Ecology

2. In order to make sense of this vast diversity, we look for ways to classify it, to simplify Looking closer at this diversity, various patterns emerge.

3. One natural classification scheme is to arrange organisms into groups that look the same. This is the approach of traditional __________. This approach leads naturally to a study of evolution - evolutionary relatedness and organismal adaptation (form and function). That is, organisms will look the same for two main reasons – they are closely related, and/or they express similar functional “designs”

4. For example, butterflies, birds and bats all fly and they all look similar because of the wings. But looking closer, there are big differences too, so they are classified as separate groups (there are many different kinds within each group)

5. Another natural classification scheme comes from noticing that some organisms tend to live together in the same places (and not in others) – that life is organized into natural “communities” of diverse organisms. This leads to the study of ________, the logic of how different organisms interact and coexist.

6. For example, major ecosystem types called ________ (deserts, rainforests etc.) have characteristic organisms and are found distributed in different places on the earth 3-5/3-6

7. And the distribution of _______ is closely related to the distribution of _________. 12-2

8. ___________ – the classification of life Both evolution and ecology are important dimensions of the multidimensional problem of understanding biodiversity. But before we could think about understanding, a huge effort had to be expended in collecting and grouping organisms into logical classes. All human cultures have developed systems for classifying life The system used by our culture was established by Carolus ________ in the 1700s in Sweden. http://www.ucmp.berkeley.edu/history/linnaeus.html

9. The _________ System This system is based on the idea that life is separated into distinct _________ that can be classified into a nested, or hierarchical, increasingly inclusive set of groups. Ultimately, each species is given a distinctive _______ – a two word name referring to the species and the group to which it belongs (this is called “binomial nomenclature”) This is similar to our method of naming people, family name and individual name e.g. Jimmy Page Leopard- Panthera pardus Genus – Panthera Species - pardus

10. Panthera onca (jaguar) Panthera pardus (leopard) Panthera tigris (tiger) Panthera uncia (snow leopard) Panthera leo (lion) http://home.globalcrossing.net/~brendel/index.html

11. The Linnaean System Some interesting examples of species names (NY Times Feb 20 2005): Bittium (mollusk) has a related genus Ittibittium Ba humbugi (snail) Insects: Heerz tooya Apopyllus now Pieza pi, Pieza rhea, Pieza deresistans Phthireia relativitae For more check this out: http://home.earthlink.net/~misaak/taxonomy.html

12. The Linnaean System Hierarchical classification is totally natural for us – although the “ideal” system of classification can be elusive Music groups English Rock Bands Led Zeppelin Jimmy Page Dec. 10, 2007

13. The Linnaean System The Linnaean system uses a particular set of levels that has been modified over time – genus, family, order, etc.

14. The Tree of Life The Linnaean system was developed before ideas about evolution and the relatedness of all life, yet it is consistent with that view (and inspired it) and has remained in wide use The evolutionary view adds an historical component – that the species we see today derive by a process of __________ (separation of one species into two over time), creating a “family tree” of ancestral and descendant species These relationships are usually depicted as a branching tree, or _________ (or “phylogenetic tree”) The Y-axis is time – down is longer into the past, ________ implies speciation events

15. The Tree of Life The hierarchical branch “clusters” correspond to the taxonomic levels This is a “rough” correspondence but overall traditional taxonomy _____ been an excellent guide to modern phylogenetic reconstruction

16. The Tree of Life _____________ – determining these trees for taxonomic groups is a very active area of research. The ultimate goal is to construct the complete family tree of life, and to make this the basis of our taxonomic system. You can find out the current status of this effort at http://tolweb.org/tree/phylogeny.html The basic idea of this approach is to classify species by their various characteristics, or traits, and to identify which traits are newer and which older. Traits that are relatively older are called ________, more recently evolved are called __________.

17. The Tree of Life This style of reasoning is ________________ traditional taxonomy

18. The Tree of Life The current explosion in tree of life research has been fueled by our new knowledge about _________________________. This is essentially an entirely new and extremely precise array of species traits from which detailed phylogenies can be constructed – independently of traditional observable traits. This independence creates a welcome check on traditional taxonomy. So far it has mostly _________the traditional approach, but in some cases has provided interesting new insights.

19. The Tree of Life For example, traditionally reptiles and birds are separated into different classes: Reptilia and Aves But the genetic evidence suggests that crocodiles, traditionally considered reptiles, are really closer to birds than to other reptiles. Reptilia Aves Naturally, there is a lot of discussion about how to sort this out What would you suggest?

20. The Tree of Life Here are some of the contenders – is your solution here?

21. http://www.eidnesfurs.com/index.html

22. How can a gene sequence be used to create a phylogenetic tree? What is a gene sequence? Recall: Gene expression is the protein production machinery of a cell’s biochemistry. Proteins are used in various ways, but especially in the form of enzymes, that catalyze reactions – they regulate what reactions happen when – that is, they control everything. What is a protein? - a long chain molecule, or polymer, a chain of small organic molecules _____________ (20 different types), that when assembled, folds itself into a 3-dimensional shape that can catalyze a reaction.

23. The final protein structure is determined by the ___________ of amino acids in the protein polymer.

24. What controls the amino acid sequence of a protein? The _____ molecule is also a long chain of simpler organic molecules (“nucleic acids”) that contains the protein sequence in coded form, using the ___________ This molecule can be copied, keeping the sequence intact The genetic code is not a simple one-for-one code because there are only four different nucleic acids (A,T,G,C) to code for 20 amino acids.

25. It is a “triplet code” – every three nucleic acids code for each subsequent amino acid DNA sequence becomes a ______ sequence There is an intermediate step involving an___sequence

26. The genetic code As far as we know, the code is pretty _______ – could have been different and still work fine Yet, ________ use the same genetic code, supporting idea of a common origin of all life

27. The DNA stores the sequence information for all the proteins needed by the organism A “gene” is a particular DNA sequence that codes for a particular protein “____________” is this conversion – protein production. Which genes are “turned on” when Gene expression is responsive to the ____________ (internal and external) Since enzymes regulate biochemistry, including gene expression, the regulation of gene expression is the ultimate controller

28. Genes are the third key ingredient, or resource, in the recipe for life –__________ 1. Energy 2. Materials 3. __________ Information encoded in the sequences of DNA can be thought of as a kind of knowledge, often referred to as a library This information has accumulated over the billions of years of life’s history on earth. It is reasonable to think of it as a natural resource, built into the structure of living organisms.

29. The differences between organisms are due to differences in their ____ Each species carries genes that are unique to that species

30. DNA sequences can be used to create phylogenies by assuming that the more _________ the gene sequences, the more closely related the species are What is the logic behind this assumption? Reptilia Aves

31. 1. All life arose from a single common ancestor 2. Organisms differ primarily in their ______ 3. Given 1 & 2, the current diversity must have resulted from a ___________ of the genetic makeup of organisms. 4. The diversification was one step at a time – biochemistry is too complicated to change radically 5. The more______has elapsed since lineages diverged, the more steps have been taken Interestingly, these assumptions don’t require any specific knowledge about gene function – it even applies to genes that have no known function (silent or “junk” DNA)

32. Human ...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTT... Yeast ...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTT... Corn ...GCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTT... Escherichia coli ...GCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGT... Methanococcus sp. ...GCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGGCCT... Some genes have changed very little, and can help compare very distant relatives (here a segment of rRNA) Some regions change very fast – what would they reveal? http://www.bact.wisc.edu/Bact303/Phylogeny

33. This work has led to a detailed “big picture” view of the tree of life, including the establishment of the “Three _______” concept Also, much fine detailed study of evolutionary changes within-species

34. Part 2 The diversity problem: Why is there more than one species? Diversification requires two aspects 1. Speciation – division of one lineage into two 2. Differentiation of the two lineages (change in one or both) If this happens over and over, you get a lot of species – speciation itself has a kind of exponential capacity

35. Speciation A species generally exists in multiple subgroups distributed in space, each called a ___________ The populations will tend to stay similar if individuals can move between them (called __________) and reproduce. Conversely, they will have the capacity to diverge genetically if there is no gene flow, if they are ____________________ What kind of factors might cause reproductive isolation?

36. Factors that increase reproductive isolation 1. Physical separation 2. Ecological separation 3. Reproductive incompatibility, asexuality _________ speciation - populations become separated geographically (#1 - e.g. a river or mountain range), then diverge. This is considered likely the most important form of speciation. _________ speciation – populations in the same range but ecologically (#2) or reproductively (#3) separated diverge.

37. An example of a probable __________ speciation 3-4/3-3 Note that a key component of this is the change in one or both of the separated populations – evolution.

38. Evolution is defined as change in genes in a population over time. Adaptive evolution refers to changes that increase organism success, and is of central interest in understanding diversity There are many genes in an organism, even more in a population (since individuals are different) – ________ The total number of different genes in a population is called the _______________ Causes of evolution are of 2 basic types increase variation – “creative” decrease variation – “restrictive” Both are required for adaptive evolution

39. Creating variability – adding new genes 1. _________– change in DNA sequence 2. Duplication, deletion – change in number 3. Introgression, conversion Restricting variability – eliminating genes 1. Random fluctuations, losses (“drift”) 2. Natural selection _________ - Darwin proposed that in a given environment, types that were most suited would survive better and reproduce more – this would tend to create adaptation by eliminating less fit types.

40. While mutation and other processes create variation – it is generally a result of ______________, “undirected” change Natural selection continually works to to improve the “______” by favoring the most effective variants Unfinished sculpture by Michelangelo for the tomb of Pope Guilio II I saw the angel in the marble and I carved until I set him free. Michelangelo Michelangelo's Pieta was carved in 1499, when the sculptor was 24 years old.

41. For this to work, differences in ________of individuals must be due to differences in genes The genes of an individual are called the genotype, and the organism with all its traits is called the __________ Adaptation is achieved by phenotypes, but for this to result in adaptive evolution, the phenotypes must reflect the genotypes. The differences must be passed on to the offspring – called ______________ Natural selection is a powerful process that can cause adaptive evolution by favoring a subset of the existing heritable variation. The more the marbles wastes, the more the statue grows. Michelangelo

42. Darwin compared this to “_______selection”

43. Science 22 November 2002:Vol. 298. no. 5598, pp. 1610 - 1613 Genetic Evidence for an East Asian Origin of Domestic Dogs Peter Savolainen,1* Ya-ping Zhang,2 Jing Luo,2 Joakim Lundeberg,1 Thomas Leitner3 The origin of the domestic dog from wolves has been established, but the number of founding events, as well as where and whenthese occurred, is not known. To address these questions, we examinedthe mitochondrial DNA (mtDNA) sequence variation among 654 domesticdogs representing all major dog populations worldwide. Althoughour data indicate several maternal origins from wolf, >95% ofall sequences belonged to three phylogenetic groups universallyrepresented at similar frequencies, suggesting a common originfrom a single gene pool for all dog populations. A larger geneticvariation in East Asia than in other regions and the pattern ofphylogeographic variation suggest an East Asian origin for thedomestic dog, ~15,000 years ago.

44. Many examples exist of natural populations responding to selection without controlled breeding For example, evolution of _____________________

45. So the basic idea that diversification can result from speciation and adaptive divergent evolution is plausible and consistent with observation The question of what species are adapting to is an ecological question we’ll take up shortly Before that, we will look at a few features of organisms reflect uniquely “Darwinian” features And also survey the results of this diversification