Basic Biology II: Genetics and Evolution

1. Basic Biology II: Genetics and Evolution How organisms work

2. Outline Inheritance (pp. 104-110, 119-120): sexual and asexual reproduction, Mendelian genetics, crop improvement, genetic engineering Natural Selection and Evolution (pp. 131-136) Classification and Diversity (pp. 124-130, 137, 140-141)

3. Inheritance • Contrast sexual and asexual reproduction. • Understand the difference between haploid and diploid, and how the processes of meiosis and fertilization convert between the two states. • Use the vocabulary of genetics: gamete, allele, homozygote, heterozygote, dominant, recessive, phenotype, genotype, to describe explain why the offspring of a self-pollinated heterozygote appear in a ratio of 3/4 dominant phenotype to 1/4 recessive phenotype. • Define several methods of crop improvement and their general properties: single gene traits, polygenic traits, selection, polyploidy, hybridization, genetic engineering. • Describe the process of molecular cloning, using a plasmid, restriction enzymes, and DNA ligase, and transformation.

4. Sexual and Asexual Reproduction Long term survival requires reproduction. Even the longest-lived organisms are less than 10,000 years old. Cellular machinery wears out, or gets clogged with waste products. Environmental conditions change Plants often reproduce asexually, through cuttings or runners or buds (e.g. potatoes). The resulting plants are clones: they are genetically identical to the parent. Used to preserve good combinations of traits. Sexual reproduction is also found in plants, and in all animals. Sexual reproduction means combining genes from two different parents, resulting in new combinations of genes. Each parent contributes a randomly-chosen half of their genes to the offspring. This can be a good thing, because some new combinations will survive better than the old ones. It can also be bad: lack of uniformity in the offspring.

5. Sexual Reproduction • Diploid: having 2 copies of each chromosome, one set from each parent. • Humans have 46 chromosomes, 23 from each parent. • Almost any organisms you can see: plant, animal, fungus, is diploid. • Haploid: having only 1 copy of each chromosome. • Sperm and eggs (=gametes) are haploid • moss, a primitive plant, is haploid for most of its life • Plants, animals, and other eukaryotes alternate between haploid and diploid phases. This is called alternation of generations.

6. Life Cycle Diploid organism generates haploid gametes using the process of meiosis. The gametes combine during the process of fertilization to form a new diploid organism. In animals, the haploid phase is just one cell generation, the gametes, which immediately do fertilization to produce a diploid zygote, the first cell of the new individual. In plants, the haploid phase is several cell generations at least. Lower plants are mostly haploid Higher plants are haploid for only a few cell generations The diploid plant is called the sporophyte, and the haploid plant is called the gametophyte.

7. Genetics The science of genetics is devoted to understanding the patterns of how traits are inherited during sexual reproduction. It was founded by Gregor Mendel in the 1850's, using pea plants. Despite the obvious differences, humans and peas have very similar inheritance patterns. The fundamental observation of genetics: within a species, there are a fixed number of genes, and each gene has a fixed location on one of the chromosomes. This allows genes to be mapped: a gene's neighbors are always the same.

8. Genetics Alleles. Many genes have several variant forms, which are called alleles. For example, a gene the produces color in the flower might have a purple allele and a white allele. These alleles are designated P and p. Differences in alleles are what makes each human different from all others True-breeding lines. If you cross close relatives with each other for many generations, eventually all the offspring look alike. Mendel started with several true-breeding lines, which differed from each other in 7 distinctive characteristics

9. Genetics • In many plants, you can self-pollinate: cross the male parts of a plant with the female parts of the same plant. • In this case, both copies of any given gene are identical. This is called homozygous. The plants are homozygotes, either PP (purple) or pp (white). • The closest cross you can do in animals is brother x sister. • Hybrids. If you cross two true-breeding lines with each other and examine some trait where the parents had different alleles, you produce a heterozygote: the two copies of the gene are different. • Surprisingly, you often find that the heterozygote looks just like one of the parents. The Pp heterozygote is purple, just like its PP parent. • This is the F1 generation in the diagram.

10. Genetics Dominant and recessive. If a heterozygote is identical to one parent, the allele from that parent is dominant. The allele from the other parent is recessive. That is, the heterozygote looks like the dominant parent. This is why we say purple is dominant to white, and give purple the capital letter P. Phenotype and genotype. Phenotype is the physical appearance, and genotype is the genetic constitution. The heterozygote in the previous paragraph has the same phenotype as the homozygous dominant parent (i.e. purple flowers), but a different genotype (the heterozygote is Pp and the parent is PP).

11. Genetics • Now we want to move to the next generation, by self-pollinating the heterozygotes. • When a heterozygote undergoes meiosis to produce the haploid gametes, half are P and half are p. • These gametes combine randomly, producing 1/4 PP, 1/2 Pp, and 1/4 pp offspring. • Since PP and Pp have the same phenotype, 3/4 of the offspring are purple and 1/4 are white.

12. Methods of Crop Improvement • The idea that we can improve the inherited characteristics of crop species is fundamental. Very few of the plants we use are unmodified wild plants: most of them have been modified to make them easier to grow and harvest, and to increase the quality and quantity of the desired product. • We will see many examples of crop improvement this semester. Here are some of the basic methods used.

13. Single Gene Traits and Mutation • Single gene traits. Many useful traits are controlled by a single gene. Spontaneous mutations can lead to important, abrupt changes • A good example: sweet corn. The recessive mutation su (sugary) produces kernels that are 5-10% sugar. But, only when homozygous: the non-sugary allele (Su) is dominant. • Single gene mutations occur rarely, but often enough so that observant people notice and propagate them. • Sweet corn was recognized and propagated by several Native American tribes. The Iroquois introduced it to European settlers. • Mutation rate: 1 in 10,000 to 1 in 1,000,000 plants. • Artificially-induced mutation occasionally works, but most are spontaneous. • Single gene traits are inherited in a Mendelian fashion: • each individual carries one copy of the gene from each parent, • the relationship between phenotype (sweet vs. starchy corn) and genotype (homozygous or heteozygous) is determined by dominance vs. recessiveness.

14. Polygenic Traits and Selection Polygenic traits. Many traits are controlled by many genes, each of which contributes a small amount to the phenotype. Grain yield is a good example: lots of genes contribute to this. Such traits respond well to selection. In the simplest sense, selection means using the best seeds to start the next generation. If this is done consistently, the crop slowly improves over many generations. Genetic research has led to an understanding of what happens during selection. This allows much faster and more effective selection than just saving the best seeds.

15. Polyploidy • Normal diploids have 2 copies of every chromosome. Sometimes it is possible to double this number, making a tetraploid, 4 copies of every chromosome. • The drug colchicine does this by causing meiosis to produce diploid gametes instead of the normal haploids. Then, diploid sperm + diploid egg = tetraploid embryo. • Tetraploids are often bigger, healthier, more nourishing than their diploid parents. • Examples: cotton, durum wheat, potato, daylily • Tetraploid is a form of polyploid, which means having more than 2 sets of chromosomes (2 sets = diploid). • There are triploid (e.g. banana and watermelon), hexaploid (bread wheat, chrysanthemum), and octaploid (strawberry, sugar cane) crops

16. Hybridization • Plants are not as rigid in maintaining species boundaries as animals are. It is often possible to produce hybrids between two different, but closely related species. • Members of the same genus will often hybridize • The resulting plants often have characteristics different from both parents • Often sterile, but many plants can be propagated vegetatively • The grapefruit is a naturally-occurring hybrid between a pomelo (native to Indonesia) and a sweet orange (native to Asia).. It was discovered in Barbados in 1750, then brought to Florida and propagated. • Hybrids have an “x” in their species name: Citrus x paradisi • Sometimes, a hybrid will spontaneously double its chromosomes, so you end up with a tetraploid . These interspecies tetraploids are usually fertile, and they benefit from the general effect of tetraploidy: bigger, healthier plants.

17. Genetic Engineering • In the last 30 years it has become possible to take a gene out of one organism and put it into the DNA of another organism. This process is called genetic engineering. The resulting organisms are genetically modified organisms (GMOs) and the gene that has been transplanted is a transgene. • There are no real interspecies barriers here: all organisms use the same genetic code, so genes from bacteria (for example) will produce the correct protein in a corn plant. • However, some modifications must be made to the signals that control gene expression, since these are more species-specific. • A few examples: • Bt corn. Bacillus thuringiensis, a soil bacterium, produces a protein that kills many insect pests, especially the corn earworm. The gene for this protein has been transplanted into much of the US corn crop. • Roundup Ready soybeans (plus other crops). Roundup is the Monsanto brand name for the herbicide glyphosate. A bacterial gene that confers resistance to this herbicide has been transplanted to many crops. The farmer can then spray the fields with glyphosate and kill virtually all the weeds without harming the crop. About 87% of the US soybean crop is now Roundup Ready transgenic plants. • Some cultural issues here: are GMOs safe to eat?

18. Molecular Cloning The first step in genetic engineering is molecular cloning. Molecular cloning means taking a gene, a piece of DNA, out of the genome and growing it in bacteria. The bacteria (usually E. coli) produce large amounts of this particular gene. The cloned gene can then be used for further research, or to produce large amounts of protein, or to be inserted into cells of another species (to confer a useful trait). The basic tools: 1. plasmid vector: small circle of DNA that grows inside the bacteria. It carries the gene being cloned 2. Restriction enzymes: cut the DNA at specific spots, allowing the isolation of specific genes. 3. DNA ligase, an enzyme that attached pieces of DNA together. 4. transformation. Putting the DNA back into living cells and having it function.

19. The Cloning Process 1. Cut genomic DNA with a restriction enzyme. 2. Cut plasmid vector with the same restriction enzyme. 3. Mix the two DNAs together and join them with DNA ligase. 4. Put the recombinant DNA back into E. coli by transformation. 5. Grow lots of the E. coli containing your gene. The real trick, however, is to find the gene that confers your desired trait.

20. Transgenic Plants • Once a gene of interest has been identified and cloned, it must be put into the plant. • Usually done with plant tissue culture. Small pieces of a plant can be grown as an undifferentiated mass of cells on an artificial growth medium. • Then, when treated with the proper plant hormones, these cells develop roots and shoots. They can then be transferred to soil and grown as regular plants. • To make transgenic plants, DNA gets put into the tissue culture cells, by one of several methods: • One method is the gene gun: tiny gold particles are coated with the DNA, and then shot at high speed into the cells. The gold particles penetrate the cell wall and membrane. Some end up in the nucleus, where the DNA gets incorporated into the chromosomes. • An important issue: the proteins produced by transgenes are identical to those produced in the original species, because the genetic code is universal. • However, the signals needed to express these genes are plant-specific, not universal.

21. Natural Selection and Evolution Define fitness, and describe how differences in fitness and natural selection lead to changes in gene frequencies within a species. Describe how directional, stabilizing, and disruptive selection affect a population. Distinguish between the “biological species concept” and the “morphological species concept”. Distinguish between allopatric and sympatric speciation, and list possible causes of sympatric speciation. List and define several possible fates for a new species.

22. Evolution by Natural Selection Fitness: the ability to survive and reproduce healthy, fertile offspring. More fit individuals have a better chance of producing offspring than less fit individuals. The basic idea of natural selection is quite simple: those organisms that are more fit produce more offspring than other members of their species, and so they will have more descendants in future generations. Many genes increase or decrease fitness. In fact, most genes affect fitness in some way: it is hard for a gene to NOT affect fitness. Genes that increase in fitness gradually take over the species, and genes that decease fitness gradually get eliminated.

23. Selection and Evolution • A population is all members of a species that interbreed with each other. • Artificial selection works the same way as natural selection: the most fit individuals have more descendants than the less fit. However, in artificial selection, humans determine which individuals are more fit: we decide which individuals will be allowed to reproduce. • Evolution on the small scale (microevolution) is just changes in the frequency of genes in the population. This can lead to large changes in appearance over the long term.

24. Directional Selection Selection can be artificial: caused by humans, or natural: caused by environmental conditions. The simplest form of selection is directional selection: one extreme phenotype is less fit than the rest of the phenotypes. Caused by outside forces like climate change or disease. Or, by the appearance of a new gene that confers greater fitness. Plot the distribution of the trait being selected on a graph. Usually get a bell-shaped curve (normal distribution, Gaussian distribution)—most individuals are more or less average, with a few extremes at each end Don’t let individuals at one extreme breed. In later generations, the population average shifts away from the less fit extreme .

25. Stabilizing Selection Selection can act to favor the most common type, the middle of the distribution. This can happen when both extreme types are attacked. The status quo is maintained. This is stabilizing selection. Most selection is stabilizing: most characteristics of a species stay pretty constant over many generations. Example: human birth weight. Too small leads to unhealthy babies and high infant mortality. Too large leads to mothers dying in childbirth.

26. Disruptive Selection Disruptive selection is the opposite of stabilizing selection. In disruptive selection, the average type is the least fit. Only the extremes survive, creating a population with two different alternatives. This is one of the forces that drives the splitting of one species into 2. Example: grasses that find themselves near mines. Mine tailings containing heavy metals are toxic to most plants. Some grasses are resistant to heavy metal poisoning, so they can grow on the mine tailings. Less resistant members of the species grow on uncontaminated ground. Since heavy metal resistance is expensive, the resistant plants are less successful on uncontaminated ground. So, the species is being cut into 2 groups: the resistant variety growing on the mine tailings and the sensitive variety growing on clean soil.

27. What is a Species? • What is a species? Based on ability to reproduce. • “Biological species concept”: a species is a group of organisms that interbreed under natural conditions and that are reproductively isolated from each other. • Reproductively isolated: don’t produce fertile hybrids. • Natural conditions: artificial breeding doesn’t count. For example, artificial insemination, keeping 2 species locked up together. • In contrast, the older “morphological species concept”: members of the same species look similar to each other. Many examples of organisms that look similar but can’t produce fertile offspring. • Problems with biological species concept: • Doesn’t work with fossils or extinct species. • Doesn’t work with asexual species , such as most bacteria. • How to deal with what is “natural”.

28. Speciation • Speciation: splitting of one species into 2 different species. Very common. • If a species is split into two groups that don’t interbreed, they mutate and change independently, and soon are unable to produce fertile, healthy offspring. • Traits that directly affect reproduction are especially prone to changing: what is attractive to members of the opposite sex is prone to changes in fashion in the non-human world as well as the human. • Selection for traits directly affecting reproductive success is called sexual selection.

29. Allopatric Speciation The simplest and most common mechanism of speciation is allopatric speciation: 2 groups of one species are isolated geographically, and diverge into separate species. Once isolated from each other, random mutations alter appearance and the ability to create a viable offspring very quickly. If members of the two groups meet, they won’t be able to reproduce together.

30. More Allopatric Speciation The most common cause of allopatric speciation is geographical barriers: mountains, oceans, rivers. A few members of a species manage to cross by a rare chance event. This is the mechanism by which Darwin’s finches evolved into separate species in the Galapagos islands. Only very rarely can birds cross the ocean to get to other islands. Or, the barrier develops slowly as conditions change: the gradual formation of the Grand Canyon split a population into 2 isolated groups, that have diverged into separate species, the Kaibab and Albert squirrels.

31. Sympatric Speciation Geographical isolation is the easiest way for species to form, but there are other possible mechanisms. Sympatric speciation means speciation that occurs within the same geographical location. Disruptive selection can cause sympatric speciation. So can polyploidy An example: cichlid fish in Lake Barombi Mbo in Cameroon, Africa—an isolated volcanic lake. Nine species, all more closely related to each other (by DNA evidence) than to similar fish in other lakes. Lake has no distinct geographical zones, and the fish can easily swim anywhere in it. They feed in different locations, but all breed in the same location, close to the bottom. the speciation mechanism is not clear.

32. Sympatric Speciation by Polyploidy About half of all flowering plants are polyploid: more than 2 copies of each gene. Polyploids are the result of failure of cell division (mitosis or meiosis) to separate the chromosomes into 2 cells. Most common is a tetraploid: 4 sets of chromsomes. When a tetraploid crosses with a diploid, the result is a triploid (3 sets of chromosomes). Triploids are sterile: there is no way to evenly divide 3 sets of chromosomes into 2 cells during cell division. Seedless bananas, watermelons, and apples are triploids. Result is instantaneous speciation: the tetraploid can’t produce offspring with its diploid parent. Only tetraploid x tetraploid or diploid x diploid works.

33. Hybrid Zones When two populations of a species are separated by a geographical barrier, they diverge genetically. Sometimes the barrier is removed and the two groups come into contact with one another. The region of contact is a “hybrid zone”. Several possibilities exist: If the two groups have only diverged a bit, fertile offspring will result, and the two groups will merge back into a single species. Geographical differences may exist within the species: different subspecies or varieties, but all can interbreed freely. If the two groups have diverged to the point that no fertile or healthy offspring result from their matings, selection pressure occurs to deter further matings. They are now two different species.

34. Patterns of Speciation What happens after 2 species separate from each other? In some cases, the species exists for millions of years, gradually changing in response to external conditions but always maintaining as a single distinct species. horseshoe crabs today are almost identical to 450 million year old fossil horseshoe crabs In other cases, many new species will form from a single species in a very short time: this is “adaptive radiation”. This often happens on isolated islands, where a new species is blown in by a storm, and finds many different ecological niches to fill. Darwin’s finches are an example of this. They are thought to have originated with a small group of finches that blew over about 1 million years ago, to islands with no dangerous predators and very few other land birds.

35. Extinction Extinction can happen: none left of the species. Various events can cause extinction: being outcompeted for a critical resource, having the climate change too rapidly to adapt. “Mass extinctions” are caused by catastrophic events. The Earth has had several mass extinction events, where the vast majority of species die out over a short period of time. This is what is seen when one moves between various geological ages. Asteroids hitting the Earth are responsible for at least some of these, but probably not all. Disasters that lead to the extinction of some species often open up niches for other species to expand into: the extinction of the dinosaurs led to a major adaptive radiation of mammals.

36. Classification and Diversity • Be able to recognize a proper binomial species name. • Distinguish between taxonomic classification and phylogenetic classification. • Distinguish between and recognize monophyletic groups and polyphyletic groups. • List the three domains of life, which domains are prokaryotic, which domain contains plants and animals, and which domains contain microorganisms.

37. Uniform Naming Communication worldwide is facilitated by having a set of agreed-upon names. Lots of plants have several different common names, and the same common name is often given to several different (and very unrelated) plants. To solve this problem, each species is given a unique scientific name, or binomial name. Same name in all languages. System invented by Carolus Linnaeus (Carl Linne) in 1753. In 1867, an international botany congress in Paris met to standardize rules for naming plant species. Rules are constantly revised. Most recent was the 17th Congress, which met in Vienna Austria in 2005. Published in the International Code of Botanical Nomenclature All organisms are classified into a hierarchical arrangement, as in the figure. Dolphin fish (mahi-mahi) Dolphin mammal (porpoise)

38. Linnaeus Carolus Linnaeus (1707-1778) a.k.a. Carl Linne Swedish naturalist Latin was the scientific language of the day, and the name he published under was a latinized version of the name he used with family and friends. Published Species Plantorum in 1753 Plants were grouped into genera and given multi-word Latin names. Linnaeus shortened this to the binomial: genus followed by species. He also grouped them into larger groups (classes) based on sexual characteristics: the Sexual System For example: "Nine men in the same bride's chamber, with one woman“. This meant 9 stamens with 1 pistil in the same flower. (All in Latin, of course) although this system was invented for convenience, it fit evolutionary reality fairly well, and we still basically use it (with modifications and corrections) also had a system for animals (and one for minerals, long abandoned):

39. Binomial Name Details Form: a binomial name is 2 Latin words, which are the genus and the species of the organism First word (genus) is capitalized, second (species) is not capitalized both words are italicized (or underlined). Sometimes followed by the "authority", the first person to publish a description of the species. Authority is NOT italicized. It is often abbreviated: L. - Linnaeus For example: common name: Peppermint (in English) genus: Mentha species: piperita authority: Linnaeus Mentha piperita L. Cirsium arvense Scop is the Canada thistle; Scop stands for Giovanni Scopoli, who first described it. Special rules for smaller groups like cultivars, landraces, hybrids genus name is supposed to be unique throughout the entire world of life. Species name is often reused: for example, aquaticus = found near water, glabra means smooth or hairless, sinensis means from China

40. Recent Developments in Classification Phylogeny: how different organisms descended from a common ancestor Taxonomy: classification based on similar characteristics. It is now the goal of taxonomists to make taxonomy fit phylogeny. A phylogenetic classification is better at predicting how similar other characteristics are than one based solely on superficial traits (like presence or absence of wings). Linnaeus’s taxonomy was based on a hierarchy of groups: kingdom, phylum, class, order, family, genus, species. Organisms were grouped according to overall similarities. The phylogenetic approach is called cladistics. Its primary goal is to group organisms by "shared derived characteristics": characteristics that are shared within the group but not found in any closely related species.

41. Cladistics • In phylogeny, every evolutionary event is the splitting of one species into two species. Groups above the species level are for convenience only. • In recent times, the higher level groups of plants have been greatly rearranged, with many traditional families split or combined. The biggest case of this: the dicots are now put into two very different groups, the eudicots and the paleodicots. This split is based on a difference in the number of pores in the pollen grains, plus a great deal of DNA evidence.

42. Monophyletic Groups • The goal is to make all named groups monophyletic. This means that every group consists of all organisms that descended from a single common ancestor. • In contrast: many of Linnaeus’s groups were polyphyletic: mixing the descendants of two or more ancestors together. For example: “winged animals” is a polyphyletic group consisting of birds, bats, and insects. • Polyphyletic groups need to be split up. • Paraphyletic groups contain some, but not all descendants of a common ancestor. Reptiles are a good example: don’t contain the birds. • The use of paraphyletic groups is discouraged, but probably unavoidable.

43. DNA Evidence in Phylogeny • Much work with DNA sequences instead of physical characteristics. • The changes that occur in DNA are much simpler and easier to understand than changes in body characteristics. • Also, much of the DNA in an organism's genome has virtually no effect on the organism's phenotype. For this reason, it is not subject natural selection: it is selectively neutral. • Selectively neutral DNA mutates freely and randomly. Random events are easy to model with statistics, making it easier to determine the true relationships between species. • Also, DNA data is much easier to gather and less subject to bias on the part of the observer than physical data.

44. The Tree of Life We are quite convinced that all living things on Earth descended from a common ancestor. NOT the first living organism: lots of things became extinct and have no living descendants. All organisms have ribosomes (which are used to translate messenger RNA into proteins). By comparing ribosomal RNA sequences, it is possible to get develop a tree of how all organisms are related. The idea comes from Carl Woese Three main branches: eukaryotes, bacteria, and archaea. Bacteria and archaea are both prokaryotes (DNA not in a nucleus), but they are very different from each other in many details. Many archaea thrive in extreme conditions of heat and salinity. Eukaryotes divided into 4 main types: animals, plants, fungi, and protists. Fungi are more similar to animals than to plants Protists are the single-celled eukaryotes, plus the algae. A very polyphyletic group that someday will be better differentiated than it is today.

46. Older View • In this view, multicellular eukaryotes dominate, and most of what is in the modern view (previous slide) is relegated to the primordial slime at the bottom.