Evolution and Ecology: Artificial Selection, Evolutionary Theory, and Ecological Concepts , Study notes of Biology

Download Evolution and Ecology: Artificial Selection, Evolutionary Theory, and Ecological Concepts and more Study notes Biology in PDF only on Docsity! BSCI106, Spring 2010 Instructor: Dr. Gerald Borgia January 28 Intro - Darwin and Natural Selection, & Selfish Gene • Darwin used the scientific method • He made predictions about what he expected based on his hypothesis • He collected data to test the hypothesis • Then he considered whether the data confirmed or denied the hypothesis. • Darwin didn’t really do too many experiments, since he has to use comparative data. You really can manipulate them. In history. • Artificial Selection o Darwin was aware of the ability of animal and plan breeders to improve crops and create new varieties o Breeders selectively propagate varieties with characteristics they want o Under natural section nature takes over the role of the breeder “selecting” who will survive and reproduce. o From the wild:  Pigeons… there are many kinds with significant differences.  Darwin concluded that they may have come from the same species. o Artificial selection leading to variation under domestication o Darwin found that in a great variety of species under cultivation there had been great radiations in the number of breeds/varieties o Among these breeds there was as much variation as is commonly seen between species • Why was AS leading to variation under domestication important o Because it showd that during the short time humans have been practicing AS there had been rapid evolution, sufficient to caruse phenotypic differences as great as commonly seen betwn diff o Provided a model for explaining natural radiations as a result of natural selection there is initial variation, artificial selection…… • Biogeography o Study of distribution of plants and animals o Darwin’s Finches  Represent a unique set of species, none of which are found elsewhere in the world  Each has unique adaptions for life on these islands  BIG Question! Where were the finches before the new Galapagos islands were formed.  Darwin knew that there was a similar species on the west coast of South America about 500 miles away. He Hypothesized that a finch ancestor colonlized the Galapagos islands not long after they were formed then settled there.  2 major grouping of Finches • Tree Finches (insectivorers) HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Ground Finches (Granivores) • Evolve to the particular environment of the island. o Tortoises on different islands have different shaped shells.  Mound shaped on wet islands and saddleback shells on dry islands  Suggest that there has been separate evolution on diff islands caused by different environment  Similar patters occur w/ other species on other volcanic island chains. o Darwin saw a parallel between artificial selection leading to variation under domestication and the adaptive radiations • Principle of imperfection o Early opponents of evolution argued that the perfection of life supported the hypothesis of Divine creation o But many organisms have imperfect design more consistent with the evolution o Important point – it isn’t that NS can’t produce relatively perfect structure but that often structures are borrowed (coopted) for secondary functions and this compromise creates the “imperfection” o Vestigial organs – organs that are in a reduced state and have a diminished functional role relative to their ancestors o Male snakes (boa) have its hind legs (bones) o Fetal whales have teeth and hair (traits not seen in adults, but which are consistent with a bear-like land dwelling ancestor. o Wings of flightless birds are vestigial structures in that they are not used for flight but may still be used for balance. o Ernst Haekel – a 19th  You can see the history (the ancestry) century biologist – hypothesized that the evolutionary history of a lineage is recorded in its development o Haekle’s law of recapitulation:  “ontogeny recapitulates phylogeny”  Its not completely correct o Gill slits and tails in fetal position o Homology: Does homology provide evidence for evolution  It is consistent with evolution  It explains complex trait evolution because traits are borrowed from ancestors and modified  But we have homology in the creationist world?  Maybe a lazy creator who recycled his/her designs?  May not refute/deny creation hypothesis  This recycling of structure is certainly economical but does it always lead to the best designs?  It may be a violation of the principle of perfection. Maybe o Serial Homology:  Common in among complex organisms.  Re-using the same structure. HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Changes in subunits represent evolutionary change • Commonly studied molecules are DNA, RNA, Proteins • Changes in subunits defines different forms of these molecules and represents molecular evolution • DNA, RNA, Proteins are functionally linked and represent different levels at which molecular evolution can be studied • Protein Synthesis o DNA  mRNA  Amino acid + tRNA  Protein • Molecular info provides a novel set of traits not available to Darwin. This capability is important because o It provides independent test of phylogenies (trees of life) constructed from fossils and other evidence o Allows reconstruction of patterns of evolution where fossils are missing or rare o Provides, through molecular clock, a mechanism of timing when evolution changes occurred  Mutations – occurs at a relative constant rate o Allows independent tests of predictions of evolutionary hypotheses (i.e. that life has few origins, is old, how genes evolve, etc.) • Using biological molecules to reconstruct phylogenetic trees o Biological molecules can be used to infer phylogenetic relationships among organisms o For ancient spits and phylogenies of prokaryotes, molecular data are the only sources of info about phylogenetic relationships o Molecules that have evolved slowly are useful for determining ancient lineage splits. • Determining and Comparing the structure of macromolecules o Biological molecules can be compared by aligning their sequences o In the following example, amino acid sequences are compared for a gene common to 6 species o Similar comparisons can be made for DNA bases. • How does one make a (molecular) phylogeny? o Generate possible trees consistent with observed changes o Choose the one that requires the fewest changes (law of parsimony) • Molecular phylogenies match patterns we observe nonmolecular characters. • Molecular Clock o Rates of amino acid substitutions in some molecules are relatively constant over evolutionary time o By counting genetic substitution we can estimate times of divergence between species  The more closely related, recently evolved, and had less time  The less related, later evolution occurred, more changes, longer evolution time. HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o The number of amino acid substitutions is proportional to the time of divergence between two taxa (grouping of organisms – i.e. family, genus, species) o Calibrate the clock can occurred using events of known age o Molecular dates of separation for species (and other taxa) generally shows a good fit with fossils and geological evidence supports evolution • Molecular clock and studies of human evolution o If good fossil or other data isn’t available the clock can be used to time events such as human divergence o Common African ancestor about 120,000 years ago. • Does the fit btwn molecular & nonmolecular phylogeny only support evolution? o If DNA codes for the organisms phenotype then shouldn’t the amount of genetic difference correlate w/ phenotypic change under other hypotheses • Test using noncoding or synonymous changes o A good test is to look at DNA changes that do not affect the protein coding o Prediction:  Noncoding regions should show more change  Phylogenies from noncoding regions should also accurately predict phylogenetic relationships.  Phylogenies are using synonymous mutations are still accurate • Phylogenies from noncoding regions give a good fit w/ nonmolecular phylogenies • Conclusion: evolution is the only hypothesis that predicts accurate phylogenies using noncoding DNA • Evidence for evolution: The common genetic code among organisms suggest common ancestry o The genetic code is the same for all organisms suggests that there is a common origin for life o It is consistent w/ a common ancestor for living systems which is supports the evolution hypothesis • Evolutionary theory should help us understand where new genes come from o More recent complex taxa generally have more genes o Much of the molecular diversity we see is a result of the diversification of gene families – co-option of existing genes for new functions • Where do new genes come from? o Gene duplication creates multiple copies of the same gene sequence o One copy retains its original and still important function, the redundant sequence is free to change (mutate) • Common ancestory of genes is shown by their consistent function in very different organiam.a • Homeobox genes: conserved genes that function in regulating development, • Conclusions – consistent with the evolution hypothesis February 16 Origins of the Earth and selfish genes HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Two step model for the origin of life o The origin of prebiotic molecules  Miller-Urey Experiment o The origin of life from prebiotic molecules  RNA World Hypothesis  RNA World Hypothesis – the world started with a RNA-like molecule  Possible similarities (and differences) of viruses with likely first organisms  does this fit with the RNA world? • They do things in ways that help their own reproduction o Selfish gene theory and viruses as sets of selfish genes • The Origin of Life – the most difficult problem for evolution o There is no clear evidence of how this happened; there is no fossil record; no development history; “molecular history” vanished o We don’t have the opportunity to observe incipient life forms evolve in nature that might duplicate what happened at the origin of life. • Hypothesis about the origin of life o Came from meteorites – but it must have evolved elsewhere after the big bang, adds an extra step o We were created – but how was the creator created? o Evolved on earth – how did that happen? • How can we study a unique event that happened 3.8+ billion years ago? o Re-create conditions similar to those that were present at the time life was once was (experimentally) • Conditions for the origin of life o Earth at the time of life’s origin had a reducing atmosphere. o In this atmosphere molecules essential to living systems could form and accumulate  There was low amount of oxygen, (shown in ancient rocks) and slowly had a large amount in the atmosphere • Hypothesis o Before life appeared carbs, lipids, amino acids. And nucleuc acids molecules accumulated (Darwin suggested warm pools) • Miller-Urey Experiment o Electric sparks were to simulate the effects of lightning and heat mimicked the origins of life o Within hours, they were able to produce simple organic compounds • But prebiotic molecules don’t seem to be assembling today • Evidence of prebiotic molecules from outer space. o More than 90 amino acids, the vast majority of which do not occur naturally in life on Earth • Step 2: the first life o Several macromolecules (protein, DNA, RNA) have been proposed as the basis for the first living systems o How did life (self reproduction) evolve from prebiotic molecules • The protein world o Proteins cannot duplicate themselves – so they are not a likely to be the basis for a self replicating (living) system HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S ll Te xt bo ok s Chapter 26: Bacteria and Archie: the Prokaryotic Domains • The Selfish gene – Richard Dawkins o Genes in all organisms are like those in viruses – designed to maximize their own reproduction o Genes that are less efficient in reproducing lose out to those that are more efficient o This led Dawkins to argue that all organisms are byproducts of natural selection acting on genes to favor the best reproducers. o “We exist largely to reproduce our genes” o Net result of this process is that genes and the individuals that express them will be selected to show adaptive behaviors that enhance their genes’ reproduction! • The Prokaryotes: Bacteria and Archaea o Antibiotic resistance – real time evolution o Male Killer’s – strange bacterial strategies for reproduction o We and the prokaryotes had a common ancestor 3 billion years ago o 2 billion years ago, we separated from archaea • Prokaryotes are important o They are an old group, but it doesn’t mean they aren’t important o Most likely the most successful group on earth o Show greater diversity in metabolism than any other group o Constitute the first half of life’s history. o Bacteria have been found at a depth up to 4 miles into the earth o 10% of our human mass is bacteria with more bacterial cells than human cells  we have bacteria on our skin that helps protect us from diseases o Bacteria account for many human diseases • Prokaryote Biology o Most are cocci, bacilli, or spiral forms o Some link together to form association, but very few are truly multicellular o Prokaryotes reproduce asexually by fission, but also can exchange genetic information • Prokaryotes vs Eukaryotes Prokaryotes Eukaryotes No membrane-enclosed nucleus Membrane-enclosed nucleus Circular DNA Chromosome No (m-e) organelles Mitochondria, chloroplasts, glogi, endoplasmic reticulum 70s ribosomes (size) 80s ribosomes (size) Binary fission Mitosis, meiosis conjugation, transformation, transduction Meiosis Cell wall Cellulose membrane when present HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Binary Fission – asexual • Bacterial cell wall – all bacteria have different cell walls o Peptidoglycan o Plasma membrane o Cytoplasm o Capsule o Outer Membrane o Peptidoglycan o Plasma membrane o Cytoplasm • Bacteria o An important source of disease o Most are not pathogenic – beneficially crowd out pathogens o Important in ecnolgy  Decomposers/degraders  Nitrogen fixation – plants develop a symbiotic relation that benefits both.  Cellulose breakdown  Photosynthesis • Exchange of genetic information o Transduction o – DNA carried from one bacterium to another by a virus/plasmid – sex pili – enable plasmid transfer Transformation • Bacterial classification – DNA released from a broken cell is taken up by another cell. o Based on shape  Cocci  Rod-shaped  Helical • Bacteria Groupings o Firmicutes  diverse; some produce endospores, resting structures resistant to harsh conditions o Actinomycetes  grow as branching filaments and produce important antibiotics o Chlamydias  tiny parasites that live within the cells of other organism o Mycoplasmas  o Cyanobacteria  photosynthesize using the same pathways pplants use. Many fix nitrogen • Sources of energy o Autotrophs  Photoautotrophs – make own food through photosynthesis  Chemoautotrophs – use oxidation of chemicals instead of light as energy o Heterotrophs – must absorb organic molecules from other organisms. • Nitrogen Fixation – symbiosis with plants o Bacteria convert atmospheric N2 to ammonia – NH3 HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S ll Te xt bo ok s o Fixed nitrogen is a key ingredient for plant growth o Nitrogen fixing bacteria commonly live in special modules…… • Humans dependence on bacteria o We could not digest and absorb food properly without out guy “flora.” o Grazing animals, depend upon bacteria in their complex, quadripartite stomachs to digest grasses int eh process of rumination o Dispersion of oceanic oil spills; the production of cheeses, yougurt by fermentation; the bacterial production of vinegar from alcohol and of MSG from sugars o Bacteria (along with fungi) are the main reducers of dead organic matter allowing recycling of nutrients. • Human diseases caused by bacteria o Tetanus; gangrene’ gonorrhea; bubonic plague; strep throat; ulcers (we used to think they resulted from stress) • Human gut microbes and obesity o Two major groups of beneficial bacteria are prevalent in the human gut, the bacteroidetes and the Firmicutes. o Proportion of bacteroidetes in lower in obese people and non-obese people • Archaea o Methanogens – anaerobic chemosynthesizers who live in bogs and the guts of herbivores  CO2 + 4H  CH4 + H2O o Halophiles grow in salty water and in alkaline environments o Thermoacidophyles – oxidize sulfur in around volcanoes and hydrothermal vents; tiny genome o Sulfur reducers • Hydrothermal vents and associated organisms with energy derived from thermoacidophyles. • Bacterial antibiotic resistance – short term evolutionary change o Antibiotics were hailed as the magic bullet for medicine – patent bacterial killers o Not long after antibiotics were developed resistant bacteria began to evolve o The bacteria soon develops a resistance to the antibiotic, which makes it difficult for doctors to develop antibiotics (i.e. flu) o R plasmids carry antibiotic resistance traits between cells. o Pili form and allow the plasmid DNA to move from one to another (jumping genes) • Causes of antibiotic resistance o Inappropriate prescriptions – use for viral infection o Failure to use full prescription or take as directed  Once you take your first dose, it kills off the less resistance bacteria. But the more resistance is still alive. If you don’t use the full prescription, the more resistance bacteria would multiply HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks  Celsl with cooperation between host and “talented” invaders gain special benefits (e.g. more efficient aerobic metabolism, photosynthesis)  Invader had a place to live in an advanced cell. o Evidence for the endosymbiont hypothesis  Chloroplast and mitochondrial DNA is circular like the bacteria chromosome  Chloroplasts and mitochondria have 70s ribosomes similar to bacteria ribosomes  tRNA and rRNA genes of mitochondria and chloroplasts similar to bacteria • affects their ability to grow  Chloroplast genes similar to those of cyanobactereia  Many bacterial genes from invader have migrated to the nucleus of the host. • Genes that originally came from an organelle migrated to nucleus.  In dinoflagellates multiple invasions are common with a Russian doll pattern. • Archezoa – A “missing link” in the evolution of eukaryots o Archezoa – the most primitive eurkaryotes o No mitochondria, ER, or Golgi Apparatus o Have 3 species of endosymbiotic bacteria to ka eup for not having mitochondria • Evolution of Multicellurlarity – 1 o Involves initially colonies of related cells o Enables cell specialization (i.e. weapons, digestion, reproduction, etc) o Ulothrix  A multicellular chlorophyte with celluar division of labor  Specialized photosynthesis, reproductive and holdfast cells. • Evolution of Multicellularity – 2 • Formation of larger bodier with specialization of function to a new life style • Reproductive division of labor • With alternation of generations the haploid or diplosid (or both) parts of the life cycle may be emphasized • Slime molds o Are interesting life cycles o Dictyostelium life cycle  Spore germination  Feeding amoebas  Aggregation  Tip formation  Migrating slug  Fruiting body formation o Big slime mold issue – which cells form the stalk HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S ll Te xt bo ok s o February 25 • Today’s Lecture o Mendel’s experiments and Mendel’s laws of inheritance o Description of mitosis and meiosis and their functions o Relationship between meiosis and Mendel’s laws o Evolutionary importance of recombination. • Genetic Inheritance o It was known that both parents contribute traits of offspring o Before Mendel’s time it was believed that the units of inheritance blended and could never be separated. o Darwin knew blending inheritance didn’t work – phenotypic variation would rapidly disappear – but he presented no alternative • Gregor Mendel discovered basic laws of eukaryote genetics by following traits from crosses of peas o Cross-pollination  Remove male organs from one individual  Collect pollen from a different individual  Transfer pollen to the female organs of the individual whose male organs have been removed. • Mendel’s experiments and laws of inheritance o He produced very consistent results (ratio of traits) from his crosses o He started with pure bred lines dominant and recessive and phenotypes o In his crosses only dominant parental traits appeared in the first generation progeny (F1) w/ recessive seen only in the second generation of crosses (F2) o Terminology  Homozygous genotypes have 2 copies of the same allele (i.e. AA)  Heterozygous genotypes have two different alleles (Aa)  Dominance the same phenotype can result from different genotypes (i.e. AA & Aa) that have one copy of the dominant allele. o Mendel’s first law of segregation  During gamete formation each allele for a trait (at a particular locus) has an equal chance of appearing in offspring. o Mendel could determine if a plant with the dominant phenotype was homozygous or heterozygous by backcrossing with the recessive phenotype o If trying to find... S- x ss.  Homozygous : SS x ss  all dominant S  Heterozygous : Ss x ss  50% Ss and 50% ss o Mendel’s second law-independent assortment  From studies of the simultaneous inheritance of two characters, Mendel concluded that alleles of different genes can have multiple possibilities HTTP://NOTES.BOOKHOLDERS.COM Bo ok H ld r .c om Bu y a nd S el l T ex tb oo ks  Ex. YR x yr • YyRr: will be split up into YR, Yr, yR, yr x YR, Yr, yR, yr • Phenotype ratio – 9:3:3:1 o 9 – all dominant o 3 – only Y is dominant, not R o 3 – only R is dominant, not Y o 1 – all recessive  The two traits cross (dihybrid) produces a consistent phenotypic  Individuals expressing the dominant phenotype for both traits are most common, the double recessive is rare. • Mendel’s laws and meiosis o Thomas Hunt Morgan showed that genes are carried on chromosomes and linked genetics with meiosis • Mitosis and Meiosis o Mitosis – producing genetically exact copies o Meiosis – producing genetically different haploid descendent cells • Mitosis o Used for asexually replicating somatic cells in multicellular organisms o Exact copies allows close genetic relationship of somatic cells to reproductive (germ line) cells o Allows for multicellularity to work in that germ line cells can be effective reproductive proxies for somatic cells. o DNA replication occurs before cell division o During interphase, there are three sub-phases: S, G1, G2 o After mitosis, chromosomes initially appear double; two sister chromatids are held together at the centromere o Each sister chromatid consists of one double-stranded DNA molecule complexed with histone proteins (chromatin) o After separating, they are chromosomes o Prophase – chromosomes condense and move toward the middle of the cell o Metaphase – chromosomes move to the equatorial plate, then centromeres holding the chromatid pairs together separate.  Line up on metaphase plate o Anaphase – each daughter chromosome migrates to its pole along the spindle fiber/microtubule track o Telophase – the chromosomes become less condensed and the cell divides • Meiosis o Two successive divisions that reduce the chromosome number from diploid to haploid in two divisions o Each resulting haploid cell randomly receive one of the homologous paternal or maternal chromotids o Crossing over allows for mixing genes between homologous (parental) chromosomes o Crossing over  Occurs during prophase of meiosis 1 HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a d Se ll Te xt bo ok s • Stabilizing selection o In newborn infants – reduces the amount of variation in a trait. Pretty much the average is the better. The extremes are not good enough. • Directional selection o Cliff swallows causes population to move to a new mean • Disruptive selection o Increases the range of variation in a trait. The extremes do the best. o Favors the two extremes relative to intermediates o May create polymorphism (i.e. sexual reproduction)  Can be absolute or relative • Hard (threshold cut off) – fish larger that a 50 cm die because they are caught in gill nets o You can survive if you are at a certain level. Achieve a certain phenotype • Soft (relative) – the smallest 50% of fish in a population die from predators that eat the smallest fish – (grading on the curve) o Achieve phenotype that can be relative. Only small would be eaten  Kinds of traits • Mendelian traits – genes w/ large effects – a single gene causes a single effect – discrete changes (i.e. eye color, genetic disases…) • Polygenic (quantitative) traits – multiple genes with small effects – causes continuous variation (i.e. height, running speed…)  Multiple Effects of NS • Directional/disruptive selection – adaptation • The selection sieve (purifying/stabilizing selection) – removes deleterious mutations – is critical in maintaining adaptation. • Can reduce (i.e. thought purifying selection) or increase (by favoring heterozygote’s or variables directional selection) genetic variation • Hard (threshold) and soft (relative)  Stabilizing selection is critical for maintaining adaptions • Biologists thought that when organisms/traits stayed the same over evolutionary time that there was no selection • Its now recognized that stabilizing selection is necessary to maintain adaptations by removing deleterious mutations  Stabilizing selection is critical for creasing mutations from chromosomes. HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks  Stabilizing selection and sex are critical for the removal of deleterious mutations • Deleterious mutations can accumulate on chromosomes unless there is a removal mechanism • Crossing over (part of sex) can produce mutation free chromosomes • Selection can then favors individuals with mutation free chromosomes increasing their frequency.  Frequency dependent selection • When alleles get rare, they becomes favored • Selection may favor (or oppose) traits based on their frequency o o Equal sex – related investment in males and females.  People with more heterozygous MHC loci live longer since infection with HIV • The MHC (major histocompatability) locus codes for cell surface proteins involved in immune response to viruses and bacteria. Its harder for pathogens to copy heterozygotes o Mutation  Change in the genetic material  Creates new variants that are critical for directional evolution  Can change gene frequencies (mutation pressure – weak)  Cumulative effects can destroy adaptations  Kinds of mutation • Point o Change in dna base… usually it doesn’t really • Frame shift • Gene duplication o Important, where genes are duplicated. • Chromosomal o Deletions – genetic material lost o Duplication – part of chromosome replicated twice.. hence have extra geness o Inversion – certain part of the gene is changed in sequence. (a-b-c  c-b-a) o Translocation – Some material of one chromosome would move to another chromosome.  Occurrences: 10^-4 in bacteria and 10^-9 in vertebrates (in humans about 1/genome/gen.) • Mostly random but hotspots exist • Most harmful (1/100 – 1/1000 beneficial)(i.e. factors that affect the stability of DNA – gamma radiation or formaldehyde) • Can be induced by factors the environment HTTP://NOTES.BOOKHOLDERS.COM B ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Repair mechanisms exist but not always effective (thyamie dymer) • Can occur in germ line or somatic cells (cancer)  Mutation paradox • Because individuals are typically harmed by mutations selection should favor lower mutation rates in individuals (repair mechanisms) • Theoretically, species with too low mutation rates have too few new beneficial mutations and ently may go extinct because they cannot adapt to change • Fortunately because it may be too costly to reduce… o Migration/gene flow  Migration of individuals/genes among populations  Immigrants may bring in new beneficial genetic variants. (i.e. warfram (poison) resistance in rats. They soon became warfram resistant and spread through out Europe.  Migration form large populations may swamp genes in small populations and can lower adaptations in the small population o Drift  The sampling error that occurs in time or space b/c of small sample size  In stats, the law of large numbers says that small samples represent the whole population less well than large samples  Thus, when small samples are used to start a new population (or generation), we expect that gene frequencies will tend to differ from the original population by chance.  Founder effects: • New populations established by a few founding individuals may, by chance, have gene frequencies that differ from those in the parent population  Population bottleneck March 4 • Making evolutionary predictions : convergence • Levels of selection: individual/population/species/intragenomic conflicts o What is it selecting for? • Evolution is a predictive model by showing that adaptation can be precise (examples of convergence & mimicry) • Limits on prediction – constraints o Genetic constraints on genetic variation not available top make new traits o Past adaptation affecting future evolution o Constraints should be more important with big changes (with little time) and less for small changes o There are lots of examples of convergence – it shows that natural selection is often not limited by constraints  Euphorbia and cactus HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld rs .c om Bu y a nd S el l T ex tb oo ks  Transduction  Transformation • Paradox of sex o In meiosis, in females, ½ of the genetic material is kicked out of her high investment egg and the egg is designed to accept the input of genes from an unrelated male o This seems to violate “selfish gene” rules o Suggest that sex is important for females to pay this cost! o Producing cells with ½ of genes missing. • Sex has immediate and long term benefits o Recent explanations for its origins emphasize immediate (individual) benefits o This is b/c highly designed mechanisms like meiosis are only likely to evolve at the individual level o However, long term benefits can lead up to extinctions • Short term benefits o Better disease resistance o The ability to produce extremely high quality offspring o Generating mutation free chromosomes • Sex as part of parasite resistance o Parasites and diseases often have faster generation time and higher fecundity than hosts o Red Queen Hypothesis – emphasizes producing a few good offspring  Sex allows individuals/species to keep up with continuously changing conditions. • Benefits of sex o Gains from producing exceptional offspring in high fecundity populations o Sex produces a higher variation in fitness • Populations with more parasites are sexual • Through crossing over mutation free chromosomes can be produced • But there are asexual species o Often live in “disturbed” habitats o They are often: polyploidy or hybrid. o Asexual lineages are short lived. • Hybridogenic fish o Coordinate with another species, get their sperm, and develop a diploid cell. • Reduction in the 2 for 1 cost of sex – not all sexual species pay the fill cost of sex o Facultative sexuality  Occasionally sexual  Common in aphids and other insects  There are multiple generations per year and then, before the winter males and sexual females are produced that mate and prodive offspring sexually.  Sexually usually have wings o Egg trading in simultaneous hermaphrodities HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er .c om Bu y a n S el l T ex tb oo ks  Being male pays off. Both male and female at the same time. Trading places. Little investment in one, more in the other.  Reciprocity can reduce the investment in males and ultimately the cost of sex  They find partners and take turns playing male and female roles o Female biased sex ration  Investment is shifted from males to females where sons mate with daughters  Brother-sister mating are common females often produce strongly female biased sex ratios. o Male parental care  Males help females rear more young and potentially double the number of offspring that can be reared – so their cost is repaid.  If parental care is limiting, so if males give care then the number of offspring a pair can have goes up and perhaps doubles • Sex organisms design and intragenomic conflict o In Wollbachia and organelles genes have been transferred from the invader genome to the host nucleus o Two reasons fro this are:  These genes can be reproduced sexually (can gain benefits for sex, i.e. remove harmful mutations)  B/c they are transferred by both sexes when in the host genome male killing tendencies are eliminated. • Conclusions o Asexuals can suffer in several ways:  Less able to produce extremely high quality offspring  May not be able to keep up with disease changes – fitness lowers over time  Cannot do mutation repair  The 2 for 1 disadvantage to sex may be lessened by inbreeding associated with sex ratio adjustment March 11 • Inclusive Fitness and Reciprocity o Cooperation evolves under limited sets of conditions o Kin selection (inclusive fitness) – helping relatives – extreme case; eusociality  Shouldn’t help other animals, but only their kin  Pretty much accepted. o Reciprocity – cooperating with others in ones own species  Controversial issue o Mutualisms – win-win situations between species  later lecture • Darwin saw the evolution of eusociolality as a special problem critical to his evolution hypothesis but one that he couldn’t answer • Hamilton suggested that in addition to person (direct) reproduction individuals could reproduce indirectly by helping relatives (kin) HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Hamilton’s 2 paths to reproductive success o Direct (personal) reproduction o Indirect (nepotistic) reproduction o Both transmit genes like yours each of these options may be used, but it depends on conditions • Why does kin selection work o Identity by descent – how many genes of one is that one’s relative. Seeing how related they are. Provides a measure of the probability that a mutant that occurred in recent ancestor is shared in two related individuals • Hamilton’s inclusive fitness model o Equation: Br/Cd o B > 1/r r = benefit to the recipient, Cd o The r value gets smaller by that distance of relatives (parents = ½; grandparents, grandchildren = ¼, cousins = 1/8. = cost to the donor, r = coefficient of relatedness between recipient and donor through identity by descent o A historical refinement of thinking about altruistic behavior  Group/species selection – cause individuals to at their own expense for the benefit of their group.  Individual selection – causes individuals act only to enhance their own personal (direct) reproduction ‐ incomplete  Kin selection (inclusive fitness, nepotism) – causes individuals act so as to maximize benefits from direct and indirect reproduction – correct and complete  Some key points on kin selection (quote “explains helping relatives and the evolution of eusociality (individuals trade direct for indirect reproduction)  probably derived from parental care ‐ borrows many of the same behaviors and retargets them  Organisms do not have to “do fractions” to do KS – genes can evolve to set the right switch point.  There is no conflict in the genome because under kin selection rules all genes in the individual gain equally from this decision rule.” • Kin selection does not happen b/c individuals share a certain fraction of genes • Eusciality o Sterile workers and reproductive divisions of labor. o Individuals evolve sterility and specialize in helping a (related) queen reproduce) o Relatedness can vary in different species and this affects the degree of specialization and worker sterility o Honeybees  Signal quality, direction and distance of food sources with a complex waggle dance- such detailed information sharing is rare in animals o Termites HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o Small eggs so as to maximize number of possible offspring when there are few egg/newborn predators o Large eggs when predators of small individuals are present so that young grow quickly out of the size range used by predators. • Live bearing vs. egg laying o Almost all lizard lay eggs o In most Sceloporus lizard species females lay eggs in nests. But in high altitude sceloporus jarrovii females retain eggs and move out into sunny areas to bask with eggs inside. This parental care speeds up development in cold but sunny habitats. o Lower altitude, eggs ; higher altitude, live birth • Paedomorphic salamanders o Most salamanders have a larval stage in the pond and then metamorphose and live on land as adults o Some salamanders remain larval in general appearance and stay in the pond even though they are reproductively mature  Stay in the water and never leave • Semelparous vs. Iteroparous o Iteroparous – a little reproduction at a time – females lay multiple clutches of eggs o Semelparous – indiv does all its reproduction at once. So-called “big band” reproduction  Extreme semelparity – big bang is associated with high cost of initiating reproduction  Agave (the tequila plant) live for 14+ years without reproduction and then sends out a huge reproductive spike. After which it dies  Insect pollinators need a big reward to cross open desert to pollinate the Agave  Salmon • Born in the headwaters of streams and take about one year to reach the ocean • They grown in the ocean for 4-7 years and then return to the headwaters of streams to spawn • They head out to the same area which they were born to • West coast salmon endure many risks and use much energy to reach the headwaters of streams. • r vs K selection – characterizes extremes in life history o some conditions favor explosive reproduction and short life (r-selection) and others that favor slow reproduction and long life (K- selection) o r-selected species have traits that allow them to do well in habitats that turn over rapidly and are initially empty (river flood plane) o K-selected species have traits that allows them to do well in habitats that are filled (rain forest) o Under r-selection fast reproduction results in a short life b/c of a trade off between life length and reproductive rate. o Predicted traits HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks r-selection K-selection Use ephemeral habitats Use permanent habitats Many small eggs Few large eggs Early first reproduction Delayed reproduction Rapid growth Slow growth No parental care Parental care Short lived Long lived Few predator defense Well-developed defenses • Diapause – Cessation of normal growth – overwintering o Allows organisms to pass through severe conditions – drought, winter, etc o Spores – fungi o Insect pupae, egg stages o Plant seeds o Red kangaroo embryonic diapause – occurs in drought. • Hibernation – depressed metabolic rate and a prolonged “sleeping” phase o Ground squirrels – true hibernators o Black bears – shallow hibernators o Hummingbirds – torpor (turn down body temp for the night) • Senesence o Alternatives models that have been use to explain deterioration associated with aging o Aging occurs in all species with somatic tissue o Shouldn’t be considered just wearing out o There are age-related effects that result from design. In humans: only two sets of teeth, fixed number of eggs in females, menopause, gray hair  Menopause – argue that this is the time where females go from making babies to taking care of babies  We could have more sets of teeth but costs involved prohibit it. o In insects: adult mayflies and male fig wasps are born with no mouth! • Hypotheses to explain why we might be built to have a limited life span o Mutation Accumulation hypothesis – o Antogonistic pleiotrophy hypothesis – traits have multiple effects (pleiotropy) over an individual’s lifetime.  These can be antagonistic with some beneficial and others harmful  Traits with good effects early in life (while most individuals are still alive) have a greater benefits than similar traits late in life • Prediction: There is a trade off between early and late reproduction o Good traits early, bad traits late o Evidence  Drosophila for early age of first reproduction and found that life length decreased • Phenotypic Plasticity o The same genotype can make multiple phenotypes that allow it to respond to current conditions  Trees (willow) exposed to predators make more leaf toxins HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks  Immune system – exposure to a disease agent increases the production of antibodies. • Migratory Locusts: o Two distinct morphs determined by crowding Solitary Gregarious Low density High density Green Brown Small Wings Long Wings Not aggressive Aggressive Does not migrate Migrates in large swarms. o **Gregarious are the ones that is talked about in the Bible** • Daphnia react to its predator Chaoborus by growing spines o Daphnia can sense Chaoborus chemical cues are react by growing spines and other characteristics that make them more difficult to eat by predators. • Protandrous Hermaphrodites – • Protandry – start with male then to female • Protogy – start with female then to male March 30 • Sexual Selection o Darwin’s book “Sexual selection and the descent of man” was published in 1871. o This book outlined the basic issues of sexual selection – female choice and male-male competition o His work is still highly relevant today. • Darwin’s theory of sexual selection has two main elements o Male-male competition  Male directly compete with each other for access to female o Female Choice  Female choose • In sexual selection based on female choice the female becomes selective agent: She takes the place of the breeder in artificial selection • Darwin noted that males and females differ in secondary traits (sexual dimorphisms) that are usually more developed in males o Where differences exist males have  Brighter feathers or plumage  Larger weapons (i.e. antlers)  A greater tendency to vocalize  Larger muscle  Greater aggressive tendencies  Higher intensity in seeking matings o In ungulates (deer) sexual dimorphism is related to harem size  also true in pinnipeds (seals) o Male birds use plumage & behavior to impress females and rivals o Male bowerbirds build and decorate display structures the females are attracted to. HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o Males are larger than female – share wives with kin  i.e. acorn woodpeckers o the brothers share females… males fight as a group to hold a territory. o Technically one female is with multiple males. o Jacanas – true sex role reversal – female holds territory in swamps that is occupied by multiple smaller males who tend the young. o Mature females larger than males (i.e. spiders) April 1 • Sexual Conflict -- Males and females often have different interests and this shows up interactions across species o Extra pair copulations o Sperm competition and associated adaptations (Female mate with more than one male in a certain time) o Sexual antagonism (conflict between male and female) o Conflict over parental care – who gives care (usually the female) o Parent-offspring conflict • Stealing Parental Care – American coots are subjects to intraspecfic brood parasitism o Parasitism is costly in that enlarged clutches have higher starvation o Female use multiple mechanisms to reduce the effects of parasitism. o Female nests with other females, and try to steal their offspring  Burying of parasite eggs  Moving eggs to the outside where they are incubated less  Adjusting egg counts to include only their own eggs o Birds have evolved color and spots on eggs so they could tell which one is their eggs • Sperm precedence can affect the nature of sexual competition o Yellow dung fly – sperm precedence – last male to mate fertilizes 80% of eggs o Males mate guard females to protect their sperm o Males fight for access to females o It pretty much the male fights for his sperm to fertilize eggs o The last male who mates, usually has the eggs fertilized • Sperm Competition o Black winged damsel fly – male pumps out sperm from previous male o Honeybees – male leave genitals in female to pump in sperm o Biting midge – male is eaten with genitalia functioning as sperm plug o Sharks – males spray seawater into the female to clean out other male sperms • Sexually antagonistic o Male adaptations triggered by experimental arrest of female evolution. o When female D. melanogaster are experimentally prevented from coevolving with males, males rapidly adapt to the static female phenotype HTTP://NOTES.BOOKHOLDERS.COM Bo kH ol de rs .c om Bu y a nd S el l T ex tb oo ks o After 41 generations apart, mate males from population with intense male- male sperm competition and females from pop without selection on males o There was a reduction in female survivorship associated with an increased rate of remating and increased toxicity of seminal fluid. • Kinds of parental care o Uniparental  Only female gives care  Only male gives care o Biparental – both parents give care (often active feeding of altricial offspring) • What affects the male tendency to give parental care o Males have multiple reproductive options  Stay and give care  Leave and try to gain matings with…. • Why should male stay and give care? o Need two parents to rear young (penguins) o Sometimes males can give care and attract females – males attract females to nests (stickleback fish) o New territories needed to attract females are hard to set up so there is a bigger payoff from staying • Male confidence of paternity should affect their tendency to give parental care: o Male confidence of paternity is higher  If delay between fertilization and production of young is less  In species with external rather than internal fertilization should more often have male parental care • Female care giving in fish and amphibians is more common with internal fertilization • Why males may give more parental care in fish and amphibians o In fish and amphibians care by males may not be particularly expensive, unlike the intensive feeding in atrilcial off spring. • Male fish often form aggregations of nests where they attract females. • Sometimes male nests have become display structures as in cichlid “bowers” • Brush turkeys: a bird in which males exclusively give parental care o Males build a mound o Then fermenting leaves generate heath o Females are attracted to the mound and after mating with the male lay… • The genetics of parental care – vole species differ in their tendency for males to give parental care • Parent-offspring conflict o Parents and offspring may conflict over how much care should be given o A parent should distribute care equally among its offspring (a parent should distribute care equally among its offspring b/c it is equally related to them o An offspring is related to itself by 1 and its sibs by at best ½, so it should want more for itself. o More interested in itself HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o Offspring attempts at control:  Weaning conflict – common in mammals – parents quit giving milk but its young is persistent in demanding more  Birds loud begging  Temper tantrums – offspring “embarrasses” parent into giving in to demands  Regression – acting more helpless that the offspring really is o Conflict arises because of parents have a greater interest in all offspring whereas a single offspring does not o The parent usually have the upper hand b/c if its larger size and greater development o Parental manipulation o In social insects (wasps) – parents makes one offspring larger so it can dominate and force others into becoming workers o Birds – parent can choose to incubate as eggs are laid or wait until they are all laid. The former increases differences and occurs under unpredictable conditions. o Infanticide  In humans parents will often kill babies – one twin when it can’t feed two  Girl babies – when a son (first son) is important to have  In animals (lions, langurs) males who takes over kill previous male’s offspring  Bruce effect – female rodents abort pregnancy when exposed to new male. o Offspring in birds nests compete for food  Siblicide: • When food is scarce older, larger chicks kill their siblings • In honey bees first emerged queens kill their younger sisters still in cells • Hyenas – daughters of dominant female kill their twin sisters • Outbreeding sex ratio o Parents gain most by investing in the sex short supply in an open system o Since each sex contributes equally (1/2 per offspring) to the nest generation so overall aggregate reproduction by each sex must be equal o Those that invest in the overrepresented sex have a lower probability of reproduction through that sex o This sets up a frequency dependent balance that favors a 50/50 sex related investment ratio. • Conflict over sex ratio o In hymenoptera queens are equally related to daughters and sons (by ½) but workers are more related to sisters (up to ¾) than brothers (1/4) o Therefore sisters favor sisters over brothers April 6 HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T xt bo ok s o Patrilocal societies primarily have local warfare o Matrilocal societies – long distance warfare specialists causing husbands to be absent over long periods. Females prefer to stay with their maternal rather than their husband’s relatives • In matrilocal groups there is lower confidence of paternity o Males and their relatives are less able to “mate guard” females – males are gone and females can seek alternative mates • Sexual behavior in preindustrial societies o The Bateman effect explains human behaviors  Polygyny is most common and males are larger, more aggressive sexually – some males accumulate wealth (resource based system) are able to pay bride price for multiple females  Matrilocal systems may be more like leks where ostentatious displays ostentatious displays (counting coup) are valued  Polyandry is very rare – males are poor and invite their brothers to stay and help – share a wife. • Dowry in human societies o Dowry – wealth paid by the female (and family) as a price for marriage – that balances the male’s inheritance o Common in medieval Europe, China, India – where b/c of intensive agriculture and population growth land is scarce relative to females o The excess of females relative to positions as wives causes females to compete for the opportunity to be married – they use wealth (dowry) as an attractant o Males who inherit land can bargain for a large dowry commensurate with the quality of land they hold o Sons and daughters with no inheritance or dowry have limited opportunity to marry and have careers as soldiers, priests/monks/nuns, servants, etc • The development of nation states reduces dependence on the family o Laws enable highly organized exchange systems (reciprocity), protect individual rights, and increased wealth increase the opportunity… • Hypothesis: with social change it may take time for social adaptation to develop o we need to learn many adaptive behaviors by watching other successful individuals • Demographic transition o Occurs before invention of birth pills o Why does fertility decrease in relation to wealth?  People are becoming more wealthier, thus People having less babies… becoming expensive to have  Educate women, they tend to have less babies April 8 • Darwinian Medicine o Applying principles of evolutionary biology to understand medical practice. HTTP://NOTES.BOOKHOLDERS.COM Bo kH ol de s.c om Bu y a nd S el l T ex tb oo ks o Modern Medicine is mechanism oriented but often fails to consider how evolution has shaped…… • Nesse and Williams 1994 o Organisms have evolved natural defenses that we need to respect o Its not always obvious which symptoms associated with infection are caused by the disease o Not usually considered – some “symptoms” may be caused by the body as part of its host defense. • Should we always suppress the symptoms of disease o i.e. Does the Diarrhea serve the host or the pathogen?  Diarrhea helps host: Shigella Bacteria (pathogen emulation)  Diarrhea helps pathogen: Cholera bacteria (dispersal) o Are drugs always helpful?  Drugs that treat the symptom, e.g. Lomotil that decreases guy contractions and reduces purging, prolongs disease in the case of Shigella • Can evolutionary thinking inform medical practices? – Fever o Two alternative hypotheses  Fever is an adaptation by the pathogen  Fever is an adaptation by the host o Fever as a disease defense: desert iguana  Lizards are ectotherms that behaviorally regulate body temperature  Control vs. Dead bacteria – latter caused the lizard to raise their temperature • With live lizards, lizards prevented from developing fever, died. o “Fever” and disease  Lizards injected with dead bacteria showed a preference for higher temperature.  Injected lizards held at high temperatures survive longer o Anti-fever medicines interfere with the immune response to the rhinovirus (common cold) • Anemia and disease (Malaria) o Many children wit malaria have anemia o It is common practices for doctors to treat the anemia by prescribing iron o But the body uses anemia to fight the malaria o So by treating the anemia doctors may actually helping the malaria parasite. • Effects of novel behaviors in modern society: increased breast cancer o In modern industrial societies breast cancer is common, buy in hunter- gatherers societies it is 12 times less common. o Why? o In preindustrial societies most women are pregnant or breast feeding o Breast feeding lasts for 3.-5 years, and causes females spend only a small part of their adult life in the menstrual cycle (about 29% of the time of females industrial societies) HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd Se ll Te xt bo ok s • Darwinian medicine – HRT o As we age the levels of many key hormones decrease o Hormone replacement therapy (HPT) was developed to reduce the effects of aging in the post menopausal women o This hormone therapy was suggested to reduce the risk or delay the onset of cardiovascular disease, bone loss and Alzheimer disease. o HRT thereapy is based on the hypothesis that older bodies just can’t make sufficient hormone o The alternative evolution……. o In 2002 – the Women’s Health Initiative (WHI) reports that combined estrogen/progestin HRT increased the risk of coronary disease, breast cancer stroke and blood clots in postmenopausal women, compared with placebo o HRT treatment reduced hot flashes, risk of fracture and colon cancer o WHI recommendation: avoid HRT and use less risky treatments to reduce fractures and hot flashes. o Consider the possibility of the body developing hormones. You have to take into consider the effects of having extras. Think about changing natural levels • Morning Sickness – is it adaptive o In the first trimester of pregnancy some women experience morning sickness o During this period the developing fetus is especially sensitive to environmental chemicals that can cause birth defects o Hypothesis: Morning sickness causes mothers to avoid strong tasting foods • The evolution of virulence: what is the best strategy for a pathogen? o General rule: virulence = reproductive rate o Host-pathogen: if the parasite is too virulent it can handicap its own spread (reproduction by killing the host before its gets transmitted to a new host o Pathogens from single infections should evolve a low growth rate (virulence) to maximize their transmission. • Disease evolves its virulence o Pathogen-pathogen competition: o Prediction: evolution of virulence is related to the ease of transmission between hosts • Can trade-offs explain patterns of virulence in human pathogens? o Paul Ewald – transmission hypothesis:  Transmission by direct contact (cold, flu): selects for low virulence (to allow hosts to move around and transmit the disease)  Transmission by indirect contact (mosquito carrying malaria): can select for high virulence, because the host need not be mobile, the mosquito can bit someone immobilized in a coma. • Trade offs: virulence and reproductive rates in a pathogen o Analysis of E. coli (host) infected by phage f1 (Pathogen) o Two modes of pathogen transmission HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o Only one combination • Postzygotic barriers o Under geographic speciation psotxygotic barriers evolve first as a side effect of genetic differentialtion in separated populations o Failure of hybrids to reproduce  Hybrid infertility  Low hybrid offspring viability  Failure of zygote to develop • Hybrid zones o If intrinsic barriers to gene flow fail to develop then there may be long term hybrid zones o There are  Static zones  Dynamic • Evolutionary Radiations o Radiations and high speciation rates often occur when species invade islands and this geographic separation…. o Commonly on islands o Hawaii has had dramatic radiations of Drosophila, snails, crickets • Sympatric speciation o Polyploidization o Allochronic speciation o Microaallopatric  Host shift  Driving xhromosome o Parthenogenesis o Creates hybrid offspring, less viable. • Polyploidization – o Chromosomes sets leads to speciation o Polyploid organisms typically cannot interbreed with the parent species. . o A form of sympatric speciation o Meiotic errors may cause unreduced gametes o More common in plants because they can self-fertilize • Polyploid vertebrates are often asexual hybrid • Asexuality assists in getting through meiosis • Many crop plants are polyploids o Polyploidization increases genome size directly and increases repetitive DNA (transposable elements) o Includes: potato, coffee, banana, peanut, tobacco, wheat, oats, sugarcane, plum, loganberry, strawberry, clover, rey, turnip, dill, spinach, apples, radish, grapes, zinnias, sugar beets, petunia, tea, watermelons. o They are often more drought resistant, grow better with fewer nutrients, have less branching, have larger size etc. • Allochronic (Time shift) Speciation HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om B y a nd S el l T ex tb oo ks o Rhagoletes flies have breeding seasons that match available hosts. Where applies are present they can breed from June to October, but if they are not, then separate species can develop on cherry and hawthorne. • Host shift Speciation o Occurs when individuals start using a new host. o It they are hightly faithful to their host, there may be effective isolation o Could also be considered geographic…………….. • Sympatric speciation in three-spined stickleback. o Two different species of three-spined stickebacks in each of five different lakes o A large bottom dwelling species with a large mouth that feeds on large prey o A smaller open water species – with a smaller mouth – that feeds on the small plankton. • Speciation by sexual selection o Sexual selection leading to sexual antagonism o As males evolve to manipulate females counter local male traits – this males females from different populations less fit with strange males o Differences in female mating preferences can cause speciation o This can occur in sympatry or allopathy April 15 • Population Growth o Two models:  Exponential growth  Logistic growth o Age structure in populations o Density dependence o Change in population size over time  Births (B) – Deaths (D)  Delta N / Delta t = B-D • Exponential population Growth o Unlimited growth o Is only appropriate for describing the initial phases of population growth in empty habitats • Logistic Population Growth o Assumes an upper limit to population size that is dictated by the carrying capacity (K) o All populations have an upper limit to growth and because this is taken into account in the logistic equation is a more reasonable model. o Math model: dN/dt = rN(1-N/K) o When N is small, (1-N/K)  1, so growth is like the exponential (rN) o But as N approaches K, the term (1-N/K)  0. This makes the rate of growth go to 0. o Population w/ different carrying capacity and the same growth rate all approach different equilibrium population growth. HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Age Structure o Population growth models treat all individuals as the same in their effect on population growth, but this is unrealistic • Survivorship curves o In type I, species most death occur in old age, relatively more deaths occur among young in type III species o All else being equal, type I species should reproduce at a height rate because a greater proportion of individuals reach reproductive age. • Age Structure – with lots of individuals in reproductive age classes populations have high growth rates o Age distributions may not be stable. o Sometimes historical events cause birth rates to change over time o Baby boomers and their children represent population bulges • In natural populations per capita birth rates are often density dependent – usually higher at low density. • Per capita death rates are also often density dependent – higher at high density. • Population numbers may stabilize at an equilibrium between birth and death rates • In some species there is a cycle with the population fluctuating in relation to the number of predators present. • Human population Growth o Thomas Malthus: in 1798 published An Essay on the Principle of Population  The human grows geometrically, while the resources available to support it tends to grow arithmetically  Unchecked populations will outgrow their food supply o Recently Human population growth has been relatively unchecked and has grown greatly o Population growth – some current figures o Current world population = close to 7 billion people  About 93 billion net gain in people per year  Net gain in people during lecture = 9000  Net gain in people per second = 3 o The number of people added in the 1990’s exceed the total number of people in 1600 o U.S. population – about 300 million  one birth every 8 seconds  one death every 12 seconds  one international migrant 26 seconds  net gain of one person every 11 seconds o Doubling Time  Historically, about 1500 years (starting @ 1600) • 0.5  2 billion: 200 years • 1  2 billion: 80 years • 2  4 billion: 45 years • 4 8 billion: 47 years. o Reduced death rate – Major technical/scientific advances HTTP://NOTES.BOOKHOLDERS.COM Bo kH ol de rs .c om Bu y a nd S el l T ex tb oo ks  Allowed for the control of Opuntia o Currently there is much work on using biological control agents (predators) to control plants pests o Common agents:  Ladybug beetles to control aphids  Wasps to capture and lay eggs in butterfly and moth larvae. o Introduction of cattle and sheep (and dung) in Australia has caused a terrible fly problem  Dung beetles that bury dung for their larvae where the flies can’t use it were introduced as a control.  But cane toads sat near the dung and ate the beetles as they landed  Some success was found when beetles were introduced that burrowed out of the toads stomach and killed them • Stability of predator and prey populations – does one drive the other to extinction or are they able to coexist? o Huffaker’s mites  Six-spotted mite ate organs and Typhlodromus occidentalis ate the herbivore  When mites had no predators on a single orange they went to K, with some variation and persisted  When predators were introduced the mites went extinct. • Long-term persistence of predator-prey interactions are promoted by: o Refuges for prey at low prey density o Predator inefficiency o Density-dependent limitation by other factors o Alternative food for the predator o Some prey that are easier to catch (young, sick, and old) while healthy individuals are predator resistant. • Populations of predators and prey cycle o Examples: voles, grouse, snowshoe hare, lynx o In some species there is a cycle with the population fluctuating in relation to the numbers of predators present • Predator population tracks prey population with a time delay • Different possible relationships between predator and prey – not always stable o Population stabilizes o Unstable – population outbreak and possible extinction o Stable oscillation • Prey response to predators – anti-predator adaptations o Escape detection: camouflage  can help some predators capture prey o Static defense: weapons, shells, spines, warning coloration and unpalatability, large body size.  Chemical defenses – often sequestered compounds from prey species cantharidin in blister beetles; • Formic acid in ants – made by the ants alkaloids, terpenoids, phenolics, and others • Cocoa  cocane HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Tobacco  nicotine • Coffee  caffeine • Chincona  quinine • Monarch – milkweed o milkweed has poisonous o Deception: aggressive and Batsian mimicry o Flight: running/flight, startles. o Acacia plants from mutualisms with ants to provide protection from predators and competing plants o Daphnia develop spined morphs o Cicada swarms – emerge at 13 or 17 year intervals in large numbers to swamp bird predators o 17 year species wait 4 years after the second instar apparently to synchronize o Anti predator behaviors  Alarm calls – wan relatives – ground squirrels, babblers  Studding – signs of health – deer  I see you calls – don’t chase me because I see you and you can’t sneak up on me • Herbivore and plant populations o Proportions of plant production consumed by herbivores depends on digestibility of vegetation o Consume about 10% of forest vegetation o Consume 30-60% above-ground vegetation in grasslands o Consume most of algal production in littoral zone o Occasional outbreaks of forest insects can defoliate vegetation o Mast crops – oak trees have big years and this allows some seeds to escape predators o Fruit adjust toxins according to what they want animals to do – at first poisons, then later when ripe bright color and sugar, no toxins. April 22 Symbiosis & Mutualism • Cellular Endosymbionts o Mitochondria – aerobic respiration o Chloroplasts – photosynthesis o Dinoflagellate endosymbionts of the genus Symbiodinium, commonly known as zooxanthellae, are found in corals, mollusks, sponges, and foraminifera o These endosymbionts drive the amazing formation of coral reefs by capturing sunlight and providing their hosts with energy • Secondary endosymbionts o More recent association, horizontally transferred between hosts, live in the haemolymph of the insects, are not obligate o The pea aphid is known to contain at least three secondary endosymbionts. HTTP://NOTES.BOOKHOLDERS.COM B ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Cellulose digestion o A large proportion of plant energy is tied up in cellulose but most organisms cannot digest it. o Symbiosis with microbes is a major means by which cellulose is used by animals o Occurs in vertebrates (ruminants like cattle) and in insects (termites and leaf cutter ants) • Termites can’t actually digest wood – they must have either microbial gut endosymbionts (new world) or an exosymbiont in the form of a fungus (old world). • Leaf cutter ants – symbiosis between ant and fungus – animal agriculture o Leaf cutter ants make gardens by growing fungus on leaves they cut and collect. o They are the major herbivore of the new world tropics consuming 10-15% of vegetation o They provide a major source of leaf recycling in tropical forests (side effect) o Agriculture in leaf cutter ants as a mutualism  Ants carry the fungus to new nests  Each ant species has its own strain/species of fungus  Ants provide for the needs of their fungus feeds them  An additional mutualism exists between the ants, fungus and bacteria that make antibiotics that controls mold. • Ant – Acacia symbiosis – predator defense o Symbiotic ants protect the Acacia o Pseudomyrmex ants have special behaviors that make them valuable to bullthorn acacias. • Acacia adaptations for sustaining ants o Hollow thorns o Beltian bodies o Extra-floral nectaries o Plant has evolved to keep the ants preoccupied • Ants appear to function in place of alkaloids (protective chemicals in leaves) that are present in leaves of related Acacias. o Predator damage can slow the growth of the Acacia allowing fast- growing, competing vegetation to shade them out. o Acacias represent an extreme form of obligate symbiosis, but it is common for plants to attract ants for defense o Extra-floral nectaries are widespread – occur on a variety of plants – E.g. sweet peas, peonies, roses, cucumbers, milkweeds, lilies, sunflowers, beans • Pollination – large flowers have evolved to facilitate the spread of pollen in an organism that cannot move. Adaptations include: o Bright colors of flowers o Nectaries in the flowers o Specialized positioning of flower parts for pollen transfer HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o Two species cannot coexist indefinitely on the same limiting resources (same niche) o Although similar species with similar species with similar requirements can coexist, studies usually reveal that they differ in their niche. • Gause’s Paramecium competition experiment o When grew separately, they were normal o When grew together, one outgrew the other • Evidence for competition o Fundamental niche: species’ niche in the absence of competition – the conditions under which can survive and reproduce o Realized niche: species’ niche in the presence of competition • Plankton paradox • All plankton species use approx the same mineral and resources • Why are there so many plankton species? • How can similar species coexist? o Niche multidimensionality ‐ many aspects define the a niche (e.g. Temp, salinity, pH etc.) and these are sufficiently different among species to allow coexistence o Spatial and temporal heterogeneity among species ‐ not really coexisting in the same space and time o Disturbance - reduces competition and populations are kept below K - one species is not dominant under all conditions (e.g. density) • Disturbance can allow more species to persist o Predation can influence the outcome of competition  A predator may prey on the best competitor species and thus allow a species that would otherwise be excluded to persist.  Keystone predator – predator species that when present allow for more species to coexist  i.e. Starfish • Evolutionary consequences of competition o Conflicting effects of intra- and interspecific competition  Intraspecific: competition often tends to widen niche breadth  Interspecific: competition tends to narrow niche breadth o Competition and species overlap  High degree of overlap between speices results in high competition  Divergence lowers overlap and reduces competition between species. o Character displacement – evolutionary effects of competition  Species show greater difference where they are sympatric than when they are allopatric  Competition in the past has caused divergence in areas where they are sympatric  In allopatry, without interspecific competition.  Islands with multiple Galapagos finch species have character displacement. HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks • Under competition, there were not enough food resources for the largest finches.  When character displacement occurs among multiple speices along a resource gradient this is called resource partitioning this can explain how communities with multiple speices. • Ecological Consequences of competition o Coexistence with a reduction in abundance, survival, and/or fecundity o Ecological exclusion (local elimination) o Habitat portioning • Evolutionary consequences of competition o Greater morphological differences between species when together (character displacement) o Ghost of past competition – current lack of interaction as the result of past competition leading to resource partitioning o Evolution of traits that enhance competitive ability. i.e. allelopathy. April 29 Community Ecology • Energy Pyramids • Food chains, Food webs • Succession • Food Chains and Pyramids o Communities show identifiable patterns of predation among species called food chains o Food chains are “schematic diagrams” o Food chains start with primary producers (autotrophs) that fix energy (photosynthesis) o They are eaten by heterotroph consumers o There can be multiple trophic levels as one set of heterotrophs is eaten by another set. o The links in the food chains are trophic levels  Level 1: Primary producers  Level 2: Herbivores  Level 3: Primary carnivore  Level 4: Secondary carnivore • Biomass Pyramid o Similar levels as food chains o The pyramid shape mostly results from conversion inefficiencies (energy loss) associated with changing prey biomass into predator biomass o Energy flow is up the pyramid o Ecological efficiency is the ration of the energy stored in a trophic level divided by the energy stored in the next lower trophic level o On average, 10% of the energy from biomass at lower trophic levels moves to biomass at the next higher levels HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks o This difference in stored energy is due to losses in metabolism (heat) and inefficiencies in processing food • Toxic Chemicals flow up and are concentrated in higher levels of food chains o Some problematic toxins: mercury, dioxin, PCBs, DDT • Toxic chemicals in fish o Methylmercury is a potent neurotoxin that affects the nervous system and brain development o PCBs affect the mental and physical development of children and may cause cancer o Dioxins have reproductive, developmental and immune systems effects • Safe Fish (fish w/ little fat where toxins are stored o Flounder, haddock, Pacific halibut • Grasshopper Effect o High level of toxic pollutants (Hg) transported to the arctic by winds from temperate power plants and industries o Seals are top predators and concentrate pollutants such as Hg o Seal bodies have such high levels of Hg they qualify as hazardous waste o Large problems for the Inuit who get 60% of their protein from seals • Food webs offer a more realistic characterization of species relationship o Most prey are eaten by more than one predator o Most predators eat more than one pretty o There is a controversy over the extent predation affects population size in food chains and webs o Top-down effects means that the top of the food chain (predators) sets the size of populations lower down the chain  i.e. Removal of predator increases deer herds; intro of gypsy moths and Opunita cactus without predators lead to uncontrolled growth • Bottom-up o Farmers increase nutrients soil for larger crops that can feed more cattle. o Nutrients (P) added to lakes primary productivity and increase population and higher trophic levels o Areas of upwelling in sears have highest productivity • Succession o Temporal changes in spices composition associated with colonizing an empty habitat. . o Ecological succession involves a series of communities (called seral stages) that co-occupy the same site through time o When an open space is cleared opportunistic pioneer species colonize it o More permanent communists may develop under a mature climax stage takes over. • Off-field Succession o Change over time. • A pioneer species – among the first colonists was Lupin which change all soil environment • Characteristics of plants in early and late succession stages HTTP://NOTES.BOOKHOLDERS.COM B kH ol de rs .c om Bu y a nd S el l T ex tb oo ks  In the U.S. the water from the north (Alaska) changes flow o Early Spanish fishermen named this change “El Niño” in reference to the Christ Child o Variable patterns of rainfall in Mojave Desert Related to El Niño oscillations o Species must be able to deal with this variation o Effects on temp in N and S American West Coast  Sea level rise > increased coastal erosion  Etc • La Niña o Atlantic storms are stronger, resulting in more damage from wind, storm surge, and rain-related flooding • Variation in precipitation can be tracked in ice logs and trees • What causes global differences in species diversity o Many different contributing explanations but factors like latitudinal gradients and altitudinal gradients are key. • More species around the tropics (generally)  close to the equator o As you move towards the equator, species population increases. As you move away from the equator, species population decreases o Some reasons for higher species diversity in the tropics  More different habitats at lower latitudes  Etc • Anthropogenic Threats o Global warming o Deforestation o Desertification o Acid rain o Smog o Ozone depletion • Latitudinal gradients and human disease • Deforestation o Forests covert CO2 to oxygen, reduce flossing, and help provide habitats for many species o In tropical areas there is a high rate of deforestation. o People clear land for farming and use wood to make charcoal o Arc of deforestation in Brazil moving to reduce the largest tropical forest in the world • Desertification o If the land surrounding the desert is overused, it will erode into desert. o 1/3 of the land on the earth’s surface is arid or semiarid and more than half of it is in danger of desertification • Desertification in China o Immediate causes  Overgrazing of marginal grazing land  Over plowing of marginal farming o Results HTTP://NOTES.BOOKHOLDERS.COM B ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks  ~900 square miles of land lost • ACID RAIN! o Midwest burns a lot of coal. The bad stuff (main sulfur) becomes sulfuric acid o Winds spread the acid in the clouds, and changes the pH of the rain, making it more acidic o High pH harms pant growth o Species are lost as acid levels increase o Partial success  Since the Clear Air Act of 1970, U.S. emissions of SO2 have declined 39%, but the emissions of NOx • UV-B is a significant health hazard have held steadily or possibly increased o Ozone layer of gas 20-30 km above the Earth’s surface HTTP://NOTES.BOOKHOLDERS.COM Bo ok Ho ld er s.c om Bu y a nd S el l T ex tb oo ks