Ecology & Evolution
Ecology & Evolution
Popular in Course
verified elite notetaker
Popular in Biology
One Day of Notes
verified elite notetaker
This 10 page Bundle was uploaded by Jacqueline Puliatti on Thursday May 1, 2014. The Bundle belongs to a course at University of California - Santa Cruz taught by a professor in Fall. Since its upload, it has received 163 views.
Reviews for Ecology & Evolution
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 05/01/14
Week 1 Science before Darwin Concept of eidos and the role it played in preventing evolutionary thinking eidos was the essentialist belief that all species have a perfect essence variation was seen as a failure of essence It prevented evolutionary thinking because variation in species was not seen as possibly evolution but rather a failure of achieving essence Contributions of the following towards the development of the theory of evolution Hutton uniformitarianism the belief that changes in the earth s geology have resulted from continuous and uniform processes Lyell principles of geology and gradual geological change Malthus looked at principle population as population grew RESOURCES BECAME LIMITED Studied demography and economics Smith important illustration in social science concerning free market system of limited resources where advantage leads to ourishing and COMPETITIVE ADVANTAGE the idea of edge and advantage goes on to formulate natural selection Linneaus father of modern TAXONOMY gave species and genus a binomial system using greek and latin roots Lamarck developed theory that CHANGE ACQUIRED IN THEIR LIFETIME Terms Eidos essentialism all species had perfect essence Unifomitarianism the belief that changes in the earth s geology have resulted from continuous and uniform processes Scala naturae The Great Chain of Being Essentialism led to the concept of scala naturae Species seen as fixed rungs of the ladder Darwin and the theory of evolution is modi cation through descent and the mechanism is natural selection Role the following played in in uencing Darwin during the voyage of the Beagle Biogeography tells about the geography of a organism Fossils Fossils show us where and when organisms lived in the past and give us an idea of what they looked like amp provide important evidence that helps us distinguish ancestral from derived traits Geology provided evidence that earth was much older than previously thought and provided fossils Theory of evolution 2 Components of the mechanism of Natural Selection Struggle for existence not all individuals will survive and reproduce Survival of the fittest selective advantage over others Population as the smallest unit capable of evolution Concepts of Fitness the reproductive contribution to a phenotype to subsequent generations relative to the contributions of other genotypes The tness of a phenotype is determined by the relative rates of survival and reproduction of individuals with that phenotype Adaptation A favored trait that evolves through natural selection Describes both the trait itself and the process that describes the trait Week 2 Evidence supporting evolution Support for idea that species change through time Fossils Fossils show us where and when organisms lived in the past and give us an idea of what they looked like amp provide important evidence that helps us distinguish ancestral from derived traits Vestigial traits traits that change go away arise because of change in the environment or behavior of an organism tail bone in humans Observations on natural populations Experiments Support for idea that species share common ancestors Biogeography ISLAND BIOGEOGRAPHY provided the major stimuli for development of theory of evolution Recall Darwin39s experiences with tortoises and nches on Galapagos shared many homologous traits Homologous traits a trait from a common ancestor any feature shared by two or more species that have been inherited from a common ancestor Homologous features may be any inheritable traits including DNA sequences protein structures anatomical structure and some behavior patterns o Anatomical bones of forearm in mammals o Embryological gill pouch and tail found in mammals o Molecular Hox genes responsible for development in different parts of the body certain parts of Hox gene Vertical evolution of genomes vertical evolution creates branches vertical evolution is the change through time Paralogs gene copies within the same species both homologs homologous genes whose divergence can be traced to gene duplication events vs orthologs are genes in different species that have evolved from a common ancestral homologous genes whose divergence can be traced to speciation events Horizontal evolution merges branches of a tree to form a new branch involves gene transfer between species most common in bacteria endosymbiotic theory Microevolutionary processes mutation small changes the shortterm changes in allele frequencies within populations These changes can be observed directly they can be manipulated experimentally and they demonstrate the actual processes by which evolution occurs Concept of gene Locus a location on a genetic sequence Allele Measuring for changes in allele frequency HardyWeinberg equation pquot22pqqquot2 l pAA l 2Aa amp qaa l 2Aa Assumptions for HardyWeinberg equilibrium N O Natural selection genetic drift gene ow mutation no random mating Fixed vs lost alleles If there is only one allele in a given locus in a population its frequency is one The population is then monomorphic one form at that locus and the allele is said to be fixed Concept of genetic diversity for single gene or entire gene pool Natural Selection De nition of four types effects on genetic diversityg examples Directional selection changes the characteristics of a population by favoring individuals that vary in one direction from the mean of the population Directional selection is operating when individuals at one extreme of a character distribution contribute more offspring to the next generation than other individuals do shifting the average value of that character in the population toward the extreme Results in a increase of the frequencies of alleles that produce the favored phenotype If directional selection operates over many generations an evolutionary trend is seen in the population Stabilizing selection preserves the average characteristics of a population by favoring average individuals Reduces variation in populations but it does not change the mean Natural selection is often stabilizing Disruptive selection changes the characteristics of the population by favoring individuals that vary in both directions from the mean of the population Operating when individuals at opposite extremes of a character distribution contribute more offspring to the next generation than do individuals close to the mean Increases variation in the population Natural Selection Sexual selection Mechanisms of sexual selection result in high rates of speciation 0 Female choice when a female actively chooses a male due to some trait that makes them appealing colorful body long tail special dance or sounds o Malemale competition when two males ght each other to win a female The female passively chooses the male because she chooses the one that wins Balancing polymorphism maintains less t alleles in population Two mechanisms Heterozygote advantage amp frequency dependent selection o Heterozygote advantage sometimes being a heterozygote has higher tness than if there were two dominant alleles BB versus Bb or bb this bb is usually the weakest both alleles are recessive 0 Negative frequency selection if there is a high frequency Genetic drift the random change in allele frequencies from one generation to the next o Mechanism 0 Founder effect When a few pioneering individuals colonize a new region the small population is unlikely to possess all the alleles found in the gene pool in its source population resulting in the reduction of genetic variation equivalent to bottleneck vs genetic bottleneck When a population goes through environmental conditions in which only a few individuals survive Gene ow Migration of individuals and movements of gametes between populations that can change allele frequencies in the population Mechanism Effects on genetic diversity for donor amp recipient populations it increases genetic diversity because the individuals moving to a different population will have different allele frequencies than the population they are entering changing the traits within the population Mutation a random mistranslation of DNA when it is copied into chromosomes It affects the allele frequencies of whatever locus the mutation occurs Inbreeding mating between individuals that are closely related to each other example of non random mating Allele frequencies don t change but genotype frequencies do change see a decrease in heterozygotes because when heterozygotes mate with themselves they produce homozygotes and heterozygotes whereas homozygotes breeding together just create more homozygotes so eventually there will be no more heterozygotes cause their offspring will more likely be homozygotes Neutral Evolution Speciation two phases genetic isolation Genetically similar pairs of species show little reproductive isolation Genetically distant pairs of species show high reproductive isolation genetic divergence natural selection genetic drift and mutation cause genetic divergence Concept of species Biological species Species are groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups Reproductive isolation is what allows sexual species to evolve independently of one another Actually says that the individuals live in the same area and interbreed with one another Potentially says that even tough the individuals do not live in the same area and therefore do not interbreed other information suggests that they would do so if they were able to get together morphospecies Morphological species concept a construct that assumes that a species comprises individuals that look alike and that individuals that do not look alike belong to different species Linneaus used this Week 4 Punctuated equilibrium change occurs in short bursts long periods of little change predicts new species to appear rapidly vs gradualism genetic change continuous accumulates through time leads to change in phenotype and new species Evolutionarydevelopmental biology Interdisciplinary approach paleontology anatomy developmental biology molecular biology genetics attempts to explain rapid development of new body plans Homeotic Hox genes genes that control developmental processes in a body Can be speci c to regions of the body Are turned on off by their own regulatory years There are different Hox genes that are responsible for developing many different regions of the body say creating head features or abdominal features etc Hox genes and body complexity more hox genes should allow for more axes of development More hox genes should allow for more axes of development You can compartmentalize Different genes from up down forward back left right Different Hox genes can control development of specific parts of the body Gene duplication mutations produce more Hox genes getting paralogs Easy to create new Hox genes These are simple mutations Then these hox genes will start doing something different for the body Gene duplications Over time gene duplication and other genetic changes produced many more genes that added to eye complexity These additional genes remained under the control of the Pax6 gene and its homologs Paralogs gene copies within the same species both homologs homologous genes whose divergence can be traced to gene duplication events vs orthologs are genes in different species that have evolved from a common ancestral homologous genes whose divergence can be traced to speciation events Mutations affecting spatialtemporal expression of regulatory genes Examples of regulatory gene mutations that cause morphological change How genes have their own regulatory These are genes that turn on Hox genes Vary if or when a particular hox gene is turned on Can result in changes in structures existing structures not to form or existing structures to form in new places Example Ubx gene and abdominal leg growth Mutation in Ubx gene inhibits dll gene which causes legs to grow Example Ubx gene and thoracic wing growth Deletion of ubx gene causes wing to grow on 3rd thoracic segment Gremlin in chicken VS duck feet changes in when and where regulatory genes are expressed Can lead to big changes in structure Example Clawed vs webbed feet in fowl Both chicken an duck have webbed feet as embryos BMP4 gene that causes tissue to degenerate Gremlin gene produces protein in inhibits BMP4 expression Presence of growth results in webbed feet Ubx in arthropod appendages insects vs others HoX dll expression in sh VS limb buds Both mouse limbs and sh ns form from limb buds in embryos Hoxdl l and shh sonic hedgehog are both genes that regulate the direction of limb bud growth Fish n only express hoxdl l and shh in rear of limb bud and early Mouse limb initially similar but there is additional expression in headtail axis later in development Allometric growth human vs chimp skulls human vs giraffe neck vertebrae Example chimp vs human skull Genes promoting a skull growth suppressed as chimp grows Genes promoting jaw growth continue Result larger brain cavity in human adults and chimps have bigger jaws Peadomorphosis copepodslancelets retention of larval juvenile characteristics in adult Can lead to new body plans Example copepod crustaceans Using orthologs to infer evolutionary relationships of structures Eg eyes in animals Pax6 in mice vs eyeless in ies Transplant experiments in ies experiment transplant tissue expressing eyeless gene to different part of the body to see if you put a gene that tells the body to make an eye somewhere else if an eye would be built result eye grow in funny places Experiment insert mouse pax6 gene in y genome Repeat transplant experiment and result is that mouse gene cause y eye to grow in transplant area conclusion eyeless and pax6 genes are orthologs So the eye initiating genes are orthologs from a common ancestor The ancestral pax6 gene controlled other genes that produced a primitive 2celled eye During evolutionspecies diverged from each other but each species retained a Pax6 homolog Over time gene duplication and other genetic changes produced many more genes that added to eye complexity These additional genes remained under the control of the Pax6 gene and its homologs Phylogenies evolutionary history for group of organisms typically depicted as a tree Phylogenetic tree branches nodes tips root outgroup ingroup sister taxa polytomy Branches populations through time Nodes forks where ancestor splits into two or more descendants you can rotate the node that gives rise to the species and you don t change the information Tips extinct or extant still living species Sister taxa Groups that occupy adjacent branches linked by a node Clade ancestor and all its descendants all the branches that emerge from the ancestor Polytomy more than 2 groups emerge from a node AKA star phylogeny constitute rapid speciation Tree rootedbottom node most ancient Outgroup taxon that diverged prior to most ancient node of a tree Monophyletic vs polyphyletic vs paraphyletic group Monophyletic group true clade ancestor and all its descendants good we want these Paraphyletic groups group with common ancestor but only some of its descendants incomplete left out some species bad but not so bad Polyphyletic group groups of species with different common ancestors putting species with different ancestors in the same group not related species worst we don t want that Adaptive radiations Appear in phylogenies as polytomies star phylogenies Represents a period of rapid speciation causes of effects on phylogenetic trees Colonization events honeycreeperssilverswords when species are physically separated from one another and quickly adapt to the new different environment Habitat unoccupied by competitors is colonized by a species Colonizing species quickly radiates to exploit new resources Can also occur as a consequence of a mass extinction Morphological innovation feathers flOWCI39S mouthparts some radical mutation gives you a new morphology that gives you access to resources that you couldn t get before the mutation Ends up creating a whole species because the mutation helps the species survive Allows new resources to be exploited examples owers owering plants have a unique reproductive structure feathers highly modi ed scales mouthpart modi cations Mass extinctions mammal radiation in Cenozoic Remove major competitors from the system Allows surviving species to exploits resources that were previously unavailable Fossils physical trace of organism that lived in the past fossil record all the fossils we have found if a new fossil is found it adds to the fossil record biases associated with fossils Habitat bias habitat rich in sediment produce more fossils Burrowing organisms and soft brown organisms more likely to make fossils Taxonomic bias organisms with hard parts are more likely to leave fossils The forms survive long enough after death for the fossil to form Temporal bias older organisms like reaally old are less likely to have fossils because they had time for the earth to decay or break the fossil Abundance bias more numerous organisms more likely to leave fossils Organic fossils organically preserved pollen insects in amber compressed fossils carbon rich lms cast fossils imprint of an organism preserved by rock the shape of organism permineralized fossils eg petri ed wood fossils Molecular clock uses amp limitations Looking at the DNA to see it they shared ca common ancestor Mutation rate constant Most mutations are neutral Can use neutral mutations to estimate time divergence for lineages Relationship should be linear CASE STUDIES USING MOLECULAR CLOCK Shorter term use DNA with ca high rate of change Eg introns of mitDNA split between chimps and bonobos stopwatch Longer term use slow changing Eg SSU rRNA or Short Subunit of the ribosomal RNA Split between chimps and humans Calendar Cladistics Tool for estimating phylogeny Tries to organize a group of organisms till it gets to the smallest clay the smallest group which is a species Draws input from Morphology Development Paleontology Molecular data Even sometimes behavior cladogram Can be depicted as a tree cladogram it is a phylogeny All cladograms are phylogenies vs phylogeny Based on ancestral analysis evolutionary history for group of organisms typically depicted as a tree Sympleisomorphy Trait shared with an ancestor ancestral trait vs Synapomorphy Shared derived trait not present in ancestor ingroup clade the shares of ingroup vs outgroup closest ancestor of ingroup Lacks synapomorphy problems associated with scoring characters in the matrix Homoplasies similar traits are not homologous Can be caused by convergent evolution eg bird and bat wings reverse mutations Evolutionary reversals loss of a trait Solution maximum parsimony maximum parsimony for selecting between different possible cladograms
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'