Bio 1204 Lecture Notes PDF

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Lecture Notes Things to do:  Go on one zoom What is this course about? -Biodiversity: -The richness of life as reflected in: -Genetic variability within species -Differences between species -Number of individuals and species on earth -Variety of communities and ecosystems -Evolution: -Descent with modification (Genetic change from generation to next) Why is evolution important? -Nothing makes sense in biology except in the light of evolution -Managing diseases (Tasmanian devils can transmit cancer through tumors on their skin) -Agriculture (e.g. Harvest, herbicide, pesticide resistance) -Managing wildlife (e.g. harvest induced evolution, when we harvest too much animals we force evolution onto them) Life on Earth -Phylogenetic tree of life shows different species and common ancestors -4 Kingdoms: Animals, plants, fungi and others -3 Domains: Bacteria, Archaea and Eukarya -This course mainly focuses on Eukarya -Recently people have begun to think Eukarya arose from archaea, which would mean that there are only 2 domains -Life arose 2.5 billion years ago -2 billion years ago eukaryotes evolved -600 million years ago animals evolved -Major extinctions are part of a pattern on earth -When Cambrian fauna went extinct, Paleozoic fauna became more diverse and present, when Paleozoic fauna went extinct, Modern fauna became more diverse and present -There has been series of extinctions -Dinosaurs went extinct 65 million years ago -There have been 5 major extinctions Life on Earth -Features of life on earth over geological time -5 mass extinctions (Know when they occurred) -Turnover of species diversity, replacement of species -Origin of a group doesn’t necessarily coincide with its radiation (Diversification)

-There were mammals when dinosaurs were present, but mammals diversified when dinosaurs went extinct Evidence for Evolution: -The fossil record -Anatomy and embryology -Biogeography (Study of distribution and diversification over planet) -Molecular biology (genetics) -Direct observation of evolution in action -Antibiotics and herbicides work until the target evolves to resist it -Not a question of if it will evolve, but how quickly it will -Richard Lenski’s experiment showed bacteria can evolve to use citrate instead of glucose, something that it could not do before evolving -There has been evolutionary decline in horn size and body size due to humans preferring to hunt sheep with bigger bodies and bigger horns -HIV evolves very quickly to combat treatments The Tree of Life -Phylogenetic tree of life shows how organisms evolved and how they are related -There is also a eukaryotic tree of life -Eukaryotes have a true nucleus -Eukaryotes have linear chromosomes Eukaryotes -All have cells with nuclei surrounded by nuclear envelope with nuclear pores -Single characteristic that is necessary and sufficient to define an organism as a Eukaryote -Eukaryotes evolved two major innovations: -Internal membranes -Multicellularity -Unicellular Eukaryotes are called protists Multicellularity 1. Unicellular flagellated protist 2. Multiple flagellates make an aggregate 3. The unspecialized flagellates can’t function alone 4. Specialized reproductive cells form 5. Cells begin to fold in to make tissues -Green algae species show a range of independence -Some are single celled, some form together and can no longer be independent -Colonies may provide protection from predation because you can become too big to eat

Internal Membranes -Internal membranes of Eukaryotic cell are known as Endomembrane System (E.R, nuclear membrane, Golgi complex) -Internal membranes likely evolved via infoldings and pinching off of the plasma membrane -Mitochondria and chloroplasts evolved via a different pathway -Endosymbiotic theory explains how mitochondria and chloroplasts evolved -A cell took in mitochondria and chloroplasts -Called endosymbiosis because they were taken into cell -Endosymbiosis theory was proposed by Dr. Lynn Margulis and was rejected 15 times 4 Lines of Evidence Support That Support This Theory 1. Mitochondria and Chloroplasts have double membrane 2. Morphology of chloroplasts is similar to cyanobacteria and morphology of mitochondria similar to aerobic bacteria 3. Mitochondria and chloroplasts divide on a different schedule than the rest of the cell, they divide via binary fission like prokaryotes 4. Mitochondria and chloroplast DNA sequences are not the same as the nuclear DNA, and they are most similar to certain prokaryotes Horizontal Gene Transfer -Endosymbiont is an example of horizontal gene transfer -Vertical gene transfer is reproduction -The introduction of genetic material from one species to another species by mechanisms other than reproduction -Scientists believe that Red Aphids became red through HGT after eating red fungi -People have said that all 3 domains of life evolved from a pool of primitive prokaryotes -Domain of Eukarya was originally divided into 6 supergroups -Within each super group are multiple kingdoms th -A 7 supergroup was discovered recently Protist -Typically, the term protist refers to only Eukaryotes that are not: -Plant -Animal -Fungi -Movement: Cilia, pseudopod, flagellum -Metabolism: Autotrophs, mixotrophs, heterotrophs Endosymbiotic Hypothesis for Origin of Mitochondria and Chloroplasts -In first endosymbiotic event, a eukaryote likely consumed aerobic bacteria that eventually evolved into mitochondria -In second endosymbiotic event, early Eukaryote consumed photosynthetic bacteria that evolved into chloroplasts

Chloroplast Evolution -All Eukaryote cells have mitochondria, but not all have chloroplasts 1. Primary Endosymbiosis of photosynthetic bacteria ancestor (Already looked at) 2. Secondary Endosymbiosis of a red or green algae -Occurred between 2 eukaryotes -Mitochondria was lost in Excavates -Mitochondrial DNA was transferred to the nuclear genome -After secondary endosymbiosis, the chloroplast would have had 4 membranes -Serial Endosymbiosis Theory said that the first Eukarya took in mitochondria, then a chloroplast -Most Excavates don’t have mitochondria -Excavates used endosymbiotic gene transfer (HGT) to transfer mitochondrial DNA to nuclear genome allowing them to undergo aerobic respiration without a mitochondria -Humans have some genes in their mitochondria, some genes in the nucleus -Excavate have 0 genes in the mitochondria, all in the nucleus

Classification and Phylogeny Biodiversity Classification -Darwin drew the first tree -Carl von Linnaeus (Swedish Botanist) -Considered father of classical taxonomy -Invented binomial nomenclature (System) -Believed in immutability of species -Suggested world’s biodiversity came from Mount Ararat where Noah’s ark was said to have landed -Linnaeus developed system of naming and classifying organisms -Taxonomic classification system uses a hierarchical model to organize organisms into increasingly specific categories -Common dog (Canis Lupus Familiars) is subspecies of canis lupus -At each sublevel in the system, organisms become more similar -Dogs and wolves are the same species but are different enough to be classified as different subspecies -Taxonomy: The science and system of classifying organisms -Taxon (Taxa Plural): A single level in the taxonomic system -Levels of Hierarchy: Kingdom, domain, phylum, class, order, family, genus, species, subspecies -To Remember Levels: Katy Perry came over for good soup Binomial Nomenclature -Each species is assigned a Latinized 2-part name -The first name is the genus and is always capitalized -The second part is the species and is always lowercase -Either both words are italicized or underlined separately Classification of Biodiversity Below Species Level

-Subspecies: Add a subspecies name (Lower Case) that is italicized or underlined after species name -The problem with subspecies is that they don’t always have evolutionary interpretation -They could be based on political or geographic boundaries, minor morphology differences or things that aren’t related to evolutionary history -Land plants evolved from green algae not red algae -Endosymbiotic gene transfer led to loss of mitochondria in Excavata Classification and Phylogeny -Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, Subspecies -At each sublevel of system, differences between organisms become smaller -Dogs and wolves are the same species but are different enough to be considered different subspecies -Species is the only level of hierarchy of taxonomy that is clearly defined -Taxonomy: Science and system of classifying organisms -Taxon (Taxa Plural): Single level in taxonomic classification system -For Latinized 2-part name: -First part of name is the Genus and it is capitalized -Second part of name is the species and it is lowercase -Both words are either italicized or underlined -The taxonomic system makes species clear across countries and languages -Buffalo and bison are the same scientific name, and subspecies but we call them different common names -Giant elephant shrew and prairie shrew may sound similar but are actually different genus -There are so many species that lots of them don’t have common English names we would know -Because of this lots of species only have Latinized name -Latinized name tells us how similar species are, same genus or same species -To add subspecies, write it lower case after the species Problem with Subspecies: Hard to decide when we should call something a different subspecies, it is often only due to geographic boundaries or minor differences -In many jurisdictions, relevant taxonomic unit for conservation is based on evolutionary significance -In Canada, relevant taxonomic unit for conservation is a designable unit (DU) -In USA, it is ESU (Evolutionary Significance Unit) -In Canada, subspecies must be distinct and have evolutionary significant differences to be considered different -Canada has 12 different caribou subspecies -Some common names have several synonyms, scientific name provides consistency -Consistent and clear communication between languages -Some species have no common names -Makes clear distinction between subspecies and species

-Binomial nomenclature has evolutionary interpretation Phylogeny and Systematics -Systematics: Science and system of organizing and classifying taxa, and understanding evolution of traits based on their phylogenetic relationships -Systematics usually put this into a tree -Scientific nomenclature is meant to reflect phylogenetic relationships, all members of a taxon should share a single common ancestor -How can we figure out phylogenetic relationships if we can’t go back in time? -We can use evolutionary principles to compare characteristics among taxa -Example: All mammals produce milk and have fur Cladistics-Building Trees -Cladistics: Philosophy and methodology for reconstruction of ancestor-descendant (Relationships amongst a set of taxa) -Basic Assumptions of Cladistics: 1. Characters are modifications of pre-existing characters, changing within lineages over time 2. Any group of organisms is related by descent from a common ancestor 3. Lineages bifurcate (Split into 2) when new lineages evolve -Monophyletic Group: Individuals in a monophyletic group share a single ancestor, and compromise all the descendants of that ancestor -A monophyletic group is also called a clade -IMPORTANT: A phylogenetic tree is a hypothesis about the evolutionary relationships between species To Determine if a Group of Taxa is Monophyletic: 1. Find the most common ancestor of all taxa in group 2. Determine whether the group includes all descendants of the most recent common ancestor -There will be question on midterm about what monophyletic group means -Phylogenetic tree only represents our best idea, or the most likely tree -Review: -Taxonomy is system of classifying animals -Phylogenetics is science -All members of clade have common ancestor -Monophyletic group are also called clade -Derived trait is a trait that has evolved in lineage, meaning it didn’t exist in an ancestor -Ancestral trait is a trait that is present in an ancestor

-Characters used to reconstruct a phylogeny can come from: -Fossil record

-Morphological traits of living species (or museum specimens) -Genetic sequences -Shared derived traits are used to identify clades ‘ Vertebrae Bony Four Amniotic Skeleton Limbs Egg

Hair

Two PostOrbital Face No No No No No No Yes Yes

Out Group No No No No No Shark Yes No No No No Ray-Finned Fish Yes Yes No No No Amphibians Yes Yes Yes No No Primates Yes Yes Yes Yes Yes Rodents Yes Yes Yes Yes Yes Crocodiles Yes Yes Yes Yes No Birds/Dinosaurs Yes Yes Yes Yes No -Can use chart like this to determine how closely organisms are related -After determining which character to study, and making a hypothesis about the ancestral state, you can build a tree by: 1. Grouping taxa by shared derived traits 2. Working out any conflicts (None in example above) -Homology: A similarity in character due to shared ancestry evolving from the same ancestral state common ancestor -Homologous characters can appear very different -Example: Whales have small pelvic bone that evolved from hind legs -Analogy: A similarity in a character due to evolutionary convergence not due to shared ancestry -Convergence in phenotype is usually the result of natural selection (Animals need blubber to live in cold water) -European mole and southern marsupial mole look very similar even though they are not related -Bat and bird wings are an example of both homologous and analogous characteristics -Wings: Analogy: Wings evolved from different ancestors that did not have wings, therefore convergent evolution -Forelimbs: Homology: Both inherited from a common ancestor with forelimbs, therefore shared ancestry -Homology and Analogy: It’s not always easy to tell if a phenotype is similar due to shared ancestry or due to convergence -Convergent evolution is actually a process that we expect when organisms evolve by natural selection -Shared ancestry is expected to result in more similar structures among more closely related organisms -Solutions to this:

-Use traits that are very likely to be selectively neutral -Use many selectively neutral traits -DNA -Neutral traits are not affected by selection -An organism’s evolutionary history is documented in its genome -Molecular systematics uses DNA to infer relatedness -Scientists have sequenced more than 110 billion bases of DNA from thousands of species -This enormous database has fueled a boom in study of phylogeny and clarified many evolutionary relationships -About 1% of human DNA actually codes for something -The more recently two species have branched from a common ancestor, the more similar their DNA sequences should be -The longer the two species have been on separate paths, the more their DNA should have diverged and become different Using and Interpreting Trees -Neutral variation among DNA sequences can be used to infer a molecular clock -A molecular clock is a known constant mutation rate of DNA sequences (For example, 2 mutations per 100 base pairs per 100 million years) -Molecular clock can be used to calculate the time since taxa have diverged -Molecular clock has been used to date origin of HIV infection in humans -Morphological traits and DNA are most often used to determine phylogenetic traits -Species evolutionary history is documented in genome -Mutations arise at a fairly constant rate Using a Molecular Clock -If there is 15 nucleotide substitutions per 100 codons per 100 million years, then there is 0.005 substitutions per base pair per million years -If you find one substitution in 20 base pairs, that is 0.05 substitutions per base, 0.05/0.0005 = 100 million years since species diverged -Pleistocene was last major ice event Phylogenies Help us Understand Evolutionary Histories -Traditionally (Since Linnaeus), there have been 5 classes of vertebrates -Fish -Amphibians -Reptiles (Including dinosaurs) -Birds -Mammals -Since then, phylogenetic evidence suggests that traditional groups don’t accurately reflect evolution -Reptiles are not a true clade (Therefore not monophyletic)

-Dinosaurs are also not a true clade unless birds are included with them -Birds are now included with dinosaurs -Phylogenies allow us to evaluate hypothesis about origins of biodiversity -Vertebrae’s that live on land were derived from fish -Amphibians are close to a transition state between fish and animals -Phylogenetically, lungfish are closest relatives to land animals -We should be able to find transitional from between lungfish and amphibians -Tiktaalik has been found that was the transition species

Mechanisms of Evolution -Evolution: Descent with modification (Moving from generation to generation with changes) Variation -Genotype: The underlying genetic makeup of an organism or a phenotype -Phenotype: An observable trait expressed by an organism -Gene: A physical and functional unit of DNA (Could be a sequence of DNA that codes for a protein or could be noncoding) -Locus: A position on a chromosome -Allele: Variations that arise by mutation and exist at the same locus on homologous chromosomes2 -DNA -> Organelles -> Cells -> Tissues -> Organs and organ systems -> Organisms, populations and communities -> Ecosystems -> Biosphere -Traditional/functional perspective -DNA -> Genotype -> Individual -> Population -> Subspecies -> Species -Evolutionary perspective -Species: Group of individuals capable of breeding -Subspecies: Recognized taxon below species level -Population: Group of individuals with roughly equivalent probability of mating with each other -We find variation amongst species -We also find variation within species -Northern flicker is found throughout Canada, on the west they are red and in the east they are yellow, in Alberta a mixed orange one is found -Variations within populations -Variation in nature can be continuous or discontinuous -Height is continuous, lots of people are average height, less are very tall or very short -Most continuous traits show a bell curve -Eye color is discontinuous, there is no gradient -Variation within individuals -Genetic variation is a DNA sequence can vary -There is variation within heterozygous individuals -If there are two alleles (c and T) you can be homologous dominant (TT), homologous recessive (cc) or heterozygous (cT)

-Population Genetics: The study of allele frequencies in a population over time -Hardy Weinberg Equilibrium -Two alleles at a genetic locus: A and a -In a diploid organism, there are 3 possible genotypes: AA, Aa, aa -p2 + 2pq + q2 = 1 -p + q = 1 -Frequency of AA = p2 -Frequency of Aa = 2pq -Frequency of aa = q2 -Used when looking at 1 genetic locus and 2 alleles -Can also be written as A1 A1, A1 A2, A2 A2 -Dominant alleles aren’t necessarily better than recessive alleles, in fact the opposite is sometimes the case -All variation does not have genetic basis, environment also has a role The Role of the Environment -An individual’s phenotype represents the combined effect of genotype and environment -Phenotype = Genotype + Environment + (Genotype*Environment) -P = G + E + (G*E) -G: Genetic Effects -E: Environmental effects -G*E: Genetic effects whose expression depends on environment, or environmental effects which only occur for certain genotypes The Role of Environment: Phenotypic Plasticity -Phenotypic Plasticity: The environmentally sensitive production of alternative phenotypes by a given genotype (Same genotype) -Peppered moth caterpillars can be green, or brown based on what color of tree they hatch on Heritability -Heritability (Symbol=h2) -The fraction of the total phenotype variation in a population that is caused by genetic differences among individuals -Inheritance: The transmission of traits (Inherited features) from one generation to the next -How do we measure heritability? -You can calculate heritability of a trait if you know the amount of phenotypic and genetic variation -Vp: Phenotypic variation -VG: Genetic Variation -VE: Environmental variation -Vp = VG + VE -h2 = VG/Vp -Heritability is a property of a population, not an inherent property of a trait

-Slope of a lone is an estimate of heritability -Alternatively, slope of relationship between parent a...