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Biology II Midterm Review

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BIOL 1020U
Mary Olavson

Chapter 26 – Phylogeny & the Tree of Life Overview  Phylogeny is the evolutionary history of a species or a group of related species  The discipline of systematics classifies organisms and determines their evolutionary relationships  Systematists use fossil, molecular, and genetic data to infer evolutionary relationships Concept 26.1 – Phylogenies show Evolutionary Relationships  Taxonomy is the ordered division and naming of organisms  Binomial Nomenclature o In the 18 century, Carolus Linnaeus published a system of taxonomy based on resemblances o Two key features of his system remain useful today: two-part names for species and hierarchical classification o The two-part scientific name of a species is called binomial o The first part of the name is the genus o The second part, called the specific epithet, is unique for each species within the genus o The first letter of the genus is capitalized, and the entire species name is italicized o Both parts together name the species (not the specific epithet alone)  Hierarchical Classification o Linnaeus introduced a system for grouping species in increasingly broad categories o The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species o A taxonomic unit at any level of hierarchy is called taxon  Linking Classification and Phylogeny o Systematists depict evolutionary relationships in branching phylogenetic trees o Linnaean classification and phylogeny can differ from each other o Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents o A phylogenetic tree represents a hypothesis about evolutionary relationships o Each branch point (node) represents the divergence of two species o Sister taxa are groups that share an immediate common ancestor o A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree o A polytomy is a branch from which more than two groups emerge  What We Can and Cannot Learn from Phylogenetic Trees o Phylogenetic trees do show patterns of descent o Phylogenetic trees do not indicate when species evolved how much genetic change occurred in a lineage o It shouldn’t be assumed that a taxon evolved from the taxon next to it Concept 26.2 – Phylogenies are Inferred from Morphological and Molecular Data  To infer phylogenies, Systematists gather information about morphologies, genes, and biochemistry of living organisms  Morphological and Molecular Homologies o Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences  Sorting Homology from Analogy o When constructing a phylogeny, Systematists need to distinguish whether a similarity is the result of homology or analogy o Homology is similarity due to shared ancestry o Analogy is similarity due to convergent evolution o Convergent evolution occurs when similar environmental pressures and natural selection produces similar (analogous) adaptations in organisms from different evolutionary lineages o Bat and bird wings are homologous as forelimbs, but analogous as functional wings o Analogous structures or molecular sequences that evolved independently are also called homoplasies o Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity o The more complex two similar structures are, the more likely it is they are homologous  Evaluating Molecular Homologies o Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms o It is also important to distinguish homology from analogy in molecular similarities o Mathematical tools help identify molecular homoplasies, or coincidences o Molecular systematics uses DNA and other molecular data to determine evolutionary relationships Concept 26.3 – Shared Characters are used to construct Phylogenetic Trees  Once homologous characters have been identified, they can be used to infer a phylogeny  Cladistics o Cladistics groups organisms by common descent o A clade is a group of species that includes an ancestral species and all its descendants o Clades can be nested in larger clades, but not all groupings of organisms qualify as clades o A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants o A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants o A polyphyletic grouping consists of various species that lack a common ancestor  Shared Ancestral and Shared Derived Characters o In comparison with its ancestor, an organism has both shared and different characteristics o A shared ancestral character is a character that originated in an ancestor of the taxon o A shared derived character is an evolutionary novelty unique to a particular clade o A character can be both ancestral and derived, depending on the context  Inferring Phylogenies using Derived Characters o When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared o An outgroup is a species or group of species that is closely related to the ingroup, the carious species being studied o Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics o Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor  Phylogenetic Trees with Proportional Branch Lengths o In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage o In other trees, branch length can represent chronological time, and branching points can be determined form the fossil record Concept 26.4 – An Organism’s Evolutionary History is documented in its Genome  Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history  DNA that codes for rRNA changes relatively slowly and is useful fir investigating branching points hundreds of millions of years ago  mtDNA evolves rapidly and can be used to explore recent evolutionary events  Gene Duplications and Gene Families o Gene duplication increases the number if genes in the genome, providing more opportunities for evolutionary changes o Like homologous genes, duplicated genes can be traced to a common ancestor o Orthologous genes are found in a single copy in the genome and are homologous between species; they can diverge only after speciation occurs o Paralogous genes result from gene duplication, so are found in more than one copy in the genome; they can diverge within the clade that carries them an often evolve new functions  Genome Evolution o Orthologous genes are widespread and extend across many widely varied species o Gene number and the complexity of an organism are not strongly linked o Genes in complex organisms appear to be very versatile and each gene can perform many functions Concept 26.6 – New Information continues to revise our understanding of the Tree of Life  Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics  From 2 Kingdoms to 3 Domains o Early taxonomists classified all species as either plants or animals o Later, 5 Kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia o More recently, the 3 domain system has been adopted: bacteria, Archaea, and Eukarya; supported by data from many sequenced genomes Chapter 27 – Bacteria and Archaea Overview – Masters of Adaption  Prokaryotes thrive almost everywhere, including places too acidic, salty, cold, or hot for most other organisms  Most prokaryotes are microscopic, but what they lack in size they make up for in numbers  There are more in a handful of fertile soil than the number of people who have ever lived  Lord May, president of the Royal Society (the UK’s national academy of sciences), has said: “Most conservation effort goes into birds and mammals – creatures like the panda, a dim, dead- end animal that was probably on the way out anyway. Yet arguably it’s the little things that run the world, things like soil microbes. They’re the least-known species of all.” Concept 27.5 – Prokaryotes play Crucial Roles in the Biosphere  Prokaryotes are so important to the biosphere that if they were to disappear the prospects for any other life surviving would be dim  Chemical Cycling o Prokaryotes play a major role in the recycling of chemical elements between the living and nonliving components of ecosystems o Chemoheterotrophic prokaryotes function as decomposers, breaking down corpses, dead vegetation, and waste products o Nitrogen-fixing prokaryotes add usable nitrogen to the environment o Prokaryotes can sometimes increase the availability of nitrogen, phosphorus, and potassium for plant growth o Prokaryotes can also “immobilize” or decrease the availability of nutrients Concept 27.1 – Structural and Functional Adaptations Contribute to Prokaryotic Success  Most prokaryotes are unicellular, although some species form colonies  Most prokaryote cells are 0.5-5µm, much smaller than the 10-100µm of many eukaryotic cells  Prokaryotic cells have a variety of shapes  The thee most common shapes are spheres (cocci), rods (bacilli), and spirals (reduces drag while moving)  Cell-Surface Structures o An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, provides physical protection, and prevents the cell from bursting in an hypotonic environment o Eukaryote cell walls are made of cellulose or chitin o Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides o Archaea contain polysaccharides and proteins but lack peptidoglycan o Using the Gram stain, scientists classify many bacterial species into Gram-positive and Gram-negative groups based on cell wall composition o Gram-negative bacteria have less peptidoglycan and an outer membrane that can be toxic, and they are more likely to be antibiotic resistant o Many antibiotics target peptidoglycan and damage bacterial cell walls o Gram staining (pink for negative and purple for positive) o A polysaccharide or protein layer called a capsule covers many prokaryotes o Some prokaryotes have fimbriae (also called attachment pili), which allow them to stick to their substrate or other individuals in a colony; the fimbriae can also create biofilms (biofilms are bad because they are resistant to antibiotics and the films can be created over catheters and other medical tools) o Sex pili are longer than fimbriae and allow prokaryotes to exchange DNA  Motility o Most motile bacteria propel themselves by flagella that are structurally and functionally different from eukaryotic flagella; the flagella allows the bacteria to move towards food sources and away from predators (the flagella are loaded with receptors which allow them to detect the presence of certain chemicals) o In a heterogeneous environment, many bacteria exhibit taxis, the ability to move toward or away from certain stimuli  Internal and Genomic Organization o Prokaryotic cells usually lack complex compartmentalization o Some prokaryotes do have specialized membranes that perform metabolic functions o The prokaryotic genome has less DNA than the eukaryotic genome o Most of the genome consists of a circular chromosome o Some species of bacteria also have smaller rings of DNA called plasmids o plasmids are often present within the cell in multiple copies whereas the chromosomal DNA has only one copy (different plasmids have different amounts of copies ranging from 2 to 100s of copies) o the typical prokaryotic genome is a ring of DNA that is not surrounded by a membrane (not bound by a double membrane like eukaryotes) and that is located in a nucleoid region  Reproduction and Adaptation o Prokaryotes reproduce quickly by binary fission and can divide every 1-3 hours o Many prokaryotes form metabolically inactive endospores, which can remain viable in harsh conditions for centuries o Prokaryotes can evolve rapidly because of their short generation times o Prokaryotes can stay dormant when times are bad, and when times are good they will regenerate and evolve rapidly Concept 27.2 – Rapid Reproduction, Mutation, and Genetic Recombination promote Genetic Diversity in Prokaryotes  Prokaryotes have considerable genetic variation  Three factors contribute to this genetic diversity o Rapid reproduction o Mutation o Genetic recombination  Rapid Reproduction and Mutation o Prokaryotes reproduce by binary fission, and offspring cells are generally identical o Mutation rates during binary fission are low, but because of rapid reproduction, mutations ca accumulate rapidly in a population o High diversity from mutations allows for rapid evolution o Basically the prokaryotes are clones of each other but within a population there will be lots of diversity because they are evolving fast  Genetic Recombination o Additional diversity arises from genetic recombination o Prokaryotic DNA from different individuals can be brought together by transformation, transduction, and conjugation o Transformation and Transduction  A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation  Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria); the bacterial DNA of a donor cell is fragmented and the phage will replicate inside the donor bacteria cell and the bacteria cell will die, then the phage transfers the “new” DNA from one bacterial cell (the donor/dead cell) to another cell and the recipient will have a new function that it never had before (in some cases the recipient cell will die if the DNA being transferred is viral, but if the DNA being transferred is not viral then it is beneficial to the recipient cell) o Conjugation and Plasmids  Conjugation is the process where genetic material is transferred between bacterial cells  Sex pili allows cells to connect and pull together for DNA transfer  A piece of DNA called the F factor is required for the production of sex pili  The F factor can exist as a separate plasmid or as DNA within the bacterial chromosome  The F Factor as a Plasmid – cells containing the F plasmid function as DNA donors during conjugation and cells without the F factor function as DNA recipients during conjugation; the F factor is transferable during conjugation (The donor cell, F factor positive, is considered “male”, and once the recipient, F factor negative, considered “female”, cell has the F factor transferred via conjugation it becomes F factor positive and “male”)  The F Factor in the Chromosome – a cell with the F factor built into its chromosomes functions as a donor during conjugation (the recipient becomes a recombinant bacterium with DNA from two different cells); it is assumed that horizontal gene transfer is also important in Archaea  R Plasmids and Antibiotic Resistance – R plasmids carry genes for antibiotic resistance (antibiotics select for bacteria with genes that are resistant to the antibiotics; antibiotic resistant strains of bacteria are becoming more common; bacteria spreads much more quickly than we can treat with antibiotics) Concept 27.3 – Diverse Nutritional and Metabolic Adaptations have evolved in Prokaryotes  Phototrophs obtain energy from light  Chemotrophs obtain energy from chemicals  Autotrophs require CO 2s a carbon source  Heterotrophs require an organic nutrient to make organic compounds  These factors can be combined to give the four major modes of nutrition – photoautotrophy, chemoautotrophy, photoheterotrophy, and chemoheterotrophy  The role of Oxygen in Metabolism o Prokaryotic metabolism varies with respect to O2  Obligate aerobes require O 2or cellular respiration  Obligate anaerobes are poisoned by O a2d use fermentation of anaerobic respiration  Facultative anaerobes can survive with or without O 2  Nitrogen Metabolism o Prokaryotes can metabolize nitrogen in a variety of ways o In nitrogen fixation, some prokaryotes will convert atmospheric nitrogen (NH2) to ammonia (NH )3  Metabolic Cooperation o Cooperation between prokaryotes allows them to use environmental resources they could not use as individual cells o In cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixed cells called heterocytes exchange metabolic products o In some prokaryotic species, metabolic cooperation occurs in surface-coating colonies called biofilms Concept 27.4 – Molecular systematics is illuminating Prokaryotic Phylogeny th  Until the late 20 century, Systematists based prokaryotic taxonomy on phenotypic criteria  Applying molecular systematics to the investigation of prokaryotic phylogeny has produced dramatic results  Archaea o Archaea share certain traits with bacteria and other traits with eukaryotes o Some Archaea live in extreme environments and are called extremophiles o Extreme halophiles live in highly saline environments o Extreme thermophiles thrive in very hot environments o Methanogens live in swamps and marshes and produce methane as a waste product; they are strict anaerobes (poisoned by2O ) o in recent years, genetic prospecting has revealed many new groups of Archaea o some of these may offer clues to the early evolution of life on Earth  Bacteria o Bacteria include the vast majority of prokaryotes of which most people are aware o Diverse nutritional types are scattered among the major groups of bacteria Chapter 28 – Protists Overview – Living Small  Even a low-power microscope can reveal a great variety of organisms in a drop of pond water  Protist is the informal name of the kingdom of mostly unicellular eukaryotes  Advances in eukaryotic systematics have caused the classification of protists to change significantly  Protists constitute a paraphyletic group, and Protista is no longer valid as a kingdom Concept 28.1 – Most eukaryotes are single-celled organisms  Protists are eukaryotes and this have organelles and are more complex than prokaryotes  Most protists are unicellular, but there are some colonial and multicellular species  Structural and Functional Diversity in Protists o Protists exhibit more structural and functional diversity than any other group of eukaryotes o Single-celled protists can be very complex, as all biological functions are carried out by organelles in each individual cell o Protists, the most nutritionally diverse of all eukaryotes, include:  Photoautotrophs which contain chloroplasts  H
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