Bio 171 Exam 3

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Genetic Drift

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any change in allele frequencies in a population that is due to chance. Causes allele frequencies to drift up and down randomly over time - random w/ respect to fitness. The allele frequency changes it produces are not adaptive. - most pronounced in small populations

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sampling error

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Allele frequencies change due to blind luck

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Founder Effect

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A change in allele frequencies that occurs when a new population is established occurs when a group of individuals emigrates to a new geographic area and establishes a new population

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Genetic Bottleneck

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a sudden reduction in the # of alleles in a population. drift occurs and causes a change in allele frequencies.

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Gene Flow

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the movement of alleles from one population to another. Occurs when individuals leave one population, join another, and breed.

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Mutation

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any change in the hereditary material of an organism. creates entirely new alleles.

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Deleterious alleles

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alleles that have lower fitness.

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Beneficial allele

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an allele that allows individuals to produce more offspring, should increase in frequency in the population due to natural selection.

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Central Dogma of Molecular Biology

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summarizes the flow of info in cells. It states that DNA codes for RNA, which codes for proteins: DNA  RNA  Proteins

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Genetic code

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the rules that specify the relationship between a sequence of nucleotides in DNA or RNA and the sequence of amino acids in a protein

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Polyploidy

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change in the # of each type of chromosome present

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Aneuploidy

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the addition or deletion of a chromosome.

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Silent mutation

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point mutation that has no effect at all, said to be neutral on an individual’s fitness.

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Chromosome inversion

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segments may become flipped or rejoined

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Chromosome Translocation

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segments become attached to a different chromosome

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Speciation

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the evolution of two or more distinct species from a single ancestral species  a new branch has been added to the tree of life.

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Species

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an evolutionary independent population or group of populations

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1. Biological Species Concept

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reproductive isolation  no gene flow occurs between populations that are reproductively isolated from each other

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- Prezygotic- Isolation

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prevents individuals of different species from mating (occurs before mating can occur)

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- Postzygotic-Isolation

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offspring of matings between members of different species do not survive or reproduce (mating produces offspring w/ low fitness)

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2. Morphospecies Concept

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– identify evolutionary independent lineages by differences in size, shape, or other morphological features. Distinguishing features are most likely to arise if populations are independent and isolated from gene flow. Widely applicable.

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3. Phylogentic Species Concept

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reconstructing the evolutionary history of populations

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Monophyletic = clade = lineage

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consists of an ancestral population, all of its descendants and only those descendants.

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a species is defined as

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the smallest monophyletic group in a phylogentic tree that compares populations.

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Subspecies

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populations that live in discrete geographic areas and have distinguishing features, such as coloration or calls, but are not considered distinct enough to be called separate species.

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Allopatric speciation

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speciation that begins w/ physical isolation via either dispersal or vicariance

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dispersal

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• Populations can disperse to a new habitat, colonize it, and found a new population

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vicariance

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• A new physical barrier can split a widespread population into two or more subgroups that are physically isolated from each other. a physical splitting of habitat (mountains, river)

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populations live in sympatry when...

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When populations or species live in the same geographic area, or at least close enough to one another to make interbreeding possible

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Sympatric Speciation

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speciation that occurs even tho gene flow is possible
**Even tho sympatric populations are not physically isolated, they may be isolated by preferences for different habitats.

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Mutation called polyploidy

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mutant individuals have more than two sets of chromosomes

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Polyploidization

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genetic isolation is created by formation of polyploidy individuals that can breed only with each other

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- Autopolyploid

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individuals are produced when a mutation results in a doubling of chromosome number and the chromosomes all come from the same species.

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- Allopolyploid

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individuals are created when parents that belong to different species mate and produce offspring where chromosome number doubles. Allopolyploid individuals have chromosome sets from different species

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Reinforcement

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natural selection for traits that isolate populations  selected traits reinforce differences that developed while the populations were isolated from one another.

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Hybrid Zone

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a geographic area where interbreeding occurs and hybrid offspring are common -- Occurs when hybrid offspring are capable of mating and producing offspring and have features that are intermediate between those of the two parental populations

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Hybridization

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Hybrid offspring create a third, new species that has unique characteristics of alleles from each parental species and therefore different characteristics.

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Phylogeny

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the evolutionary history of a group of organisms (usually summarized and depicted in the form of a phylogenetic tree

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Phylogenetic tree

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shows the ancestor-descendant relationships among populations or species, and clarifies who is related to whom.

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- Branch

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a population thru time

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- Node

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the point where two branches diverge (a fork) – the point in time when an ancestral group split into two or more descendant groups

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- Tip

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the endpoint of a branch (terminal node) – a group (a species or larger taxon) living today or one that ended in extinction.

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Phenetic Approach

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estimating trees is based on computing a statistic that summarizes the overall similarity among populations, based on data`

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Cladistic Approach

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inferring trees is based on the realization that relationships among species can be reconstructed by identifying shared derived characters, or synapomorphies (“union-forms”) in the species being studied

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Synapmorphy

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a trait that certain groups of organisms have that exists in no others  allow biologists to recognize monophyletic groups – aka clades or lineages.

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Homology

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(same-source) occurs when traits are similar due to shared ancestry

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Homoplasy

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(“same-form”) occurs when traits are similar for reasons other than common ancestry.

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Convergent Evolution

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occurs when natural selection favors similar solutions to the problems posed by a similar way of making a living

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Parsimony

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the logical principle that the most likely explanation of a phenomenon is the most economical or simplest. When applied to comparison of alternative phylogentic trees, it suggests that the one requiring the fewest evolutionary changes is most likely to be correct.

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Fossil

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piece of physical evidence from an organism that lived in the past

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Fossil Record

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the total collection of fossils that have been found throughout the world

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• Habitat Bias

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organisms that live in areas where sediments are actively being deposited (beaches, mudflats, swamps) are much more likely to from fossils than are organisms that live in other habitats.

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• Taxonomic Bias

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Slow decay is almost always essential to fossilization, so organisms w/ hard parts such as bones or shells are most likely to leave fossil evidence.

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• Temporal Bias

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Recent fossils are much more common than ancient fossils. The older a fossil is, the more likely it is to be demolished.

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• Abundance Bias

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Fossil record is weighted toward common species. Organisms that are abundant, widespread, and present on Earth for long periods of time leave evidence much more often than do species that are rare, local, or ephemeral (short-lived).

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- Precambrian

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included the origin of life, photosynthesis, the oxygen atmosphere (1) life was exclusively unicellular for most of earth’s history
(2) oxygen was virtually absent from the oceans and atmosphere for almost 2 billion years after the origin of life.

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- Phanerozoic Eon

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divided into 3 eras

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1. Paleozoic Era

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“ancient life” the origin and initial diversification of the animals, land plants, and fungi, as well as the appearance of land animals.

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2. Mesozoic Era

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“middle life” Age of Reptiles – gymnosperms = dominant plants and dinosaurs = dominant vertebrates

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3. Cenozoic Era

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“recent life” Age of Mammals – mammals diversified after the disappearance of the dinosaurs. On land, angiosperms = dominant plants and mammals = dominant vertebrates. Events that occur today are considered to be part of the Cenozoic era.

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Adaptive Radiation

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occurs when a single lineage produces many descendant species that live in a wide diversity of habitats and find food in a variety of ways.

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Mass extinction

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the rapid extinction of a large number of lineages scattered throughout the tree of life  60% of the species present are wiped out w/in 1 million years

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Background extinction

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refers to the lower, average rate of extinction observed when a mass extinction is not occurring.

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Conjugation

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takes place when a physical connection, called a conjugation tube, forms between two bacterial cells. Sometimes followed by an event called plasmid transfer.
Conjugation can result in genetic recombination.

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prokaryotic

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lack a membrane bound nucleus

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Lineages in the domains of bacteria and archaea are

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ancient, diverse, ubiquitous, and abundant.

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Pathogenic

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bacteria that cause disease

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Koch’s Postulates

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to establish a causative link between a specific microbe and a specific disease, 4 criteria must be met:
1. The microbe must be present in individuals suffering from the disease and absent from healthy individuals
2. The organism must be isolated and grown in a pure culture away from the host organism
3. If organisms from the pure culture are injected into a healthy experimental animal, the disease symptoms should appear.
4. The organism should be isolated from the diseased experimental animal, again grown in pure culture, and demonstrated by its size, shape, and color to be the same as the original organism.

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Germ theory of disease

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laid the foundation for modern medicine, holds that infectious diseases are caused by bacteria and viruses

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Viruses

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acellular particles that parasitize cells

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Antibiotics

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molecules that kill bacteria

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Bioremediation –

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the use of bacteria and archaea to degrade pollutants.
- Fertilizing contaminated sites
- “seeding” or adding specific species of bacteria and archaea

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Extremophiles

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bacteria/archaea that live in high salt, high temp, low temp, high pressure habitats.

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cyanobacteria

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The oxygen we breathe comes from cyanobacteria: a lineage of photosynthetic bacteria

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Aerobic respiration

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uses oxygen

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Anaerobic respiration

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does not use oxygen, may use nitrate or sulfate

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nitrogen fixation.

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The only organisms that are capable of converting molecular nitrogen to ammonia are bacteria

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Direct sequencing

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allows biologists to identify and characterize organisms that have never been seen.

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Tree of Life

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Bacteria, Archaea, and Eukarya  bacteria were the first to diverge from the common ancestor of all living organisms. Archaea and Eukarya are more closely related than to bacteria.

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Monophyletic Group

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consists of an ancestral population and all of its descendants. Aka clades/lineages.

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Morphological Diversity

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size varies, shape varies, mobility varies. Differences in composition of cell walls and plasma membranes.

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- Phototrophs

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“light feeders” use light energy to promote electrons to the top of electron transport chains. ATP is produced by photophosphorylation

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- Chemoorganotrophs

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oxidize organic molecules w/ high potential energy, such as sugars. ATP may be produced by cellular respiration – w/ sugars serving as electron donors – or via fermentation pathways.

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- Chemolithotrophs

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“rock feeders” oxidize inorganic molecules w/ high potential energy, such as ammonia or methane. ATP is produced by cellular respiration, w/ inorganic compounds serving as the electron donor.

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Autotrophs

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organisms that manufacture their own building block compounds

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Heterotrophs

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organisms that acquire building block compounds from other organisms

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The basic chemistry required for photosynthesis, cellular respiration, and fermentation originated in

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bacteria and archaea

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Oxygenic photosynthesis

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uses oxygen

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Anoxygenic photosynthesis

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does not use oxygen

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Virus

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obligate (dependent on host cells), intracellular (cannot replicate unless they enter a cell) parasite (reproduce at the expense of their host cell).
Viruses are NOT cells and are not made up of cells  not considered organisms.

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Bacteriphage

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a virus that infects bacteria

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Epidemic

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a disease that rapidly affects a large # of individuals over a widening area

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Pandemic

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an epidemic that is worldwide in scope (Spanish flu)

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Virulent

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tending to cause severe disease.

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In overall structure, viruses fall into 2 categories

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1. Enclosed by just a shell of protein called a capsid
2. Enclosed by both a capsid and a membrane-like envelope

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Important distinction among viruses

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nonenveloped or enveloped.

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Vaccine

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a preparation that primes a host’s immune system to respond to a specific type of virus.

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Virion

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a mature virus particle

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Lytic cycle

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replicative growth.  viral genome enters host cell and viral or host enzymes make copies of it. The replicative cycle is complete when the virions exit the cell – usually killing the host cell.

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Lysogenic cycle

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viral genome enters host cell, is inserted into the hosts chromosomes, and is replicated whenever the host cell divides. When activated, the viral DNA enters the lytic cycle, leading to production of new virus particles.

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REPLICATIVE CYCLE
Six phases

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1. Entry into host cell – plant viruses = enter after a sucking insect has disrupted the cell wall. Viruses in bacterial cells bind to a specific molecule on cell wall/plasma membrane.
2. Transcription of the viral genome and production of viral proteins – viruses exploit the host cell’s biosynthetic machinery to produce viral proteins
3. Replication of the viral genome – most viruses contain a polymerase that copies the viral genome inside the infected host cell using nucleotides and ATP provided by the host cell
4. Assembly of a new generation of virions – during assembly, the capsid forms around the viral genome.
5. Exit from the infected cell – viruses leave by: budding from cellular membranes or by bursting out of the cell (in general, enveloped viruses bud; nonenveloped burst.
6. Transmission to a new host – transmission = the spread of pathogens from one individual to another

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Retrovirus

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backward virus

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Positive sense virus

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the genome contains the same sequences as the mRNA required to produce viral proteins (genome sequence is the same as viral mRNA)

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Negative sense virus

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the base sequences in the genome are complementary to those in viral mRNAs. (genome sequence is complementary to viral mRNA)

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Ambience virus

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some sections of the genome are positive sense while others are negative sense.

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Emerging disease

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– new illnesses that suddenly affect significant numbers of individuals in a host population.

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Eukarya

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largest and most morphologically complex organisms  algae, plants, fungi, and animals. Eukaryotes are defined by the presence of the shared, derived character called the nuclear envelope.

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Protist

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refers to all eukaryotes that are not green plants, fungi, or animals.

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Protists constitute a paraphyletic group

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they represent some, but not all, of the descendants of a single common ancestor. No synapomorphies define the protists. There is no trait that is found in protists but no other organisms.

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Synapomorphies

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shared, derived traits that distinguish major monophyletic groups

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Endosymbiosis Theory

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– proposes that mitochondria originated when a bacterial cell took up residence inside a eukaryote about 2 billion years ago.

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Symbiosis

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is said to occur when individuals of 2 diff species live in physical contact

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Endosymbiosis

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occurs when an organism of one species lives inside an organism of another species.

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morphological traits played a key role as protists diversified

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- The nucleus and endomembrane system
- Mitochondrion
- Structures for protection and support
- Multicellularity

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Protists feed by

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1. Ingesting packets of food  based on eating live or dead organisms or on scavenging loose bits of organic debris. Engulfing process is possible in protists that lack a cell wall.
2. Absorbing organic molecules directly from the environment  some are decomposers.
3. Performing photosynthesis  endosymbiosis theory contends that the organelle where photosynthesis takes place in eukaryotes originated when a protest engulfed a cyanobacterium.

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Secondary Endosymbiosis

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occurs when an organism engulfs a photosynthetic eukaryotic cell and retains its chloroplasts as intracellular symionts

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Amoeboid motion

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sliding movement in some protists

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Animals

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Monophyletic group of eukaryotes that can be recognized by 3 traits:
1. Multicellular
2. Ingest their food
3. Move under their own power at some point in their life cycle.

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Animals are heterotrophs

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they obtain the carbon compounds they need from other organisms.

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consumers

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heterotrophs eat producers and other organisms

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Animals of cells are distinguished by several traits:

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• Cells of animals lack walls but have an extensive extracellular matrix, which includes proteins specialized for cell-cell adhesion and communication
• Only lineage on the tree of life w/ species that have muscle tissue and nervous tissue
• Many animals reproduce sexually and asexually, but no animals undergo alternation of generations
• During an animal’s life cycle, adults of most species are diploid; the only haploid cells are gametes produced during sexual reproduction.

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Body Plan

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animal’s architecture – the major features of its structural and functional design

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Four features define the basic elements of an animal’s body plan

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1. # of tissue layers found in embryos
2. Type of body symmetry and degree of cephalization (formation of the head region)
3. The presence/absence of a fluid-filled body cavity
4. The way in which the earliest events in the development of an embryo proceed.
*The origin and early evolution of animals was based on the origin and elaboration of these 4 features.

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Tissues

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all animals have groups of similar cells that are organized into the tightly integrated structural and functional units called tissues

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Epithelium

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a layer of tightly joined cells that covers the surface (found in sponges)

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Diploblasts

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animals whose embryos have 2 types of tissue layers (“two-buds”) germ layers are called ectoderm (outer) and endoderm (inner). Derm = skin

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Triploblasts

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animals whose embryos have 3 types (“three-buds”) • Ectoderm = covering of the animal
• Endoderm = generates the digestive tract
• Mesoderm = gives rise to tissues in between

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Radial symmetry

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organisms have two planes of symmetry

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Bilateral Symmetry

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have one plane of symmetry  usually long, narrow body.

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Evolution of bilateral symmetry = cephalization =

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the evolution of a head, or anterior region, where structures for feeding, sensing the environment, and processing information are concentrated.