Emma BISC 120 Midterm 2
Terms in this set (163)
How is life defined?
metabolism, reproduction, cellular organization, homeostasis, growth, adaptation, response to stimuli
How many years ago did Earth form?
4.6 billion years ago
When did the Earth "cool down" or have a stable hydrosphere?
4.2 billion years ago
Prebiotic Chemistry-- years ago and evolution taking place
-Abiotic synthesis of small organic molecules
-Joining of these small molecules into macromolecules
-Packaging of molecules into "protocells"
simple organic compounds were changed by heat and solar radiation into more complex organic compounds
Theories/experiments around abiotic synthesis
-Stanley Miller experiment: applied formation of amino acids to volcano-like conditions
-Hypothesis that organic molecules were first produced at hydrothermal vents
-Hypothesis that meteorites were the source of organic molecules
What substrate was believed to have hosted the formation of the first macromolecules?
-aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure
-exhibit simple reproduction/metabolism
-potential spontaneous formation
Pre-RNA World- how many years ago, why RNA and not DNA?
-the first genetic material was probably RNA, not DNA
Reasons: RNA can carry out many functions
Reasons supporting the RNA world hypothesis (functions of RNA above DNA)
RNA can carry out many functions:
1. Catalyze reactions (ribozymes)
2. Central to protein synthesis
4. Stores information
First direct evolution of life? BYA?
Last Universal Common Ancestor (LUCA)
Hypothetical early cell, or group of cells, that gave rise to all subsequent life on Earth.
--> anaerobic, chemo autotrophic, thermophilic (may have lived in hydrothermal vents)
Formation of Earth --> Stable Hydrosphere --> pre biotic chemistry --> pre-RNA world --> RNA world --> first direct evidence of life --> LUCA
used ocean to create spark in atmosphere creating amino acids...hypothesis that earth's ocean and atmosphere formed a sort of "prebiotic soup" of amino acids in which life originated
principle of superposition
Exceptions to superposition
What is Original Horizontality?
Layers of sediment are originally deposited horizontally. The principle is important to the analysis of folded and tilted strata. Steno's law.
The processes that alter the Earth are uniform through time (Lyell)
Production of sediment particles
-erosion (water, wind, ice, ppl)
-volcanic eruption (minerals, volcanic glass, pulverized rocks)
-organisms (calcite, coal)
Biases in the fossil record (what kind of organism is most likely to appear?)
-Many things don't fossilize (filters exist between death of an organism and its discovery)
-Organism is more likely to appear in fossil record if it...
has hard parts
is abundant and widespread
exists for a long time
lies in a habitat conducive to deposition
method used to determine the age of rocks using the rate of decay of radioactive isotopes
Theory of Serial Endosymbiosis
mitochondria and chloroplasts were formerly small prokaryotes living within larger cells
A burst of evolutionary origins when most of the major body plans of animals appeared in a relatively brief time in geologic history
time period on the geological time scale when complex life forms were developing
Earliest terrestrial plants
-primitive vascular system
Earliest terrestrial animals
-included organisms similar to modern millipedes, centipedes, spiders
Major changes can be attributed to...
Plate tectonics/continental drift; mass extinctions; adaptive radiations
Current species estimates are bad because...
Taxonomic, geographic biases, taxonomic biases, taxonomists are going extinct, difficulty of documenting extinction
Past species estimates are bad because...
Most things don't fertilize, fossils are nearly impossible to ID to species, the fossil record is biased
~250 MYA, Biggest mass extinction event- Earth lost 96% of all marine organisms
-65 million years ago
-asteroid in Yucatan peninsula Mexico
-debris block sun
-extinction of many marine and land mammals, dinosaurs, birds spared
Adaptive radiations definition
Periods of evolutionary change where groups of organisms form many new species whose adaptations allow them to fill different ecological roles
Adaptive radiations can occur when...
-Organisms colonize a new habitat
-Groups go extinct
-Key innovations evolve
Why we may be in midst of a 6th mass extinction
-More species (or families) than ever before, and extinction rates are rising very quickly
-Current extinction rates at least 100-1000x above background
The evolutionary history of a species or group of related species
The science of naming and classifying organisms
Scientific system for classifying organisms
classification of organisms by their order of branching on an evolutionary tree
Old-school taxonomy includes...
Binomial nomenclature and hierarchical classification system
A taxonomic grouping that includes an ancestral species and all of its descendants.
ancestor and some of its descendants
descendants without an ancestor
New proposed classification system
Groups of organisms that share an immediate common ancestor and hence are each other's closest relatives.
In a specified group of organisms, a taxon whose evolutionary lineage diverged early in the history of the group.
characters in different organisms that are similar because they were inherited from a common ancestor that also had that character
similarities that arise through convergent evolution
Analogous structures that have evolved independently.
one biological system of classification that is based on phylogeny
simplest phylogeny is the best
Most likely tree given computational analysis is the best
species or group known to have diverged before the lineage that includes the species being studied
a group of organisms believed to have evolved from a common ancestor.
Two part format for scientific names
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (Dumb kids playing catch on freeway get smushed)
Which two are closely related?
Fungi, Plants, Animals
Eubacteria, Eukarya, Archaea
Annelids, Mollusks, Arthropods
1. Fungi and Animals
2. Eukarya and Archaea
3. Annelids and Mollusks
Molecular phylogenies rely on two types of homologous genes...
Orthologous and Paralogous
Homologous genes passed in a straight line from one generation to the next. (found in diff. species as a result of speciation)
Homologous genes that are found in the same genome as a result of gene duplication. (parallel)
A way of measuring absolute time of evolutionary change based on the observation that some genome regions appear to evolve at a constant range
states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection (developed by Motoo Kimura)
Came up with the Neutral theory of molecular evolution
Difficulties with molecular clocks
-Clock rates vary among genes and among species
-Clock rates need to be calibrated with independent data
- many estimates/ assumptions are likely to have a high degree of uncertainty
- many irregularities caused by natural selection and or evolutionary fluctuations
Practical applications of phylogenetic
1. Spread of HIV
2. HIV infections in Libyan hospital
3. Source of SARS
4. MERS source and transmission
5. H1N1 outbreak
alleged patient zero of HIV
How was the Libyan medics proved innocent?
2. Many children co-infected with hepatitis, and one child infected with HIV after medics were arrested
Source of SARS
Phylogeny supports the virus originated in bats (Civet or Horseshoe)
MERS source and transmission
--> diagnosed "two mutations were critical for bat-to-human transmission of MERS coronavirus"
--> why do bats host so many emerging viruses? (ex: Bats spread Ebola bc they're evolved not to fight viruses"
Source of the 2009 H1N1 Outbreak
D Virus derived from avian, swine, and human strains, all circulating in pigs
--> resulted from recombination events that incubated for years before being detected
To resolve more recent divergences we use rapidly evolving sequences like...
We used to use conserved sequences because other gene sequences are more complicated due to...
Horizontal gene transfer
What an animal does and how it does it (includes muscular and non-muscular activity)
-Focus on external/environmental stimuli that trigger a behavior
-Focus on genetic, anatomical, and physiological mechanisms underlying a behavior
-Address the evolutionary significance of a behavior
the study of animal behavior, especially under natural conditions
Fixed action pattern
A sequence of unlearned, largely unchangeable behaviors
Examples of Fixed action patterns
Yawning, goose egg retrieval, sex change in clown fish, sticklebacks (red belly of an intruding male stimulates attack from resident male)
Includes both learned and innate components.
Develops only during the critical period
3 Examples of The Evolution of Social Behavior
Sexual selection, altruism and kin selection, human sociobiology
-Selection for mating success
-May oppose natural selection
-May lead to sexual dimorphism
-Involves intra-sexual (same-sex) competition, and inter-sexual choice (female choose)
Asymmetries in sexual reproduction
-Females have larger parental investment (PI)
-Female productive success is low and stable- limited by number of pregnancies she can carry
-Male reproductive success is highly variable- limited by number of successful matings
Consequences of asymmetries in sexual reproduction
-Sex with low PI should be competitive
-Sex with high PI should be choosy (to find the best partner)
Altruism and Kin selection
Individuals do not act "for the good of the species" cause cheater alleles will win
the principle that for natural selection to favor an altruistic act, the actor must be related enough to the recipient for it to outweigh the cost to the actor...
rB > C (B = benefit to the recipients, C = cost to the actor)
Sociobiology and example
The study of social behavior based on evolutionary theory
ex: Some studies show that women prefer mates who differ at MHC loci involved in immunity
Behavior that reduces an individual's fitness while increasing the fitness of another individual (queen bee)
the total effect an individual has on proliferating its genes
Nat. selection favors individuals who perform altruistic acts for their kin (who are related...) ---> or Natural selection favors altruistic behavior by enhancing the reproductive success of relatives
Sex roles reversed in species examples
Seahorse and pipefish -- males carry young and provide parental care
The tactic an individual adopts is determined by some aspect of state (ex: clown fish -- when dominant female dies her male mate changes sex and replaces her)
Conservation biology is a young field that integrates...
Ecology, behavioral ecology, physiology, molecular biology, genetic, and evolution (focusing on the prior two-- conservation and genetics)
Why preserve diversity?
For its own sake (moral and ethical reasons.
For our own sake (pharmaceuticals)
Loss of biodiversity has economic costs due to lost economic services such as...
Pollination, nutrient cycling, purification, detoxication, moderation of weather extremes
How is genetics used to aid conservation?
1. diagnose populations or species at genetic risk
2. prioritize populations or species worthy of protection
Small populations may be at genetic risk due to...
inbreeding depression and low genetic variation
breeding with close relatives increases the chance the parents will share the same deleterious recessive alleles (inbreeding of ancestry of King Charles II of Spain)
Low genetic variation
Can result in reduced ability to adapt to environmental changes, such as alterations in climate or the introduction of new pathogens
--> can't adapt to new threats; can lead to extinction vortex
A downward population spiral in which inbreeding and genetic drift combine to cause a small population to shrink and, unless the spiral is reversed, become extinct.
(ex: prairie chicken)
Effective population size
Th size of an ideal population that would lose genetic variation due to genetic drift at the same rate as the actual population (Ne)
Does the tuatara deserve high priority conservation?
Yes- Tuatara is phylogenetically unique- not a lizard, its own lineage; they deserve high priority
Do Catalina Bison deserve high priority for conservation?
Yes- interesting because genetic data says 45% of Catalina bison have cattle mtDNA
Does the San Clemente Loggerhead Shrike deserve high priority for conservation
Pros for listing: Rare
Against listing: not clear that the subspecies is morphologically unique; genetic data suggests hybridization among subspecies
Does the San Clemente island fox deserve priority for conservation?
For listing: rare; morphologically and genetically unique
Against: foes eat endangered shrikes...
Extinction vortex steps
Small population --> inbreeding and genetic drift --> loss of genetic variability --> lower individual fitness and lower population adaptability --> lower reproduction, higher mortality --> even smaller
Ideal populations have...
Equal sex ratios, equal family size, random mating, no fluctuations in population size, no overlapping generations
Prioritize populations or species species worthy of protection...
-Things at risk for genetic drift
-Pure species rather than hybrids
(Ex: Tuatara, San Clemente Loggerhead Shrike, San Clemente Fox)
In total, ecosystem services are estimated to be worth at least...
125 trillion per year ($$$)
Are viruses alive?
Generally no, do not fit the definition of life besides "adaptation".
1st discovery of a virus
tobacco mosaic disease
What are viruses?
Viruses are not cells- rather, are infectious particles consisting of nucleic acids in a protein shell (capsid), and in some cases, a membranous envelope
What are the hosts for viruses?
Bacteria (for bacteriophage,) archaea, plants, animals, fungi, protists
Major viral groups
Tobacco mosaic virus, adenoviruses, influenza viruses, bacteriophage T4, pandoravirus
What's so special about the Pandoravirus?
-Big in size and genome size
-invent their own genes
-suggest the existing of a 4th domain of life
How can viruses (phage and animal viruses) replicate?
Only replicate in host cells, use the host's enzymes, ribosomes, tRNA, amino acids, ATP, and other molecules
Phage: Lytic or lysogenic cycle
Animal virus: often involve a viral envelope
Virulent phages undergo a(n) ____ life cycle, whereas temperate phages are capable of undergoing a(n) ____ cycle.
a. lytic (destroys host to reproduce)
b. Lytic and lysogenic (doesn't destroy host) cycles
HIV replication; why is it hard to find a cure?
inserts itself into genome and stays there for life
--> infects helper T-cells, and has a rapid rate of mutation
Influenza virus (animal)
RNA virus, not retrovirus
DNA virus, infects the nucleus of host cells (neurons), and can stay in hibernation form for years
--> in rare cases, spreads to the brain
Host range definition
range of different species/tissue types that viruses are able to infect
Host range examples
-Some viruses have broad range (West Nile virus infects mosquitos, birds, horses, and humans)
-Some are species-specific (measles only infects humans)
-Some viruses are tissue specific (human cold only infects upper respiratory tract)
-Recombinant viruses can expand host range
2 kinds of sub viral pathogens
Viroids and prions
Free, infectious circular particles that cause disease in plants
infectious protein particles (cause brain diseases)
Why is the origin of viruses so difficult to discern?
Due to horizontal gene transfer and lack of fossil record
Why cells most likely evolved before viruses
1. Viruses cannot produce without cells
2. Both viruses and bacteria may have evolved from a fully functioning, self-replicating cell that lived about 3.4 BYA
3. While bacteria have become more complex over time, viruses may have shed genes until they could no longer reproduce on their own
Viruses in the ocean
Around 10^30 viruses in ocean (v. abundant)
Around 10^23 viral infections occur every second in ocean
viruses catalyze the movement of nutrients from organisms to the DOM and POM pools -- alter carbon cycling
Morphological species concept
Defines a species by structural features (including color) --> most common
-Many species have FEW distinguishing morphological characters
Ecological species concept
Views a species in terms of its ecological niche (where it lives, what it eats)
-often have TOO LITTLE info to apply this concept
Phylogenetic species concept
Defines a species as the smallest group of individuals that share a common ancestor
-Often have too little info to apply this concept
Biological species concept
Defines a species as individuals actually or potentially capable of interbreeding
Biological species concept exceptions
Cannot be applied to...
1. Asexual organisms
3. Organisms that that don't cooperate in controlled breeding studies
Two types of Reproductive Barriers
Prezygotic and Postzygotic
Impede mating or hinder fertilization if mating does occur
Ex: Habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, gametic isolation
Prevent the hybrid zygote from developing into a viable, fertile adult
Ex: Reduced hybrid viability, reduced hybrid fertility, hybrid breakdown
Wrong place; when two species encounter each other rarely, or not at all, because they occupy diff. habitats (not isolated by physical barriers)
Wrong time; Species that breed at different times of the day, diff. seasons, or different years, and therefore cannot mix their gametes (ex: 13 and 17 year cicadas)
No attraction; Courtship rituals and other behaviors unique to a species prevent from breeding
(ex: Dayasan albatross courtship)
Morphological differences can prevent successful mating
Can't fertilize; sperm of one species may not be able to fertilize eggs of another
Reduced hybrid viability
Genes of the different parent species may interact and impair the hybrid's development
(ex: Rana pipiens x Rana sylvatica hybrids do not survive more than a day)
Reduced hybrid fertility
Even if hybrids are vigorous, they may be sterile due to problems at meiosis (ex: male lion and female tiger --> ligers (sterile males)
Some F1 hybrids are fertile, but when they mate with another F1 or with either parent species, offspring of the next gen. are feeble or sterile (ex: tide pool copepod)
Modes of speciation
Allopatric and sympatric
Gene flow impeded by physical or geographic barrier
-Selection and drift lead to reproductive isolation
The process through which new species evolve from a single ancestral species while inhabiting the same geographic region.
-Takes place in geographically overlapping locations
-Can occur through chromosome changes or through non-random mating
-Can be caused by polyploidy
-Could occur by changes in habitat, food preference, or mate choice
(ex: Maggot flies and ciclid fish)
Examples of polyploid plants
Coffee, sugar cane, bread wheat, potatoes, bananas, peanuts, apples
T or F: anthropogenic (something caused by humans) effects may cause species to merge back together?
True- global warming causing polar bears and grizzly bears to mate --> grolar bears
Critiques of Macroevolution
1. Irreducible complexity
2. The evolution of new species is rarely, if every observed
3. Punctuated equilibrium not explained by Darwinian theory
Rebuttal to Irreducible complexity
Pieces of complex systems often have functions of their own
ex: bacterial flagellum
Evolution of new species is rarely, if ever observed rebuttal
1. There has been little time to observe the origin of new species, since human history spans <.006% of biological history
2. We have observed the origin of new experiments (lab selection experiments, arising naturally, spontaneous polyploidy and/or hybridization)
Punctuated Equilibrium rebuttal
1. Punctuations that appear in the fossil record may take tens of thousands of years
2. Periods of apparent stasis bay belie extensive biochemical changes that aren't detectable in the fossil record
3. Slight genetic chances may result in major phenotypic changes
evolution of genes controlling development (ex: heterochrony --> allometry and pedomorphosis)
Important Developmental Change in Evolution
1. Changes in Rate and Timing (Heterochrony)
2. Changes in spatial pattern
Changes in rate in timing (allometry and pedomorphosis)
Sexually mature adults with juvenile morphology (ex: axolotl and puppies)
Changes in the relative growth rate of different body parts
Allometric growth: differential growth rates in different body parts (Ex: baby head)
Changes in Spatial Organization of body parts
Homeotic genes (control body plans) and Hox genes (provide positional info)
Control body plans by controlling the developmental fate of groups of cells (ex: Hox genes)
A class of homeotic cells that provide positional information in animal embryos (UBX suppresses leg formation in insects but not crustaceans; changes caused evolution from fish fins to tetrapod limbs)
Hallmarks of Evolution
1. Evolution is not goal oriented
2. Evolution is not a ladder from simple to complex
3. Novel features often arise through intermediate stages, each of which serve a function
4. Evolution recycles features and put them to new uses
5. Evolution leaves baggage behind
Many characters evolved for purposes other than those for which they are currently used
(ex: feathers from insulation to flight)
--> Hallmark of Evolution for recycling