Prelim 1 Flashcards
Fossil
remains, traces, or impressions of once living organisms ie. skeleton, impression, cast, trace, or coprolite (poop); most found in sedimentary rocks
Forces that impede fossilization
natural processes such as predators/scavengers, bacterial decay (soft tissue), dissolution in water (soft and hard tissue), or physical disturbance (wave action, wind)
Conditions that promote fossilization
rapid burial, protection from physical disturbance ie. quiet, deep water, anaerobic conditions (prevent bacterial decay)
Sedimentary rock formation
formed from the deposition of sediment falling to the bottom of a body of water
What gets preserved in fossils of animals
hard parts ie. teeth, bone, chitinous exoskeleton, or calcium carbonate shells
What gets preserved in fossils of plants
seeds, pollen, leaves, wood, rarely flowers (fragile petals)
What gets preserved in fossils of microbes
bacteria, microbial mats ie. stromatalites are formed from biofilms of cyanobacteria that trap sediment which eventually harden and form layers
Types of preservation
original remains (skeletal body, other body elements), permineralization/petrification, trace fossils, impression fossils, casts and molds
Permineralization/petrification
process where minerals are deposited in tiny holes within bones, or wood and over time completely replacing the original organism and all that remains is a stone structure
Impression fossils
made up of carbonaceous film imprint of an organism
Lagerstatten
German word that means “storage place”, place where fossils are exceptionally preserved (numerous and well preserved)
Burgess Shale
a famous Lagerstatten from the Cambrian which has yielded many of the organisms that contribute to our understanding of the Cambrian explosion
How do we know the age of a fossil?
relative and absolute dating
Geological chronology
the science of dating geological layers and fossils
4 principles relative dating is based on
superposition, original horizontality, lateral continuity, and cross-cutting
Principle of superposition
geological layers are formed by laying one on top of the other so that the youngest layer is on top
Principle of original horizontality
layers are first deposited horizontally and then they may be deformed later such as from the movement of continental plates
Principle of lateral continuity
layers continue laterally over distances; each layer is deposited at the same so that even if erosion has removed some of the layer, the layer is still the same layer after the gap
Principle of cross-cutting
if there is a cross-cutting layer or intrusion in rock layers, the intrusion is always younger than any of the layers it is cross-cutting
Index fossils
fossil organisms that are only found in a particular rock layer and are also geographically widespread so that the layers can be stratiagraphically correlated with each other in different locations according to the principle of lateral continuity
How was geological time scale (GTS) created?
by correlating layers based on index fossils; derived from the spatial distribution of rocks and the vertical sequence of rocks and contained fossils
How/when did absolute dating become possible
with the discovery of radioactivity in the late 19th century
Absolute dating
done by examining the radioactive decay of unstable isotopes
Radioactive decay
decay of a parent isotope gives rise to a stable daughter isotope at some characteristic rate of decay
Which rocks can be absolute dated
only igneous rocks; clock starts ticking when rock solidifies (daughter isotope is 0 in molten rock); sedimentary rock decays too quickly (carbon decays too quickly)
Radiometric dating: half lives
0 half lives = 100% parent isotope; 1 half life = 50%; 2 half lives = 25%; 3 half lives = 12.5% etc.
Uranium-lead effective dating range
10 million - 4.6 billion years
Potassium-argon effective dating range
100,000 - 4.6 billion years
Carbon-14 effective dating range
100 - 100,000 years
Phylogeny
a visual representation of the evolutionary history of populations, genes, and species
Tips of phylogenetic tree
represent groups of descendant taxa; most often species but can also represent molecules or populations
Branches of phylogenetic tree
lineages evolving through time between successive speciation events
Node of a phylogenetic tree
a point in a phylogeny where a lineage splits (a speciation event)
Clade/monophyletic group
an organism and all of its descendants; consists of the most recent common ancestor and all of its descendants
Paraphyletic clade
an ancestor and a group of taxa but it is not monophyletic because some of the descendants are missing
“Tree Thinking”
using data to construct trees, and reading trees to determine evolutionary relationships
Pedigree vs Phylogeny
pedigree: individuals, 2 ancestors, unlimited descendants; phylogeny: populations, 1 ancestor, 2 descendants (except for a polytomy)
How do we infer relatedness in a phylogeny
based on sharing of derived characteristics
Character
anything inherited (genetically determined, or DNA sequence itself) that can be used to determine relationships; morphological, physiological, (traits) or molecular (DNA sequence)
Ancestral state
the historical state of a character
Derived state
the more recently evolved state of a character
Synapomorphies
shared derived traits which are phylogenetically informative
Polytomy
describes an internal node of a phylogeny with more than 2 branches (the order in which the branching occurred is not resolved)
Choosing optimal phylogeny
select tree with the smallest number of character state changes (most common for morphological characters); select tree that is the most probably (based on probability methods, typically used for DNA mutations)
What are phylogenies used for?
map characters, trace the origins of epidemics, or to inform taxonomy; is it NOT a depiction of the degree of similarity
Bootstrap/posterior probability as branch support
statistical confidence assigned to certain branches
Neutral theory of molecular evolution
at the fine scale level, most new mutations are not favored or disfavored by natural selection (synonymous mutations); neutral mutations will arise at random and random processes (ie. genetic drift) will determine their fate in a population; since mutations arise at an average rate, they can be used to date the nodes on a molecular phylogeny
Graphic variations of a phylogeny
Cladogram (branching only); Phylogram (degree of change); Chronogram (calibrated to real time)
Parsimony inference
the best phylogeny is the one that explains the observed character data by positing the fewest evolutionary changes
Homology
shared traits because they are inherited from a common ancestor
Autapomorphy
a trait that does not help us distinguish between two trees because it is only in one lineage
Homoplasy
when similar characteristics are not due to common ancestry but instead arise by convergent evolution or evolutionary reversals; can create the mistaken impression that two species are closely related when they are not
Vestigial
a trait that has become functionless in the course of evolution (but still is present)
Ideal characters for phylogenies
have low rates of evolutionary convergence and/or reversal
What do different speeds of evolving characters show ie. fast vs slow)
slowly evolving characters ( including DNA sequences) can show the relationship between distant taxa while rapidly evolving characters (including DNA sequences) can reveal relationships between closely related taxa
Index case
source of the outbreak ex. someone who is initially affected brings a human pathogen to a new geographic location and transmits the disease to a few other recipients
Outbreak
when a disease continues to be transmitted
Last Universal Common Ancestor (LUCA)
molecular characteristics: used nucleic acids (DNA OR RNA) as hereditary material, used a molecular mechanism to replicate this material, used the same triplet genetic code for amino acids, used similar biochemical pathways for energy ie. ATP;
cellular characteristics: had a plasma membrane, unicellular, lacked organelles
Who are the prokaryotes?
archaea and bacteria; not monophyletic
Characteristics of Prokaryotes
always unicellular but are capable of forming large colonial groups called biofilms ie. dental plaque; divide by binary fission, horizontal (lateral) gene transfer
Stramatolites
rocks that are formed from biofilms of cyanobacteria trapping layers of sediment; 3.7 bya stramatolites are the earliest evidence of life
Prokaryotes vs Eukaryotes
eukaryotes have a membrane bound nucleus and membrane bound organelles ie. mitochondria and chloroplast
Peptidoglycan
only present in the cell walls of bacteria; gram positive: more; gram negative: less
Membrane linkages between 3 Domains of Life
bacteria and eukarya have ester-linked membrane lipids while archaea have ether-linked membrane lipids which enable arachae to live in extreme conditions since ether linkages are more stable
Coccus/cocci
round, spherical shaped bacteria
Bacillus/bacilli
rod-like shaped bacteria
Spirilium/spirilla
spiral shaped bacteria; have filaments that run along the long axis and use these filaments to move and can be highly mobile
Staphyloccocus
unnamed taxon; genus that contains bacteria which live on your skin; most of the time they are harmless but can cause harmful and even deadly staph infections
Bacillus anthracis
unnamed taxon; source of deadly anthrax
Cyanobacteria
photoautotrophs meaning that they harvest carbon from carbon dioxide and use sunlight to break up the carbon dioxide and make glucose (photosynthesis); gave rise to chloroplasts via endosymbiosis
Proteobacteria
well known human pathogens; exhibit the highest metabolic diversity of any organismal group (including animals); E.coli, Yersinia pestis, Vibrio cholerae, Salmonella
E. coli
proteobacteria; lives in our GI tract but can also cause deadly food poisoning
Yersinia pestis
proteobacteria; cause of bubonic plague
Vibrio cholera
proteobacteria; causes cholera
Salmonella
proteobacteria; causes food poisoning
Spirochetes
spiral shaped bacteria with axial filaments: motile; Lyme disease, syphillis
Chlymdias
small obligate parasites meaning that they cannot live outside of a host; can cause STDs and other strains can cause eye infection and even pneumonia
What synapomorphy unites Eukarya and Archae
having DNA with histones and certain introns
Characteristics of Viruses
don’t have a membrane bound nucleus, lack mitochondria, parasites, lack ATP and molecular machinery for replication
Why are viruses placed outside the tree of life?
they lack ATP and can’t replicate without a host
Binary fission vs. mitosis
binary fission: DNA is replicated, simple, no nucleus; mitosis: chromosomes replicated, forms 2 membrane bound nuclei; both create 2 daughter cells
Characteristics of Archae
no membrane bound nucleus, no membrane bound organelles, no peptidoglycan in cell walls, ether linked membrane lipids, extremophiles but can also be found in soil, ocean plankton and microbiomes
Methanogen
type of archaea; contribute to global warming by producing methane; also present in our gut microbiome
Halophiles
survive in highly saline environments; typically archaea
Characteristics of Eukaryotes
membrane enclosed nucleus, mitochondria, some have chloroplast, relatively large and complex
Origin of eukaryotes
flexible cell membrane (loss of cell wall) -> infolding (increases surface area: volume) -> cytoskeleton forms from microtubules -> internal membranes with ribosomes -> infolded membrane encloses DNA forming the nucleus -> flagellum formed from microtubules -> endosymbios leads to mitochondria and chloroplasts
Endosymbiosis
results from the incomplete phagocytosis of a bacterium where a mutualistic symbiotic relationship forms
Characteristics of Protists
not a monophyletic group, eukarya that are not animals, fungi, or plants,
Alveolates
unicellular protist; has sacs (alveoli) beneath cell membrane, secondary endosymbiosis of red algae; dinoflagellates, ciliates including Paramecium, Plasmodium -malaria
Ciliates
covered with cilia which allows for controlled movement ie. Paramecium
Dinoflagellates
have 2 flagella: one in an equatorial groove and the other longitudinal; tertiary endosymbiosis; themselves endosymbionts of coral; red tide, bioluminescence
Plasmodium - Malaria
intracellular parasites, chloroplast is vestigial, complex of proteins at the apical prominence attach to and penetrate the host cell
Stramenopiles
have 2 unequal flagellas one of which has tubular hairs ; brown algae and diatoms
Brown algae
multicellular, some are very large, secondary endosymbiosis of red algae, found in kelp forests
Diatoms
secondary endosymbiosis of red algae; unicellular, lost double flagella , deposit silica -> shells
Excavates
reduced or lost mitochondria; euglenids, Giardia, Tyrpanosoma-sleeping sickness, Chagas’ disease, leishmaniasis
Giardia
most common intestinal parasite, water borne
Euglenids
have mitochondria, one large anterior flagellum, secondary endosymbiosis of green algae
Trypanosoma
free living or parasite; some cause debilitating and deadly disease; single large mitochondria; sleeping sickness, Chagas’ disease, leishmaniasis
Amoebozoans
lobe-shaped pseudopods, move by cytoplasmic streaming; slime molds, amoeba
Darwin’s 3 Postulates
Natural selection will occur when: 1. individuals are variable in some trait 2. at least some of this variation is heritable 3. there is a struggle to survive or reproduce and some are better at it than others
What causes phenotypic variation?
genetic differences, environmental differences, interactions between genes and the environment; (measurement error, ontogenic differences)
Ontogenic differences
variation in phenotypes across development, occurs mostly before sexual maturation
Heritability
the proportion of within-population variation in a trait that comes from genetic factors
Natural selection
the non-random process by which biological traits become more or less common in a population as a result of the differential reproductive success of their bearers; one mechanism of evolution
Selection differential/coefficient (S)
the difference between the population mean of a trait before and after selection
Response to selection (R)
the difference between the mean of a trait before selection and the mean of that trait in the next generation
Directional selection
favors phenotypes at one end of a distribution, the population evolves in that direction
Stabilizing selection
favors values toward the middle of the distribution; fitness of organisms at either end is lower
Disruptive selection
favors phenotypes toward the ends of the distribution
Frequency dependent selection
occurs when the fitness of a genotype depends on its frequency in a population
Negative frequency dependent selection
a phenotype has the greatest selective advantage if it is rare
Positive frequency dependent selection
a phenotype has the greatest selective advantage if it is common
Hamilton’s rule
a helping behavior can spread in a population if the cost to the donor is smaller than the benefit to recipient weighted by relatedness; if rB > C
Senescence
a decline with age in per capita reproductive performance, physiological function, or the probability of survival
Antagonistic pleiotropy
when a genetic variant with beneficial effects on one trait also has a detrimental effect on some other trait
Fitness
an individual’s proportional representation in the gene pool of subsequent generations; can only be assessed relative to the fitness of other individuals
Direct fitness
determined by the number of offspring an organism produces (and that survive to maturity) over its entire lifetime
Life history
the timing and duration of key events during a liftetime (ie. age and duration of reproduction); often involves tradeoffs between present and future reproduction
Current repro success
number of offspring
Future repro success
of offspring times the likelihood of survival
Survival vs reproduction
inverse relationship; high survival, delayed reproduction; low survival, high reproduction
Extrinsic mortality
the rate at which external events (predation, starvation, infectious disease) leads to death in a population
Intrinsic mortality
the rate at which internal events (aging, disease, mutation) lead to death in a population
Individual selection
differential performance (fitness) of individuals causes some genotypes to replace others
Group selection
differential performance (fitness) of groups of individuals causes some genotypes to outcompete and replace others (populations unstable)
Altruism
behaviors that are costly to the individual performing them but benefit one or more others
Inclusive fitness
direct fitness + indirect fitness
True altruism
reduces inclusive fitness; rare because it is evolutionary disadvantageous
Kin selection
selection arising from the indirect fitness benefits of helping relatives
Locus
the position of a gene on a chromosome
Allele
one copy of a gene at a locus
Genotype
pair of alleles at a single locus; determines phenotype
Microevolutionary forces the disturb Hardy-Weinberg equilibrum
natural selection, non-random mating, genetic drift, gene flow, mutation
Hardy-Weinberg equilibrium
predicts what the allele frequencies and genotype frequencies would be if the population was not experiencing any evolution
Equation for phenotypic variance in a population
Vp = Vg + Ve; Vg = Va + Vd + Vi
Broad sense heritability
H2 = Vg/Vp; proportion of phenotypic variance that is due to genotype
Narrow sense heritability
h2 = Va/Vp; proportion of phenotypic variance that results from additive (simple) genetic variance; remember that Vp = Vg + Ve
Breeder’s equation
R = h2 * S
Plastids
organelles derived from cyanobacterial endosymbionts
