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99 Cards in this Set
- Front
- Back
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Systemic Biology
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The study of the diversity of living organisms, their relationships and evolutionary history
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Phylogeny
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Inferring evolutionary relationships, mathematical structure that models the evolutionary history of a group shows descent relationships of “tips”
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Taxonomy
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Classification
Identification Nomenclature mathematical structure that models the evolutionary history of a group -- shows descent relationships of “tips” |
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MRCA
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Most recent common ancestor
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Monophyletic group
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An ancestor and all of its descendents
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Paraphyletic group
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An ancestor and some, but not all, of its descendants
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Hierarchy
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A general integrated system
comprising two or more levels, where groups (units in the hierarchy) are nested within groups. |
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Phylogenetic Taxonomy
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• Get rid of ranks
• Define taxa by reference to their phylogenetic composition • Given a tree there is no ambiguity as to the clade to which a name applies |
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Autapomorphy
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Unique derived character state
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Synapomorphy
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Shared derived character state
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Plesiomorphy
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Ancestral character state
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Life
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• carrier of encoded information
• metabolism for generating and consuming biochemical energy • replication |
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LUCA
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Sedimentary rocks, 3.7 bya C12/C13 ratio
First cyanobacteria 3.4 bya Features probably similar to modern Bacteria, Archaea |
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Mitochondria
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Proteobacteria
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Chloroplast
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Cyanobacteria
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Proterozoic
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Before multicellular organisms
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Phanerozoic
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After multicellular organisms
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Ediacaran fauna
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Jellyfish, sponges, trace fossils of triploblasts
565–543 Ma |
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The Burgess Shale
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515-520 million years ago
Soft-bodied and hard-shelled animals, tall sponges and algae Bilaterally symmetric Every major modern phylum of animals |
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Diploblastic animals
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Two embryo levels
ectoderm and endoderm e.g. cnidarians, ctenophores |
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Triploblastic animals
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have 3 embryonic tissue types,
ectoderm, endoderm, and mesoderm e.g. bilaterally symmetrical animals |
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Cambrian
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Most animal phylogenies have occured
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Basal lineages
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occur earlier
in the fossil record |
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Phyletic gradualism
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gradullly increasing
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Punctuated Equilibrium
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old species, punctuated
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Punctuated Gradualism
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logarithmic
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Endemic Biotas
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organisms found in limited regions
along with close relatives |
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Law of Succession
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living species in an area
are frequently closely related to fossils in that area, providing evidence that the species of that area evolved there |
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microevolution
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a change in allele frequencies
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polymorphism
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more than two alleles in a population
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point mutation
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frameshift due to extra point, chance errors during synthesis or repair, creates new alleles
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chromosome inversion
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inversion of DNA sequence, radiation, alleles in the inversion are locked into an unit
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gene duplication
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unequal crossing over during meiosis, "extra" gene is free to mutate and perhaps gain a new function
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Polyploidy
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Addition of chromosomes, error in meiosis, can create new species
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variation
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mutation, migration, random genetic drift, selection
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phenotype
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any observable and measurable characteristic of an organism
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phenotypic variation
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genetic and environmental
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polygenic
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variation no longer discrete
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evolution
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change in heritable mean phenotype, variation must be heritable
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h^2
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heritability
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natural selection
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a difference, on average, between the
survival or reproduction of individuals with certain phenotypes compared to individuals with other phenotypes *because they carry those phenotypes |
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selectively advantageous
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they survive better or reproduce better
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Evolution by natural selection
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1. Individuals in the population vary in phenotype
2. Variation in phenotype is heritable 3. Some individuals survive or reproduce better than others 4. Survival and reproduction are nonrandom with respect to phenotype |
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adaptation
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the population comes to look like
(and be like genetically) the individuals that survive and reproduce the best Natural Selection produces |
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fitness
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the extent to which an individual contributes genes
to future generations |
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Directional Selection
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goes away from the mean, selection for/against homozygote
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stabilizing selection
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cause the mean to be the same but less variation
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diversifying selection
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less in the middle but the mean still stays the same
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gene pool
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the totality of the alleles of a given sexual population that
could be contributed by members of one generation to members of the next generation |
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H-W equilibrium
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no change in allele frequency
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Hardy Weinberg assumptions
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1. diploid, sexual organisms
2. random mating 3. No mutation 4. No gene flow 5. No genetic drift 6. No selection |
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gene flow
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the movement of alleles from one population to another
population by movement of individuals or gametes homogenizes allele frequencies |
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genetic drift
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The change in gene frequencies
due to chance events or sampling processes |
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chance effect
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•mortality,predation, disease
•differences in offspring # •gamete frequencies = expected •failure to mate |
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characteristics of drift
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• causes random fixation of alleles
• more powerful (changes allele frequencies faster) in small popns • leads to loss of heterozygosity |
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founder event
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establishment of a new population by a small
number of individuals |
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founder effect
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A change in allele frequencies that occurs
after a founder event due to genetic drift |
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inbreeding depression
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decline in fitness of inbred progeny
relative to outcrossed ones |
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effective population size
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The size of an idealized breeding
population that would lose genetic variation via drift at the same rate as is observed in an actual population |
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adaptation
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a trait that evolved for its current role due to natural selection
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exaptation
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evolved for some other role &
later co-opted for current role |
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preadaptation
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an earlier stage of an exaptation
(when trait had a different role) |
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aptation
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a general term for a trait that is
beneficial |
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Sarcopterygians
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walked on lake bottoms, walked on muddy surrounds of waters edge, and walked on muddy surrounds of
waters edge. |
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Hypothesis of Adaptation
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Examine current utility
A) Is structure consistent with function? 1. observation: e.g., nectar feeding & bill morphology 2. experimentation: e.g., fruit fly wing patterns 2. Historical inference A) Concentrated changes test B) Phenotypic convergence (analogous solutions to recurrent problems) |
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Concentrated changes test
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Determines if there is an evolutionary correlation between a trait and its function
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the adaptationist program
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* all traits are for something
* all traits are optimized by natural selection Flaws * some traits may be neutral * traits may not be optimal in all contexts |
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neutral variation
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1) Nucleotide variation may be neutral
2) Phenotypic variation may be neutral |
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trade-offs
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1) Ecological trade-offs
different environments favor different trait values 2) Functional trade-offs traits must adhere to physical or physiological “rules” |
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genetic constraint
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when a species lacks the genetic
variation that is required to produce a potentially adaptive trait |
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Three components of fitness
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survival, fecundity, mating success
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sexual selection
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Differential mating success (among members of same sex)
caused by heritable trait differences that confer a mating advantage |
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mating success
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number of mates secured by an individual
across lifespan |
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sexual dimorphism
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A difference between the phenotype of
females & males within a species |
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parental investment
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females more than males
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gamete investment
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female more gamete investment
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male-male selection
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type of sexual selection, fighting between men for mates, sperm competition
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material benefits
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• choosy females may benefit directly by acquiring resources
• better male competitors may acquire more mates by defending access to or providing superior resources larger nuptial gifts, better mate feeding and parental care |
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good genes benefit
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choosy females may benefit indirectly by mates with good
viability genes |
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pre-existing sensory bias
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-a signal is favored because it “exploits” a
sensory bias in the receiver (female) and thereby confers a mating advantage to the sender (male). |
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Fisher's run-away sexual selection
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1). Advantageous variation in male trait arises
2). Genetically based female preference for trait is favored intersexual selection 3). Genetic correlation established between male trait and female preference 4). Trait spreads in population because females choose it, and indirectly choose preference for it. If average female preference is slightly greater than average male trait, trait value will run-away. |
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intrasexual selection
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sperm competition
and combat |
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intersexual selection
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good genes, direct
benefits, sensory bias, and runaway mechanisms |
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altruism
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behavior that decreases the fitness of the
ACTOR and increases the fitness of the RECIPIENT |
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direct fitness
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results from personal reproduction
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indirect fitness
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results from additional reproduction
by relatives that is made possible by an individual’s actions (above and beyond what they would have achieved on their own) |
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inclusive fitness
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the sum of an individual’s reproduction through
relatives made possible by its action (indirect fitness) and its own reproduction (direct fitness) |
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kin selection
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mechanism of increasing inclusive fitness
through apparent altruism need to recognize kin |
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Hamilton's rule
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Br-c>0
B=benefit to recipient r=coefficient or relatedness c=cost to actor |
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eusociality
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extreme altruism
1. Overlapping generations 2. Cooperative brood care 3. Reproductive and non-reproductive castes |
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Haploploidy
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A reproductive system in which males
are haploid and develop from unfertilized eggs, while females are diploid and develop from fertilized eggs females maximize their inclusive fitness by helping their sisters rather than producing offspring |
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Reciprocal altruism
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an exchange of altruistic acts, separated
in time, between two individuals 1. Animals must be long-lived (lots of time for reciprocation) 2. Animals must live in stable groups (time for reciprocation) 3. Must be able to recognize cheaters (good memories…) 4. No hierarchy to altruistic interactions (symmetrical) |
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Life History
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an individual’s pattern of allocation, throughout life,
of time and energy to various fundamental activities, such as growth, repair of cell and tissue damage, and reproduction. |
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the darwinian demon
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Lives forever
Matures at birth Gives birth to huge numbers of offspring |
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Rate of living age theory
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(1) Aging rate (life span) correlated with metabolism
“live fast, die young” wrong |
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tradeoff between survival and reproduction
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more mating, less survival
invest more in early reproduction and lifetime reproduction goes down |
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ecological mortality
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mortality due to extrinsic factors like predation, accidents
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intrinsic mortality
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mortality due to intrinsic factors such as wearing down of body parts
Delayed senescence in island population -lower mortality rates -late-acting deleterious alleles are exposed to selection & purged. |
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clutch size
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more eggs would decrease
probability of offspring survival smaller than optimal |
