Evolution Exam I

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Monophyletic

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– contains all the descendants of a common ancestor

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Paraphyletic

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– contains some, but not all, the descendants of a common ancestor (e.g., Reptilia)

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Polyphyletic

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– a group that consists of unrelated lineages, each more closely related to other
species not placed in the taxon

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Convergence

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adaptation of structures for similar functions
-e.g., various modified structures that enable vines to climb
-example of homoplasy-structures with same function but different origin-occurs because different organisms are exposed to the same selective pressures like whale and fish body shape

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Suboptimal design

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making something work from what is available rather than what is ideal
– trachea would be better behind esophagus because food must pass over the trachea to reach the esophagus
-the human eye has a blind spot where the optical nerve attaches to the retina
-human body structure, e.g. prone to back and joint problems, varicose veins and unprotected internal organs

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3 types of genomes

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-nuclear, mitochondrial, and chloroplast data

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nuclear genome

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-bi-parentally inherited- 30-45 thousand genes, 2 alleles, crossover mixes chromosomes which can mess up phylogenetic trees, genes that code for protein (which are under selection because they are an expressed physically), introns are not under natural selection because they are not physically expressed-may still evolve due to things like genetic drift, multiple codons code for amino acids (often condons with different 3rd position often code for the same protein-3rd codon would not be under natural selection but the first 2 would)-different parts of the genome are evolving at different rates due to different natural selection constraints

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mitochondrial and chloroplast genomes

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- from one parent- mammalian mitochondrial DNA comes from mother as a function of fertilization (meiosis produces egg that dumps chromosomes and has 23 haploid chromosomes and organelles, sperm is little more than 23 chromosomes with just a little mitochondria to power flagella)-repair mechanisms during mitosis better in nuclear dna so end up with more mutations in mitochondria and chloroplast dna (if looking at coding data-noncoding nuclear dna might have more mutations due to lack of selection)

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Geographic distributions

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flightless bird (ostriches, emus, and rheas) are closely related and are similar morphologically, yet they are distributed in Africa, Australia and South America – they shared a common ancestor before the land masses separated

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Transitional or Intermediate forms

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show a combination of traits typical to ancestor and descendant populations
-in the fossil record, horses from 3-toed to 1, whales from land to sea, birds to dinosaurs (archaeopteryx), fish to amphibians (Tiktaalik roseae-which was found when scientists searched in fossils from the time frame when such an intermediate should have existed)
-differences in DNA sequences range from almost none among very closely related species through increasing degrees of difference as we compare more remotely related taxa

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phyletic evolution

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-linear progression of one species to another-used to think horse evolution was phyletic but is not, also used to think human evolution was phyletic but finding evidence that there were many groups of lineages with many ending-probably no organisms truly have phyletic evolution

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why is evolution the unifying concept in biology?

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-tries to explain origin in life forms
-integral to understand responses and adaptations of organisms
-explains many of the findings in scientific research
-universal-all organisms evolved
-explains similarities among organisms-all life forms have dna, many have vestigial characters, why do we have differences
-explains the why questions in biology

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Synapomorphy

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– shared, derived character (e.g., fur and lactation in mammals)

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outgroup

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used to represent common ancestor (plethedon salamanders the ingroup and outgroup should be truly outside that group and a closely related organism-ideal to choose multiple outgroups)

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what is the definition of evolution?

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originally defined as descent with modification, or the change in populations over time, currently defined as changes in allele frequencies over time-have documented that allele frequents occur

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what are forces of evolution?

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selective pressure-artificial or natural, mutation, bottlenecks and genetic drift

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need to pick a gene that is right for what you are studying

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~if you want to look at real old relationships need to choose conservative gene that doesn’t evolve very fast
~if looking at recent changes a fast evolving gene would be better so it shows changes

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Molecular clocks

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work on the fact that mutations accumulate at a certain rate

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how do you set a molecular clock?

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-varies depending on taxa, mutations accumulate faster in organisms with faster metabolism
--almost always set with the fossil record- (see paper notes )

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problems with molecular clocks

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-do you even have a fossil, is your fossil actually related, and if it is how do you know at which point in evolution and time it is from
-calibration is problematic
-mutations don’t accumulate at a consistent rate-sometimes in a new environment a lot of selective pressure occurs in a short period of time
-need to calibrate each gene
-we use them, they have problems and big error bars that need to be bracketed-molecular clocks from recent past aren’t very useful but at large time scales are better-when you read about molecular clocks see how they calibrated it and take it with a grain of salt

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Natural selection

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individuals with favorable adaptations reproduce more successfully than those without adaptations

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Genetic drift

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random variation in the survival or reproduction of different variants

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evidence of reptilian ancestor of birds and mammals

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all mammals have left aortic arches, birds have right aortic arch, ancestral reptile had left and right arches

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process of protein development

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proteins made of chain of amino acids folded into complex 3 dimensional structure

amino acids made of nucleic acids coded from dna transcribed into rna then associated with ribosome which reads mrna 3 at a time trna brings nucleic acids to build the amino acid

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evidence eyes have evolved

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amino acid sequence of development of eye is the same in humans, mouse, quail, zebrafish and only slightly different in fruit flies

all similar because they shared a common ancestor

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Charles Darwin

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The Origin of Species (1859) 20+ years in the works, finally published because Wallace was about to publish same theory based on his work with birds in the Malayan archipelago
-both presented their ideas at same meeting and published at same time
-descent with modification due to natural selection

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dogs

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illustrate the power of artificial selection-many breeds have specific genetic problems due to inbreeding -artificial selection usually much stronger than natural selection

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evolution as a fact

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descent, with modification, from common ancestors

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evolution as a theory

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causes for descent with modification
-natural selection
-genetic drift
-mutation

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Inheritance

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for evolution to function traits must be able to be passed from one generation to the next -no inheritance then every generation is a new start
-dna is the molecule of heredity

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Why is evolution so controversial??

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-contradicts biblical laws
-brings humans off pedestal to same level as other organisms
-religion usually indoctrinated as children and many children not exposed to evolution
-makes people question their beliefs and many religions are about faith not questions
-science is based in questioning and new ideas develop from proving hypothesis wrong
-very personal, many people believe we are not animals and are a higher form

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Science principles

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Ideas are questioned
Based on facts
Scientific method used
Modified with new data
Reasonable doubt allowed
More objective, public
Based on physical evidence

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Religion principles (Christian)

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Ideas are not to be questioned
Based on faith
Based on the Bible
Unchanging
Reasonable doubt not allowed
Personal decision
Based on the word of the Bible

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Young-Earth creationists

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– earth <10,000 years old-take genesis literally-represents majority of creationists in US (45% of americans) that god created man and most animals died in a world wide flood

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Old-Earth creationists

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– acknowledge modern geology- some believe in the gap theory-a gap between 1st and 2nd chapters in genesis that explains elapse of time and fossil record

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Progressive creationists

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–blend creationism and evolution but limit the powers of evolution

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Intelligent design

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–a supernatural being (God, aliens or other supernatural force) intervened in development of people and organisms-

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Theistic evolution

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–accepted by majority of christians worldwide, esp western europeans, God works thru evolutionary laws and processes- evolution and natural selection exist but god works thru them

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Deist

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–god created universe and laws and stepped back and allowed things to develop

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Atheists

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- would deny existence of god

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agnostic

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-don’t care or deny god

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Evidence for evolution

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1. The hierarchical organization of life
2. Homology
3. Embryological similarities
4. Vestigial characters
5. Convergence
6. Suboptimal design
7. Geographic distributions
8. Intermediate forms

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The hierarchical organization of life

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because evolution is a process of branching and divergence, organisms naturally fall into the hierarchical system of groups within groups
example: salamanders and newts share a common ancestor with frogs and toads who shares a common ancestor with caecilians who shares a common ancestor with mammals, reptiles and birds
-groups of organisms are nested within the evolutionary tree (think of all the family members that derived from your grandparents)
-many species developed as a result of physical separation that results in different evolutionary paths
-understand how phylogenetic trees indicate relatedness
-closely related species separated by vast distances implies a more widespread ancestor

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Homology

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-similarity between species that results from inheritance of traits from a common ancestor e.g., forelimbs of moles, wings of bats and birds, flippers of whales and penguins are all derived from the same bones
-organs of two organisms are homologous if they have been inherited from an equivalent organ in the common ancestor
forelimb adaptations in different animals (result from developmental changes that result in more or less growth in different segments)
human-grasping
horse-running
birds and bats-flight
seals and turtles- swimming

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Homoplasy

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similarity in the characters found in different species that is due to convergent evolution, parallelism or reversal – not common descent
-similar structures not based on common ancestry-bird, bat and insect wings

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Embryological similarities

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~human fetuses briefly display gill grooves during development which form lower jaw, hyoid bone, one ear ossicle
~tooth primordial appear and then are lost in the jaws of fetal anteaters
~tail starts external and regresses to form coccyx

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Vestigial characters

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~structures that once were functional but are no longer-easier to lose function than completely eliminate-holdovers from ancestors that once had function
-cave-dwelling salamanders have genes for eye pigment yet they cannot see
~some humans have rudimentary muscles that enable them to move their ears or scalp (other animals move ears to focus on sound)
-human tail-coccyx
appendix-extremely regressed in humans, some vitamin production but not very functional (bursts due to bacterial infection)-fermenter in hind gut ruminators
-rudimentary pelvis and limbs in whales-pelvis does anchor uterus in females
-snakes have regressed limbs and pelvis

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What is HIV?

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intracellular parasite-a retrovirus (virion) that carries RNA (rather than DNA) and enzymes and transcribes backwards
-virion fuses with Tcell membrane & dumps RNA and enzymes including reverse transcriptase -RNA->DNA and inserts into host DNA then every time host DNA replicates it reproduces HIV mRNA which makes viral proteins spread the infection (infected DNA (ACTG)-> transcribed into mRNA (ACUG) then translated [reads bases 3 at a time (codon) -> tRNA bring amino acids until stop codon brought (~100)] into proteins

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How does HIV cause AIDS?

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-depletes T cells and macrophages that fight bacteria and infection
most people usually die from pneumonia

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Why does AZT work in the short run, but fail in the long run?

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worked great at first but then lost efficacy
AZT looks like nucleotide but with N3 instead of OH group that prevented reverse transcription
high levels of mutation selected for reverse transcriptase that selected against AZT (evolution in the enzyme)
side effect will effect all process that are replicating DNA

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where did HIV come from?

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primates have simian SIV that doesn’t have similar effects as HIV has in humans-has coevolved with primates for a long time (co-evolution common in pollinators, and flowers-slow process over a long period of time) jumped to humans and had strong response like most invaders
HIV-1 & HIV-2 both mutate quickly
HIV-1 probably came from chimps, possibly as result of chimps kept as pets (bites...), bushmeat (exposure to blood)
HIV-2 probably came from sooty mangabey or stump-tailed macaque or something closely related

have pointed out several transmissions and possibility of new transmissions from other simian SIV strains-HIV has made the transmission many times

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Why are some people resistant to infection by HIV?

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Natural immunity: have found people infected with HIV and no symptoms, found delta 32 allele (32 base pair deletion in the gene that codes for T-cell surface protein) that prevented membrane fusion between T-cells and HIV virions-person still infected but can’t get into T-cells-virus will eventually die but unclear how long that will take
highest concentration of delta 32 allele found in NW Europe and theorized to be involved in bubonic plague immunity resulting in strong selection for delta 32 allele

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Could a vaccine provide protection from the diverse strains of HIV?

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multiple transmission limits vaccine efficacy
high mutation rate also limits efficacy of vaccine

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HIV-1 and HIV-2, explain

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actually 2 epidemics
-HIV-2 in sub-saharan africa and SE asia-heterosexual
-HIV-1 in NA and Europe- homosexual men and iv drug users

HIV-1 more virulent
HIV-2 less virulent
several hypothesis related to virulence and transmission
if you are slow to transmit but kill fast you die off (must get transmitted to new host before killing host)

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Phylogenetic tree(evolutionary tree)

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- a diagram of the relationships of ancestry and descent among a group of taxa
-may infer timing (sometimes by the length of branches, can also infer sequence differences), can apply a molecular clock if sequence data available -
-record sequence of speciation events
-document which taxa are more closely or distantly related
-composed of nodes, branches and terminal taxa
-branching pattern of a tree is called the topology

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Primitive (interchangeable with ancestral) character

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-a trait that is inferred to have been present in an ancestor; to be applied only to character states (traits) and not to organisms (relative to common ancestor in question)
ie platypus primitive characters-cloaca, lays eggs, primitive lactation and mammary glands

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Derived character

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-the opposite of primitive; a trait that has been modified from the primitive condition
ie salamander derived characters; legs, lungs
platypus derived characteristics-sensory ability of bill, venomous spur

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Nodes

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represent common ancestor

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terminal taxon

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represents an individual organism

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Phylogeny

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-the evolutionary history of a group

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Convergent evolution

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-similar environments-similar pressure-fish and whales overall characteristics (fusiform body shape, fins)

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Parallelism

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- ancestor doesn’t process a trait but it pops up independently in descendants (sister taxa) some butterfly patterns -developmental pathways are there in ancestor but not expressed

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Reversals

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character state that evolves then loss of that character, whales reverted to ancestral condition- -Dollo’s law state that complex characters, once lost, are not usually regained-genes that are turned off continue to evolve but begin to accumulate mutations that aren’t being selected against so may become dysfunctional and unable to be reactivated

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Evolution has 2 major features

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anagenisis and cladogenesis

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Anagenisis

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evolutionary change of various characteristics in each of the descendants

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Phyletic (linear evolution)

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-accumulation of genetic variation in a group over time, not usually resulting in new spp

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Cladogenesis

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– branching of a lineage into two or more descendant lines-2 or more species arising from one common ancestor-can be caused by geographic isolation (a separation event like SA and Africa separating)

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parsimony

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– a criterion for selecting among alternative patterns or explanations based on minimizing the total amount of change or complexity simplest explanation (if position 1 has a T in A and B the most parsimonious explanation is that the common ancestor had T in 1 also)

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parsimony trees

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count steps (change from the common ancestor) to determine tree length, tree length = certain number of steps, trying to minimize the number of steps

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Evaluating trees

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computer programs begin taking shortcuts-synapomorphies, exhaustive searches of trees are rare, can take a long time (days) for computers to run models, can give computer program instructions (step matrix) like: reversals so uncommon they are weighted 10x - or give different weights to A<>G, C<>T (transitions purine to purine or pyrimidine to pyrimidine) than to transversions (A<>T or G<>C) because transitions are easier due to similar sizes of molecules -third position in DNA position changes the most because it will still code for the same protein -really common cost 1 step, 1st position pretty rare cost 10 steps, 2nd position even more unlikely cost 12 steps

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bootstrapping

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-generates new data sets using your data (sampling with replacement) then generate new trees and determine how many times taxa share the questioned node, sampling with replacement draws new samples from all the data each time, if there is a lot of support for relationships they will come out again thru repeated samples

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bootstrap percentages

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-<50%-no relationship-don’t draw that tree -50-75% gray area ->75-80% strong support for relationship

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maximum likelihood

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- similar to parsimony generates a probability in that it generates a probability for each branch and adds them up for the entire tree

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genetic distances

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- was used in phyletic methods to indicate relationships many methods but most get answers between 0-1 (closer to 0 more closely related) -numbers are relative within the same data set, cannot be used to compare with other data sets -add numbers at branches to determine relatedness of different terminal taxa -similar process uses differences in base pairs instead of ratios

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radiation of hawaiian fruit flies, when did they split from other fruit fly populations?

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-Hi created volcanically, initially bare rock, has to rely on colonization from mainland, fruitflies quite diverse on Hi due to lack of competition and resulting diversification, used molecular clock to determine how long ago they diverged ~42mya but Hi is only 5-6my -why? -one theory is they diverged somewhere else and more than one spp made it to HI -molecular clock could be wrong -but most likely is that oldest islands have submerged and are no longer in existence

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phylogeny of HIV transmission-accused dentist of transmitting HIV to patients

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looked at patient and dentist HIV genetic sequences and compared them, some patients fell in a nested pattern and some fell out further away-dentist shared some similarities but tree didn’t indicate support- but very interesting that dentist and patients shared same HIV strains