Exam 1 UCF 2018 Evol Bio PCB 4683

Monophyly

aka Clade

a common ancestor and its descendants on a phylogeny tree

HIV

Infects individuals by releasing HIV RNA and HIV reverse transcriptase to integrate the RNA into the cell's DNA

Transmission rate hypothesis

The higher the transmission rate of a virus, the more virulence will be selected for

and vice versa

Trade-off hypothesis

Non-numerically dominant strains of the virus are likely to colonize a new host

- expect an increase in virulence

Mis-match of immune systems hypothesis

When HIV was transmitted from apes, where it was benign, to humans, it was more virulent than optimal

- assumes that virulence will decrease over time for increased survival

AZT

replaces thymidine to interfere with HIV reverse transcriptase and stop transcription of HIV-infected DNA

Problems with AZT

HIV with reverse transcriptase that was prone to mistakes died out within 2 years, and left only HIV with a mutation that helped them differentiate between AZT and thymidine, which could survive and reproduce

HAARt

highly active antiretroviral therapy

uses multiple drugs at once to account for variance in the virus

Louisiana vs. Richard J. Schmidt

- Nurse Trahan received vitamin shots from Dr. Schmidt on the same day as a blood draw for an HIV+ patient.

- Case reconstructed phylogenetic trees using parsimony to determine that the strands of HIV were related

- Evidence that supported the conclusion of the nurse's HIV strand was phylogeny of the HIV strands in

Pre-Darwin views

- Earth is very young ~ 6000 years old

- Organisms are created independently by a deity - no extinction or mutation b/c they are created perfect

- Lamarck - inheritance of acquired traits, like giraffes stretching their necks and passing that trait onto the next generation = epigenetics

- Charles Lyell - uniformitarianism = Earth has been undergoing the same processes at the same rate since the beginning

- Sparked Darwin's conclusion of descent with modification

- Malthus - over-reproduction and overpopulation will cause famine

Darwin's Four Postulates

Species are variable

Variation is heritable

More young are born than can survive

Survival and reproduction are not random

Post Darwin view

- Questioned where variability comes from and if it runs out

- Questioned how traits are inherited - it was believed that traits were blended and lost individuality

- Questioned how all the species could have evolved in such a small amount of time (Earth was proposed to be only 20 mya)

Vestigial structures

nonfunctional (leftover) structures from speciation - salamanders with eye sockets, snakes with hind legs, humans with goosebumps

Advancements for evidence of Darwin's theories

- Relative dating used to determine that Earth is billions of years old

- Marie Tharp = continental drift

§ Collected data from all voyages and mapped the North Atlantic seafloor to discover seafloor spreading

- Absolute dating using unstable radioisotopes with known half-lives, exponential decay curve

- Mendelian genetics

Contradictions to three propositions of special creation

- Species were not created independently, they are related: Homology, fossil record, observation of speciation, transitional forms

- Species mutate: fossil records, speciation in Galapagos, transitional forms

- Earth is not young: dating, plate tectonics, fossil record

Evidence against special creation

○ Homology

○ Vestigial structures

○ Direct observation

○ Fossil record

○ Geology

○ Correspondence among data sets

Modern synthesis

- answers the questioning that followed his first 2 publications using the advancement of population genetics

- It brought to the world the ideas of:

○ Gene mutation

○ Population genetics

○ Mendelian inheritance

○ Contingency

○ Speciation and trends

Scopes Monkey Trial

A substitute biology teacher was put on trial for "teaching evolution"

- Case used as a platform to argue religion vs. evolution, when it was supposed to be a test case that would be used against future teachers

○ Was a PR win for evolution, bringing it into mainstream media

Argument for intelligent design

Extremely perfect organs, like the eye, must have been intelligently designed

Louisiana vs. Richard J. Schmidt

- Nurse Trahan received vitamin shots from Dr. Schmidt on the same day as a blood draw for an HIV+ patient.

- Case reconstructed phylogenetic trees using parsimony to determine that the strands of HIV were related

- Evidence that supported the conclusion of the nurse's HIV strand was phylogeny of the HIV strands in all of Schmidt's patients

Methodological naturalism

- Hypotheses that researchers propose for natural phenomena

- Explanations that involve strictly natural processes and cause

Preadaptation/Exaptation

repurposing traits for new functions - panda's thumb

Phylogeny

hypothesis of evolutionary relationships

Principle of parsimony

Fewest new assumptions, fewest new explanations is most likely to be true

- "Keep it simple, stupid" -US Navy

Homology

similarity in traits resulting from common ancestry

Synapomorphy

derived characteristics shared by all members of a group

Homoplasy

convergence and reversal

Convergence

same traits that were independently derived from different lineages

Reversal

reverting back to the ancestral form of traits

Phyelogram

phylogeny trees with informative branch lengths

Bootstrapping

Uses multiple subsets of a whole data set to see if a tree differs from chance

- used to statistically evaluate confidence in each node on a tree

Distance based method

Uses a table of genetic similarities to determine genetic distance

Maximum Likelihood

Calculates the probability of the data given the tree

- Accounts for complex patterns of nucleotide evolution across regions of genes

Bayesian Methods

Probability of the tree given the data

Coalescent methods

Models genetic drift backward in time

- Reconstruct gene variants backward in time, until they coalesce in common ancestors

Ancestral State Reconstruction

- Mapping features on a phylogenetic tree to determine what features were present in an ancestor

- Tracing the evolution of a trait along a phylogeny

- See how many times a trait has evolved

- Build a phylogeny based on a table of genetic traits and looking at correlations among them

Genotype-by-environment interaction

Unequal effects of the environment on different genotypes, resulting in different phenotypes.

phenotypic plasticity

the ability of an organism to change its phenotype in response to changes in the environment.

- plant defenses induced by the environment

Point mutation

mutation that affects a single nucleotide, usually by substituting one nucleotide for another

Transition

more common point mutation; Purine to purine or pyrimidine to pyrimidine

Transversion

nucleotide change between purine and pyrimidine

Synonymous

Silent mutation

Non-synonymous

a nucleotide mutation that alters the amino acid sequence of a protein

Frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

Nonsense mutation

changes a normal codon into a stop codon

Gene duplications

- duplication of whole segments of a chromosome

- Unequal crossing over in meiosis

- One copy is free to accumulate mutations

Globin gene family

- Alpha and beta clusters from gene duplications

- Need 2 subunits from each cluster for hemoglobin

Paralogs

homologous genes in the same species

- Like the globins (alpha and epsilon in a human, for example)

Orthologs

genes in different species that evolved from a common ancestral gene by speciation

- Human alpha and beta are ___ to the mouse alpha and beta b/c we come from the same ancestor

Retroposition

The duplication of a genetic sequence resulting from the retrotranscription of a processed mRNA followed by integration back into the genome.

- Chondrodysplasia in corgis

Triploid salamanders

Use sperm of a male of another species to ACTIVATE their eggs, then the sperm nucleus is eliminated = kleptogenesis

deleterious point mutations

Albinism

Color blindness

Hemophilia

Mutation rate variations

- DNA polymerase varies in error rate

- Mismatch repair systems vary in effectiveness

- Coding regions have fewer mutations than non-coding regions

~ Due to purifying selection