Evolution #1`

Theory

complex set of ideas that can be tested

Biological evolution

Inherited change in a group of organisms across generations

How many genes are in the SARS-CoV-2 genome

11

Why have certain covid strains become more dominant

strains have evolved to become more infectious; they usually have become less deadly as they evolved to be more infectious (tradeoff)

What is one key thing that has led to rapid evolution in viruses?

recombination

occurs when two viruses with different mutations infect the same host

Spike gene sequence in SARS-CoV-2

not similar to any other known human virus

not the most effective spike protein (why it most likely wasn’t lab created)

SARS-CoV-1

led to an asian epidemic in the early 2000s

closely related to a bat virus

What were the two hypothesized intermediate hosts for covid?

pangolin

raccoon dog

What were the convergent evolution examples provided in class?

pangolin and giant anteater

raccoon dog and raccoon

Aristotle

350 BC
greece

“great chain of being” based on complexity of organisms

Carl Linnaeus

1700s, Sweden

Gave every species a latin name

developed the modern system for classifying life

“Systema Naturae”

Charles Darwin

1800s, UK

Beagle Expedition (1830s)

On the Origin of Species (1859)- presented theory of evolution with ample evidence

Gregor Mendel

1800s, Austria

Studied inheritance in peas and recorded in lab notebook

1865- published his theory describing rules of genetic inheritance

Population Genetics

Started by RA Fischer, Sewell Wright, and JBS haldane

modern synthesis combined mendelian inheritance, natural selection, and genetic variation

used statistics to describe populations

provided current understanding of how evolution works and how it applies to all fields of biology

two requirements for evolution to occur

individuals with certain traits have a greater chance of survival and reproduction, offspring resemble their parents

Darwin’s hypothesis of evolution

natural selection is a mechanism of evolution

Lamarck’s Hypothesis

organisms altered their behavior in response to environmental change. Their changed behavior, in turn, modified their organs, and their offspring inherited those "improved" structures.

organisms are often …

well adapted to their environment

Fossil records show…

changes with species and changes in the number of species

homologous structures

similar physical features in organisms that share a common ancestor, but the features serve completely different functions

Vestigial Structures

features of an organism that are considered to have lost much or all of their original function through evolution.

Inefficient designs result…

from evolutionary history (ex. windpipe and food passageway)

Hierarchical relations reflect

evolutionary tree of life

Convergent evolution

the process whereby distantly related organisms independently evolve similar traits to adapt to similar necessities

transitional stages

can be seen in fossils and living organisms, shows the evolution of complex organs

Geographical distributions

reflect evolutionary history

ex. ratite birds→ common ancestor on gondwana supercontienent

parallel evolution

occurs when independent species acquire similar characteristics while evolving together at the same time in the same ecospace

divergent evolution

the process by which interbreeding species diverged into two or more evolutionary groups.

what is the ultimate source of genetic variation

mutation

What are two general features of mutations that have a big effect

1. deleterious

2. pleiotropy

deleterious effects

harmful mutations, vast majority are not beneficial

cause loss or alteration of normal gene function, leading to reductions of organismal fitness.

pleiotropy

phenomenon in which a single locus affects two or more apparently unrelated phenotypic traits

Homeotic Mutation

cause displaced body parts (homeosis), such as antennae growing at the posterior of the fly instead of at the head

Point Mutations

alter one base pair

most common type of mutation

can be synonymous or nonsynonymous

Non-synonymous mutation

point mutation that alters the amino acid sequence

can be a missense or nonsense mutation

Synonymous mutation

point mutation that does not alter the amino acid sequence

aka a silent mutation

Deletion mutation

most are harmful, but can be occasionally beneficial (ex. partial HIV resistance)

Duplication Mutation

copies a segment of the chromosome

important source of biological novelty

duplications can evolve new functions

Fission

increases the number of chromosomes

Fusion

decreases the number of chromosomes

Inversion mutation

section of a chromosome flips in place

can link together a favorable set of alleles

alters the order of genes along a chromosome

Epigenetic mutations

mutations that do not involve the altering of base pairs

affect proteins interacting with DNA or alterations of nitrogenous bases

include histone acetylation and dna methylation

do epigenetics contribute to long term evolution?

no, they are often erased after one or a few generations

What were the two hypotheses tested in the lederburg experiment?

1. Changes in the environment cause favorable mutations to occur

2. effects of mutations are random with respect to what selection favors

What were the two big conclusions of the replicate plate experiment?

1. Mutations generate alleles with random effects

2. Adaptation happens when natural selection causes those mutation at increased survival and reproduction to spread in a population

Linkage Disequilibrium

associations between alleles at different loci

Distribution

tells us the frequency of different kinds of things

mean

typical value in a distribution, an average

Variance

measures variability/spread around the mean (sigma squared)

correlation

measures how much 2 measurements vary together, between negative 1 and positive 1 (represented by r)

regression

a line that predicts the value of y from the value of x

Hardy Weinberg Equilibrium

Tells us the relative proportions of genotypes in a population where segregation is the only factor that changes genotype frequencies

What are the 5 conditions for hardy weinberg equilibrium

infinite population size, no natural selection, no mutation, no migration, random mating

standard deviation

equal to the square root of variance

useful for measuring the differences between the means of 2 distributions

Natural Selection

The nonrandom survival and reproduction of phenotypes and genotypes

galapagos islands

archipelago off of the coast of ecuador

daphne minor

small island with a few finch species, used for research since the 1970’s

1976 daphne minor

largest drought in the island’s history, led to a large drop in finch population

Selection on finches

drought led to no new flowers/seeds

all small seeds were consumed, leaving only large seeds that required large beaks

selection on larger beak size occurred

Absolute Fitness

the number of progeny that a zygote/genotype/phenotype produces over its lifetime

relative fitness

equal to the absolute fitness divided by a decided reference fitness

natural selection acts more on relative fitness

Strength of selection depends on what?

relative fitness

Positive Selection

when 1 allele has a higher fitness than another

selection coefficient (s)

natural measure of the strength of selection acting on an allele

change in allele frequency

change in p= p(1-p)(s)

rate of evolution can be described as a product of what

genetic variance x strength of selection

How do you calculate the number of generations for an allele to go from 10 to 90%

generation number= 4/s

Peppered Moth

With industrial revolution, melanic allele became more fit for camouflage

1848- first melanic moth is found, within 50 years it had spread rapidly

s=0.5 (one of the largest coefficients measured)

Selection on humans

lactase persistence

tibetan plateau- gas exchange mutation

skin color

overdominance

heterozygotes have the highest dominance

preserves genetic variation

results in a polymorphic equilbrium

underdominance

heterozygotes have the lowest fitness

decreases genetic variation

most common allele goes to fixation

How to predict polymorphic equilibrium allele frequency

p2= (1-w11)/(2-w11-w22)

Fischers fundamental theorem of natural selection

evolutionary change in 1 generation of a population’s mean fitness is equal to the genetic variance for fitness

sewell wright’s adaptive landscape

allele frequency evolves in a direction that causes the population to move “uphill” on the adaptive landscape

what are the 2 exceptions to the fundamental theorem and adaptive landscape

1. changing environments

2. frequency dependent selection

frequency dependent selection

relative fitnesses of individuals depend on the frequencies of phenotypes or genotypes in the population

frequency dependent selection results in what

fewer individuals surviving

What are the common sources of frequency dependent selection

competition for mates

competition for resources

genotype

genetic makeup of an individual

phenotype

properties of an individual that selection can act on

what are the two influences on phenotype

genetic influence

environmental influence

Environmental variation can smooth out what

the variation between different genotypes of a gene

The number of genes involved in a trait can affect what?

how much that a trait can evolve

when many loci affect a trait, what can occur?

large changes can evolve without the introduction of new mutations

fitness functions

show how phenotypes affect fitness

Directional selection

increases or decreases the mean phenotype of a population

z-bar

mean value of a trait

delta z-bar

evolutionary change in a trait’s mean value from the beginning of the current generation to the beginning of the next generation

delta z-bar=

G times Beta

What is G

genetic variance for a trait

what is beta

selection gradient

What is phenotypic variance equal to

G+E

What is E

environmental variance

environmental variance

not transmitted from parents to offspring

largely from things like nutrition

genetic variance

part of the phenotypic variance that results from inherited genetic variation

heritability (h²)

fraction of the phenotypic variance caused by genetic variance

h²=

G/P or G/(G+E)

h² is measured from…

the resemblance between relatives

G=

P times h²