EEMB 2 Evolution

Biological evolution

• genetically based change in a line of descent over time (descent over time)
  - individuals of populations show different forms of their traits

The frequencies of different forms relative to one another can […] over successive generations

"The frequencies of different forms relative to one another can change over successive generations

what did the earliest roots of modern evolutionary theory begin with to explain the natural world

origin myths and superstition

anaximander miletus

first land dwelling ancestors of humans were born in water
fir human must have been the child of a different type of animal (fish)

xenophanes

recognized fossils (fish/shellfish) as evidence of past life

aristotle

created the "scala Naturae" hierarchy of life from simple to complex

lucretius (De rerum natura)

development of the cosmos, earth, life, and humans through mechanistic mechanisms

roman stoic philosophers

teleological view
nature as an agency concerned with "life best fitted to survival" by purposeful design

Origen of alexandria, gregory of nyssa, Augustine of Hippo 

Early christian Church philosophy
genesis as allegory and "theistic evolution" - life transformed over time directed by the creator

great chain of being

(lowest to highest forms)
linked were designed and forged at the same time at center of creation and were immutable

biogeography

examination of global distribution of animals

observations of biogeography

many plants and animals are unique to isolated places
certain species separated by great distances resemble one another

questions of biogeography

• how did so many species get from one point of creation to isolated places on earth
  - what did the similarities and differences among them mean

basic questions about life

biogeography
comparative morphology
geology
- findings from biogeography, comparative morphology, and geology did not fit well with teleological views

comparative morphology

the study of similarities and differences in body plans between major groups

comparative morphology observations

homologous structures
- human arms, whale flippers, bat wings differ in size, shape and function
- yet have similar locations in the body

comparatie morphology questions

• why are some animals that are so different in some features so much alike in others
  - why were there parts with no functions (vestigial structures)

geology

fossil remains of plants and animals

geology observations

• distinct layers of rock contained distinct fossils
  - deep layers contained simple fossils and shallow layers contained similar but more complex fossils

geology questions

• what did this increasing complexity represent
  - were these fossil layers separated in time
  - could these organisms be related

novel hypotheses

1. if dispersal of all species from a center of creation was not possible because of barriers

2. if organisms were not created in perfect states

• then species may have originated in more than one place
  - then species may have been modified over time

Georges Louis Leclerc de Buffon

• life could be generated spontaneously
  - life was not immutable but many degenerate from a perfect form
  - enviornment influences modifications
  - earth was older, 75,000 years 
  - views published in 44 volume natural histor book series Histoire Naturelle

Erasmus Darwin

• published multiple works
  - competition play role in species formation (not creation)
  - animals change in response to changes in the enviornment
  - offspring inherit these changes
  - life on earth could have descended from a common ancestor

James Hutton and Charles Lyell

Geologists

Theory of Uniformitarianism

changes in the earth occurred slowly gradually and at uniform rates
- lyell published ideas in the book principles of geology
- age of earth determined by sedimentation rates
- earth was very old (millions of years)

william smith

paleontologist
- principle of faunal succession (different layers of rock substrata contained distinct fossil assemblages), geologic map of england
- linked age of rocks to age of fossils

georges cuvier

anatomist/paleontologist
- established the science of paleontology
- fossils represent species that went extinct (extinction as fact)
theory of catastrophism

theory of catastrophism

george cuvier
(earths geology and life were determined by repeated catastrophic events)
- current diversity due to survivors and immigrants not new species

Jean Baptiste de Lamarck

• inheritance of Acquired Characteristics (traits)
  (enviornmental pressures and internal needs bring about permanent changes in body form and function) - behaviors modified traits

Charles Darwin

naturalist, geologist, biologist
- attended university of edinburgh (medicine) transferred to cambridge (clergy)
- at 22 yrs old took position as "captains companion"
- 5 years voyage 1831-1836
- survey of geography, oceanography, geology and biology
- devised the theory of natural selection draft essay did not publish

charles darwins 3 major findings

1. as enviornment changes so does species composition
   2. fossils are related to organisms today but are also structurally different
   3. galapagos islands: island animals were related to mainland species but locally different in form and function ex. finches

Thomas Malthus

• essay on the principle of population
  (geometric growth of popualtions)
  - all individuals have the capacity to produce more individuals than the enviornment can support

Alfred Russel Wallace

• independently wrote 2 page letter summarizing same ideas as Darwin's on natural selection "survival of Fittest"
  -2 papers present in 1858 (Darwin and Wallace) at the proceedings of the Linnaean Society of London

What book did Darwin publish in 1859

on the Origin of Species

Theory of Natural Selection

nature selects the individuals that are most fit

basic principles of natural selection (5)

1. members of any population vary in their traits (morphological, physiological, behavioral)
   2. all species can produce more offspring than their enviornment can support (overproduction of progeny)
   3. there is a struggle for existence among individuals and species (resource limitation)
   4. the fittest individuals (best traits) for a given enviornment have a higher probability of survival and reproduction, leave more offspring
   5. Leads to an accumulation of inheritable favorable traits in population over time (generations)

what did darwin not understand

the source of variation or how it was passed on (inheritance of traits)

what was the problem that darwin faced

the blending theory of inheritance
- offspring traits tend to be blends of the parents

fleeming jenkins

swamping argument - inaccurate
- unusual variants occasionally arose
- variant likely to mate with individuals with most common trait
- offspring will be a blend of that trait
- in only a few generations the novel trait will be "swamped" out

novel traits would be lost by […]

"novel traits would be lost by repeated intercrossing

"

what theory did darwin invent to solve the problem of blending of inheritance that ended up being wrong

pangenesis theory: gemmules (not published)
would provide mechanism for inheritance of acquired characteristics

what do we need for natural selection to work

1. need to have predicatable mechanism for inheritance
   2. but also, unpredictable production of sports/monstrosities

gregor mendel

father of genetics
- found indirect but observable experimental evidence how parents transmit genes to offspring
- sperm and egg carry distinct "factors" (genes) of information about heritable traits (2 units - male and female)
- provided the evidence to support a key premise of natural selection

what are mendels 3 laws

law of segregation
law of independent assortment
law of dominance

erich von teschermak, Carl Correns, Hugo de Vries

independently rediscovered mendels work and confirmed it

hugo de vries

theory of mutation
- spontaneous mutation was the source of variation
- inheritance of specific traits in organisms via particles

R.A. Fisher

• extends Mendels work (discreate characteristics) to continuous traits
  - 1918 published paper on Quantitative genetics
  -1930 published paper on genetical theory of natural selection (unified the theory of Natural Selection and Mendels laws of inheritance)

Huxley

neodarwinism and the modern synthesis
- combination of Darwinian natural selection and Mendelian genetics

Watson, Crick, and Franklin

established general structure of DNA
- double stranded right handed antiparallel exposed bases in grooves

stephen gould and niles eldredge

theory of punctuated equillibrum
- long periods of stability (stasis) punctuated by bursts of evolutionary change and diversication

The modern synthesis: cross disciplinary consensus

1. synthesis of Neo-Darwinian ideas and population biology (genetics)
   2. Modifications in descent can occur gradually rapidly, or by a combination of both
   3. Framework how evolution occurs at the level of populations, the mechanisms by which genetic variation is generated, inherited, and acted upon by natural selection, leading to the diversification of life

descent with modification

• evolution is the most powerful unifying principle in biology
  - explains why organisms are different from each other (accumulation) yet at the same time share many common characteristics (ancestry)

evolutionary process

1. variation
   2. natural selection
   3. genetic divergence
   4. reproductive isolation
   5. specification

Variation: populations…

• evolve not individuals
  - have variation in traits among individuals

microevolution

the change in allele frequencies in a population over generations

features that characterize a population

1. morphological traits (form)
   2. physiological traits (function)
   3. ethological traits (behavior)

In reproducing species there is….

variation in most traits in individuals 
(individuals of a population vary in their traits)
- discrete characters
- quantitative characters

discrete characters

either or basis (2 or more distinct forms)

quantitative characters

vary along a continuum (range of values)

variation

traits may be positive, negative, or neutral to individuals in a population
(survival and reproduction)

adaption

adjustment or change to meet enviornmental conditions

adaptive traits

(+)
form of trait that is an advantage in terms of survival and reproduction

maladaptive traits

(-)
form of trait that is a disadvantage in terms of survival and reproduction

neutral traits

(0)
form of trait that is neither a disadvantage or advantage in terms of survival and reproduction

almost every trait of every species is […]

"almost every trait of every species is variable

gene

hereditary unit of DNA that codes for specific traits

alleles

2 or more different molecular forms of a gene
(alternate form of a gene- dominant, recessive, incomplete dominance)

gene pool

all the genes in a population (pool of genetic resources)

genome

all the genes in a species

genotype

The genetic makeup or set of alleles, of an organism (genetic expression)

phenotype

the observable traits of an organism, determined by its genetic makeup and by enviornmental influence on those genes (physical expression)

phenotypic frequency

describes the distribution of observable traits in a population (the proportion of individuals exhibiting a specific trait)

the relationship of genotype to phenotype may not be […]

"the relationship of genotype to phenotype may not be 1:1

multuple genotypes can result in […]

"multuple genotypes can result in the same phenotype (BB, Bb)

allele frequencies

the proportion of each kind of allele in a population

how do you calculate pheno/genotypic frequency

The frequency of genotype AA = N_AA/N
The frequency of genotype Aa = N_Aa/N
The frequency of genotype aa = A_aa/N

how do you calculate allele frequencies

The frequency of allele A is called "p", and p = (2N_AA + N_Aa) / 2N
The frequency of allele a is called "q", and q = (2N_aa + N_Aa) / 2N

phenotypic and allele frequencies can be used to

track the rate of genetic change over multiple generations

how do we know whether a popualtion is evolving with respect to any trait (is there genetic change over generations?)

compare it to the genetic make-up of a population if it were not evolving for that trait

genetic equillibrium

the frequencies of alleles at a given gene locus remain stable for multiple generations

hardy-weinberg principle (1908)

mathematical formulation to describe how to maintain the frequencies of alleles of a population over time (genetic equillibrium)
- dominant allele will not drive out recessive allele
- genotype frequencies can be predicted and will not change (conditional)
- considers all alleles in the gene pool
- considers the combination of alleles in all of the crosses in a population
- select gametes at random (random mating)
- calculate the frequencies of the three possible genotypes assuming random union of gametes

in a popualtion in genetic equillibrium

the proportions of genotypes at one gene locus with two kinds of alleles (binomial expansion)

what is the hardy weinberg equation

p²(AA) + 2pq (Aa) + q²(aa) = 1

conditions for equillibrium (allele frequencies will be stable through successive generations if):

1. there has been no gene mutations
   2. the population is very large
   3. the population is isolated
   4. the gene has no effect on survival reproduction (no natural selection)
   5. mating is random

Hardy-Weinberg equillibrium example

butterfly wing color

1. assume the population is at […]
   2. pair of alleles is for wing color
       allele A = dark blue wings (homozygous dominant)
       allele a = white wings (homozygous recessive)
       Heterozygote Aa = light blue wings (incomplete dominance)
   3. the frequencies of A and a must add up to 1 in the population 
       p + q = 1
   4. During meiosis: each allele segregates from its partner and ends up in separate gametes
       p = the proportion of gametes carrying the A allele
       q = the proportion of gametes carrying the a allele

"1. assume the population is at equillibrium
2. pair of alleles is for wing color
    allele A = dark blue wings (homozygous dominant)
    allele a = white wings (homozygous recessive)
    Heterozygote Aa = light blue wings (incomplete dominance)
3. the frequencies of A and a must add up to 1 in the population 
    p + q = 1
4. During meiosis: each allele segregates from its partner and ends up in separate gametes
    p = the proportion of gametes carrying the A allele
    q = the proportion of gametes carrying the a allele

1. assume the population is at equillibrium
   2. pair of alleles is for wing color
       allele A = dark blue wings (homozygous dominant)
       allele a = white wings (homozygous recessive)
       Heterozygote Aa = light blue wings (incomplete dominance)
   3. the frequencies of A and a must add up to […] in the population 
       […]
   4. During meiosis: each allele segregates from its partner and ends up in separate gametes
       p = the proportion of gametes carrying the A allele
       q = the proportion of gametes carrying the a allele

"1. assume the population is at equillibrium
2. pair of alleles is for wing color
    allele A = dark blue wings (homozygous dominant)
    allele a = white wings (homozygous recessive)
    Heterozygote Aa = light blue wings (incomplete dominance)
3. the frequencies of A and a must add up to 1 in the population 
    p + q = 1
4. During meiosis: each allele segregates from its partner and ends up in separate gametes
    p = the proportion of gametes carrying the A allele
    q = the proportion of gametes carrying the a allele

1. assume the population is at equillibrium
   2. pair of alleles is for wing color
       allele A = dark blue wings (homozygous dominant)
       allele a = white wings (homozygous recessive)
       Heterozygote Aa = light blue wings (incomplete dominance)
   3. the frequencies of A and a must add up to 1 in the population 
       p + q = 1
   4. During meiosis: […]
       p = […]
       q = […]

"1. assume the population is at equillibrium
2. pair of alleles is for wing color
    allele A = dark blue wings (homozygous dominant)
    allele a = white wings (homozygous recessive)
    Heterozygote Aa = light blue wings (incomplete dominance)
3. the frequencies of A and a must add up to 1 in the population 
    p + q = 1
4. During meiosis: each allele segregates from its partner and ends up in separate gametes
    p = the proportion of gametes carrying the A allele
    q = the proportion of gametes carrying the a allele

1. assume the population is at equillibrium
   2. pair of alleles is for wing color
       allele A = […]
       allele a = […]
       Heterozygote Aa = […]
   3. the frequencies of A and a must add up to 1 in the population 
       p + q = 1
   4. During meiosis: each allele segregates from its partner and ends up in separate gametes
       p = the proportion of gametes carrying the A allele
       q = the proportion of gametes carrying the a allele

"1. assume the population is at equillibrium
2. pair of alleles is for wing color
    allele A = dark blue wings (homozygous dominant)
    allele a = white wings (homozygous recessive)
    Heterozygote Aa = light blue wings (incomplete dominance)
3. the frequencies of A and a must add up to 1 in the population 
    p + q = 1
4. During meiosis: each allele segregates from its partner and ends up in separate gametes
    p = the proportion of gametes carrying the A allele
    q = the proportion of gametes carrying the a allele

at fertiliation

1. gametes combine at random, give rise to the next generation
   2. assume, population remains constant at 1000 individuals

as long as the 5 basic conditions (assumptions) are met:

• the frequencies stay the same through succesive generation

how to test hardy weinberg equillibrium

by calculating frequencies in the gametes of the next generation

what can be said about the results of hardy weinberg equillibirum

they are quite general
- can be extrapolated to situations with moer than 2 alleles

hardy weinberg equillibrium is useful it allows us to….

make a prediction if various evolutionary forces are not operating

when hardy weinberg genotypes do not match the predicted proportions

1. indicates that 1 or more conditions (assumptions) of the Hardy-Weinberg Rule are violated.
   2. can then begin searching for the specific evolutionary driver of the change

rarely, do all 5 conditions operate at the same time in nature:

1. no gene mutations
   2. population is large
   3. population is isolated
   4. gene has no effect on survival and reproduction
   5. mating is random

3 processes drive the population away from equillibrium

1. natural selection
   2. gene flow
   3. genetic drift

sources of variation

1. mutation
   2. recombination

mutation

heritable changes in DNA (genes) that give rise to altered gene products