Evolution Exam 3

Genetic drift

Change in allele frequency due to random chance

Sampling error

allele frequency of the sample does not reflect the distribution of alleles in the original population, by random chance

• the “sample” is the group of alleles that make it into the next generation

Evolution by Natural Selection vs Evolution by Genetic drift

Natural selection:

Green beetles are more visible to predators and are selected against = There are more brown beetles in the next generation due to a fitness advantage

Genetic drift:

Simply by chance, more green beetles were stepped on than brown beetles =

There are more brown beetles in the next generation due to chance (sampling error)

Five fundamental features of genetic drift

1. Drift is unbiased

2. Fluctuations in allele frequency due to drift are larger in small populations

3. Drift causes genetic variation to be lost

4. Drift causes populations that were initially identical to become different over

   time

5. An allele can become fixed even if it is not beneficial

Population bottleneck

sudden decrease in population size in large population

• Commonly caused by disease outbreaks, natural catastrophes

• lead to genetic bottlenecks

Genetic bottlenecks

sudden reduction in the number of alleles in a population

Founder effect

occurs when a group of individuals establishes a new population in a new area (founder event)

• Allele frequencies likely differ in the new population from source population, especially if new population is small enough= sampling error

Effective population size (Ne)

the number of individuals in a population who contribute to offspring in the next generation

• sometimes called idealized population

• Effective population size does not include juveniles or post-reproductive individuals, and is subject to fluctuations in sex ratios

• A small value of Ne means that drift is strong, while a large value means drift is weak

Heterozygosity (π, NOT pi)

a measure of polymorphism (two or more alleles) at a specific locus

• Polymorphism is spread unevenly throughout the genome:

  higher in selectively neutral regions

• Neutral DNA = mutations can stay = more polymorphism.

  Selected DNA = harmful mutations get removed = less polymorphism.

• Much of the polymorphism in a species is due to genetic drift acting on

  selectively neutral mutations

Neutral regions in the genome

are not subject to selection only mutation and genetic drift can cause evolution in neutral regions

Silent mutation

a point mutation in an open reading frame that does not alter the amino acid encoded, due to degeneracy of the genetic code.

neutral mutation

a mutation that occurs in noncoding DNA and does not affect gene products or gene expression. A neutral locus.

selection coefficient, s

Strength of Natural Selection

1/Ne

Strength of Genetic Drift

s >>> 1/Ne

If selection is very strong (or the population is very large), drift has less effect than selection

s <<< 1/Ne

If selection is very weak (or the population is very small), drift has a stronger effect than selection

Neutral theory of molecular evolution

most alleles that become fixed are selectively neutral and evolve by drift

• Translation: the majority of molecular evolution is due to random chance (selection is rare)

• predicts selectively neutral loci will accumulate more differences than loci under strong selection

• proposed by Motoo Kimura to explain molecular clocks

• predicts that loci will evolve at a relatively constant rate

• Neutral theory also predicts that within coding regions (functional genes), synonymous (neutral) mutations should accumulate faster than nonsynonymous mutations

Molecular clock

a scientific technique in evolutionary biology that uses the mutation rates of biomolecules (such as DNA, RNA, or amino acid sequences) to estimate when two or more species diverged from a common ancestor

Pseudogenes

are nonfunctional duplicate copies of functional genes:

• mutations in pseudogenes are selectively neutral

• pseudogenes are among the fastest evolving parts of the genome

Synonymous vs Nonsynonymous (dn/ds)

• dn=# of nonsynonymous change(difference)/nonsynonymous site

• ds=# of synonymous change(difference)/synonymous site

• dn/ds < 1: fewer nonsynonymous than synonymous mutations = purifying selection

• dn/ds = 1: equal nonsynonymous and synonymous mutations = neutral evolution

• dn/ds > 1: more nonsynonymous than synonymous mutations = positive selection

You do not have to calculate this for exam

McDonald-Kreitman test (MK test)

more sensitive to positive selection than the dn/ds test

• dn/ds = πn/πs ------NEUTRAL EVOLUTION

• dn/ds > πn/πs ------ POSITIVE SELECTION

• dn/ds < πn/πs ------ PURIFYING SELECTION

Gene flow

the mixing of alleles from different populations

• Gene flow can introduce new alleles into one population from another population (like mutation)

• random with respect to fitness

• can increase genetic variation within a population

• can decrease genetic variation between populations

Dispersal

the movement of individuals and/or gametes

• passive and active

Passive dispersal

• passive movement

  • ex: dispersal of pollen or seeds by wind

Active dispersal

• active movement

  • ex: humans dispersing from Africa all over the globe

Migration

• migration does not lead to gene flow if it does not lead to mixing of alleles between populations

  • Migrants move to a new population and reproduce in their new home: gene flow

  • Migrants move to a new population and return to where they were born to reproduce (no mixing of alleles): NOT gene flow

Measuring gene flow

discrete patches or spatially continuous

Discrete patches

• gene flow is quantified with migration rate (m): the fraction of individuals in a population that arrives from another population in each generation.

  • ex: In a population of 1000 individuals, 120 are immigrants. m = 0.12

• ∆p = m(pm– p)

Spatially continuous

• there are no distinct populations so migration rate (m) cannot be used

• Gene flow is measured by migration variance

• Variance in the distribution of where individuals were born vs where they reproduce

• The square root of migration variance is equal to the average distance between birthplaces of parent and offspring.

FST

measures the genetic variance found across populations that results from genetic differences between them

isolation by distance

describes the pattern by which FST increases as the distance between pairs of populations increases

Local adaptation

occurs when a population is differentially adapted to a specific geographic area

(sometimes called geographic differentiation)

• Local adaptation causes high FST in areas of the genome that are

  associated with changes in the environment

Cline

a change in trait mean or allele frequency over geographical space

• Clines can occur for any trait over large or small distances

• ex: many groups of animals, are larger in colder climates (higher latitudes)

• pattern of distribution is called Bergmann’s rule

Gene flow and selection

• Selection is increasing genetic differences between populations.

• Gene flow decreases genetic differences between populations.

p = 1 – m/s

If s >> m, the allele will evolve primarily by selection

If s << m, local adaptation will be overwhelmed by gene flow; gene swamping

Gene swamping

a locally adapted allele could be lost entirely (p=0)

Gene flow and drift

• Genetic drift (like selection) causes populations to diverge and accumulate genetic differences, primarily through neutral mutations.

• The potential of genetic drift to accumulate differences in populations is limited by gene flow

• Gene flow moves all alleles, including neutral allele, across populations

Anisogamy

dimorphism in gamete size between male and female gametes

• females make the large gamete (egg)- large and immobile

• males make the small gamete (sperm)-small and mobile

Sexual dimorphism

Traits that are sexually dimorphic are expressed differently in males and females

Primary sexual traits

the physical organs and structures directly involved in human reproduction that are present from birth and mature during puberty

• ex: gonads, genitalia

Secondary sexual traits

physical features that differentiate males and females but are not directly part of the reproductive system

• ex: plumage, behavior/displays, tusks/antlers, mammary glands, size

Sexual selection

• is selection for traits that increases an individual’s reproductive success (ability to find a mate and contribute to offspring)

• Sexual selection can sometimes lead to the evolution of a trait that

  decreases survival, if the reproductive advantage is large enough:

  constrained by natural selection

male-male competition

males directly interfere with each other for access to mating opportunity

• male combat

• alternative mating strategies

• sperm competition

• infanticide

Male combat

the direct physical contest between males for access to females

• This often results in the evolution of sexually dimorphic “weapons”

Alternative mating strategies

different ways that males of the same species can acquire matings

• alpha morph: dominant in size and behavior, guards a harem of females

• beta morph: similar in shape and size to females, tricks alpha into gaining access to females

• gamma morph: small “sneaker”, can quickly slip past alpha unnoticed to gain access to females

All three morphs experience equal reproductive success

Sperm Competition

• Males will guard females until she has used his sperm to fertilize her eggs

• Males can deposit a sperm plug (physical barrier)

• Males will actively remove sperm that has been deposited by a previous male

In primates, testes size increases with promiscuity

Infanticide

• where a male will kill another male’s offspring

• After displacing the dominant male in a pride, the new dominant male will kill all of the previous male’s offspring

  • decreases the reproductive success of the previous male, increasing the new male’s fitness

  • causes females to become sexually receptive (in heat)

Female mate choice

Sexual selection can also occur through female choice

• direct benefits

• perceptual biases

• good genes

• Fisher’s runaway

direct benefits

Some males provide females with direct benefits which are resources that increase the female’s survival and reproductive success

Direct benefits can include:

• Nutrition:

  • food

  • spermatophore

  • cannibalism

• Parental care

Perceptual biases

Mating preferences that evolve by selection on pleiotropic effects in females are called perceptual biases

• female preferences evolve as a “side effect” of selection on another trait or bias

• Some female mating preferences can evolve before the preferred trait in males

• This occurs through perceptual biases

Good genes mechanism

Sometimes females chose males based on traits that are honest indicators of a male's health and fitness

• Females who chose mates with ”good genes” will have offspring with “good genes” and therefore experience better fitness

Fisher’s runaway

a process in which a mating preference and a sexual display become very rapidly exaggerated as the result of a genetic correlation that develops between them

• one way to explain Darwin’s observations regarding extreme, and seemingly maladaptive secondary sexual traits

• assumes that initially the sexual display signaled greater potential fitness, so preference for the display had a selective advantage

• These two traits, the display and the preference for the display, become genetically correlated: offspring off choosy females and long tailed males inherit the allele for long tails and preference for long tails

• Subsequently, if strong enough, female preference for exaggerated display could undermine constraints of natural selection

Why are males sexually selected?

Fundamental asymmetry of sex (Bateman’s principle)

• males are capable of fertilizing a large number of females

• males benefit from multiple matings

• females have fewer, larger gametes and invest more in mating events (parental care)

• females do not benefit from multiple matings

• Females invest more in acquiring resources for reproduction vs acquiring mate

• Females are a “limiting resource” for males

• Females are therefore the limiting factors in reproductive investment and males will compete in order to reproduce.

• Therefore, sexual selection is stronger on males than females

Operational sex ratio

the relative number of males to females available to mate

• Whenever the number of available males and females is unequal, the more common sex must compete for access (usually the males)

• Even when the sex ratio is equal, females often become unavailable because they are developing new eggs, carrying embryos to term, or carrying for offspring

Sex role reversal

a mating system in which females compete for access to males

• Usually associated with male parental care

• Bateman’s principle is reversed

• males DO NOT benefit from multiple matings because they invest so much in parental care

• females DO benefit from multiple mating because they do not invest in parental care

• Females experience more sexual selection than males

Sex ratio

• sex ratio is usually equal at birth, but this can depend on sex determination

  • Chromosomal sex determination: Sex ratio is roughly equal due to independent segregation of sex chromosomes during meiosis

  • Environmental sex determination (temperature): Sex ratio can vary depending on where a female lays eggs

  • Haplodiploid sex determination (diploid vs haploid): Females can adjust sex ratio behaviorally, fertilizing/not fertilizing eggs

• evolution tends to favor equal sex ratios

• but SOMETIMES skewed sex ratios are favored

  • ex: fig wasps

Advantages of asexual reproduction

• can also be called parthenogenesis

• do not need to find a mate

• no two fold cost of males

• no STD’s

• but asexual reproduction is rare

• animals who do asexually reproduce usually have a short life span

Two-fold cost of males

refers to the loss of fitness in a sexually-reproducing population caused by producing male offspring, that themselves do not make offspring

Red Queen Hypothesis

• yes this is named after the queen of hearts from Alice and wonderland

• “It takes all the running you can do, to keep in the same place”

• Species are in an evolutionary arms race with other species (like pathogens or predators)

• Recombination of alleles (through sexual reproduction) can increase the frequency of adaptive combinations of alleles

Selective interference

reduction in the spread of an advantageous alleles as a result of genetic linkage

• colonial interference

• ruby-in-the-rubbish

• muller’s ratchet

Recombination through sexual reproduction breaks down selective interference

Colonial interference

competing beneficial mutations, usually in asexual populations

Ruby-in-the-Rubbish

beneficial mutations are linked to deleterious mutations

Muller’s Ratchet

accumulation of deleterious alleles, usually in asexual populations

Hermaphrodites

have both male and female gonads

• When finding a potential mate is difficult, hermaphroditism is advantageous: and conspecific you find is a potential mate

• Some hermaphrodites have evolved a compromise between sexual and asexual reproduction: self-fertilization

Self fertilization (selfing)

a form of sexual reproduction: hermaphrodites produce gametes via meiosis and fertilize themselves

• Selfing (like asexual reproduction) provides reproductive assurance: increased chance of reproduction when mates are rare

• HOWEVER Offspring produced by self-fertilization are prone to inbreeding depression

Inbreeding depression

the decrease in offspring fitness as a result of inbreeding

• This is due to an increase in homozygous recessive deleterious mutations (Muller’s rachet)

Outcrossing

Many hermaphrodites outcross, or mate with other individuals

• animals can do this behaviorally

In plants:

• Male and female gametes (pollen, ovule) mature at different times

• Physical separation of male and female structures (anthers, stigma)

• Self-incompatibility

Self incompatibility

• gametes produced by the same individual are unable to fertilize one another (biochemical interactions)

• Outcrossing and self-incompatibility are mechanisms that reduce inbreeding depression in hermaphroditic species