EVE 100 midterm #2

Recombination

A type of inheritance where gene mixing occurs

• where genetic material from different sources is exchanged

• occurs in sexual organisms during meiosis

epistasis

The effect of an allele at one locus depends on the allele at a second locus

Additive allele

An allele that yields twice the phenotypic effect when two copies are present at a given locus than when a single copy is present

• Additive alleles are not influenced by the presence of other alleles (e.g dominance)

Qualitative traits

Simple traits, Mendelian traits

• dominance or recessive

• Phenotypic distribution; discontinuous/desecrate

• Number of genes involved; one to a few (monogenic)

• Effects of environment; small

• ex; sickle cell, blood group

Quantitive Traits

studies the genetic and environmental factors that influence variation in complex traits

• Additive alleles

• Phenotypic distribution; continuous

• number of genes involved; many (polygenic)

• Effect of environment; moderate to large

• ex; height, weight, genetic disorders

What about inheritance of continuous traits?

• Multiple genes can be involved

• impacted by environmental factors

How do we quantify continuous phenotypes?

using broad sense heritability (H2)

H² = V_G/V_{P =} V_G/V_G+V_E

• _{H= proportion of total phenotypic variation}

• _{VG= variance from genetic differences between individuals}

• _{VE= differences in individuals from environmental conditions they were raised}

Heritability

A proportion of the total phenotypic variance that is attributable to genetic variation

Broad Sense Heritability (H2)

Measures relative importance of genetic and environmental effects on trait expression

• genes

  h2=1 trait expression is influences by genes

• environment —> like parental care

  h2=0 trait expression is dominated by the environment

Narrow Sense Heritability (h2)

Proportion of phenotypic variance of a trait attributable to the additive effects of alleles within a population at a specific time

h2 = VA/VP = VA/VG+VE = VA/VA+VD+VI+VE

• VA= additive genetic variance

• VD= variance due to dominance

• VI= variance due to episastic interactions amount alleles at varous genetic loci

How do we figure out which genes contribute to the phenotype?

Genome wide association analyses (GWAS)

Method for identifying genes associated with a phenotype

• Scan genotype to find which loci is responsible for contributing to the genotype

what does narrow heritability tell us?

Allows us to understand how a trait in a a population is able to evolve in response to selection

what does narrow heritability not tell us?

• does not tell us about “nature vs nurture”

• does not tell us about differences between population

Selection on quantitative traits example

The horned lizard’s horn vary in size, phenotypic trait is being selected

• Those with larger horns are less likely to experience predation from butcher bird

• fitness function reveals increased horn size results in increased survival

Fitness function

displays the selection on quantitative traits

• The function that relates the phenotypic value for a trait to the average fitness of individuals with that trait value

Stabilizing/Normalizing Selection

Culls extreme variation, narrow width distributions

ex; birthweight

Directional Selections

Favors one extreme, shifts distribution left or right

• ex; bill depth

Disruptive/Diversifying Selection

Favors both extremes, creates bimodal distribution

ex; lower jawbone of birds (mandible)

Strength of Selection (S)

A measure of the strength of phenotypic selection

• Xp; all members of a population

• XB; the mean of the individuals that reproduced

S = X_p - X_B

• Small S; weaker selection

• Large S; stronger selection

S tells us the magnitude not the direction of selection!

Breeders Equation

R = h² * S

A population response to selection, it is dependent on heritability (h²) and selection differential (S)

• R; response to selection, changes caused by selection between generations

• h²; narrow sense heritability

• S; selection differentiation, changes caused by selection within a generation

Just because selection is present it does not mean the population will respond!

Limits of selection are?

A lack of genetic variation and genetic correlation are major causes of evolutionary constraints

• traits can be related but not one can be favored because they coexist

How do we know which genes contribute to the variation of the trait?

1. GWAS (Genome wide association study); scan genotype to find which loci is responsible for contributing to the genotype

   • GWAS has confirmed high polygenicity(influenced by two or genes) of many traits

2. Quantitative trait locus (QTL) Mapping; is a chromosome region containing at least one gene that contributes to variation in a quantitative trait

Manhattan Plot

A scatter plot that helps visualize the results of GWAS

• The plot helps identify significant SNP’s (single nucleotide polymorphs) and regions of the genome associated with a trait or disease

Polygenic scores

A value summarizing the predicted effect of an individuals genotype on their phenotype

part of using GWAS in health

Application of GWAS in health

Once loci are found to be associated with trait from using polygenic score, we can:

• Sequence the DNA of an individual

• Add up the effects of each locus

• Estimate the probability of developing a particular phenotype

QLT mapping experimental design

spur length seen within a section of the chromosome

• What will those chromosomes look like in our F₂s if we use our color scheme?

• Goal; Identify regions of genome where genotype predicts phenotype

Phenotypic Plasticity

The ability of individuals to produce different phenotypes when exposed to different environmental conditions

• ex; tadpoles were fed different diets head size and teeth strength differed

Reaction norm

The range of phenotypes expressed by a genotype along an environmental gradient

• Helps us identify whether phenotypic plasticity is present

Overview of Heritability misconceptions

1. Heritability is not a proportion of phenotype that is genetic, but rather the proportion of phenotypic variance in a pop. that is due to additive genetic variance

2. High heritability does not imply genetic determinism

3. Heritability are not constant (they can change)

4. High heritability does not imply genes of large effects

5. Heritability is a population parameter, therefore it depends on population specific factors

Speciation

Evolution of reproductive isolation within an ancestral species, resulting in two or more descendant species

Taxomony

Formal naming system

• Species delimitation(separation of 2 distinguishing species)

Cryptic species

Two or more species that are morphologically indistinguishable but genetically distinct, often requiring molecular analysis to differentiate them

Joshua Tree

Two different species of tree, it was found due to the differences of moths pollinating the tree

• style and ovipositor length different within two species of moth

Ring Species

A chain of interbeeding populations that forms a loop

• The population at the end of the loop are reproductively isolated but can interbreed with populations alongside them

• More reproductively isolated as distance increases

Why do we use species concepts?

to define species, it includes;

• Morphological

• Biological

• phylogenetic

Morphological Species Concept

A species is a group of organisms that look similar to each other and are distinct from other groups of organisms

Limitations:

• Cryptic species; different species can have similar morphology

• Same species can vary in morphology

Phylogenetic Species concept

A species in a group of organisms that share a pattern of ancestry and descendants that form a single branch of life

• Smallest monophyletic group of organism

Limitations:

• We decide the threshold of what makes a species

• Cannot be used in isolation

Biological species concept

A species is a group of organisms that are reproductively isolated from other species

• these organisms can interbreed and form fertile offspring

Limitations:

• Cannot test extinct species

• Would they mate in the wild? or are we forcing them to reproduce?

Morphological species concept pros and cons

Cons:

• Some species are diverged but look identical

• Some species have a lot of intraspecific variation

Pros:

• Easy

• Works with fossils

Phylogenetic species concept pros and cons

Pros:

• Reflects evolutionary history

• Works for asexual species and cryptic species

Cons:

• Cutoff is very subjective

• Can recognize too many species

• Needs sequence data

Biological species concept pros and cons

Pros:

• Reproductive isolation is biologically relevant

Cons:

• Limited to sexual organisms

• Cannot deal with fossils

• Complicated by hybridization

Why care about defining species?

1. Human Health

   Understanding which species transmits malaria (+ other diseases) to protect human health

   • Use ecological interactions to target species to reduce populations

2. Biodiversity Monitoring

   To monitor and further protect species who are vulnerable, we must differentiate them

   • Can easily confuse and aid species who do not require additional assistance if it resemble species

Endangered species act

Lists species as endangered or threatened

• Monitoring and species assessment

• Establishes protections for listed species

• Species recovery

Barriers to Gene Flow

Reproductive Barriers:

• Before fertilization (Ecological, Behavioral)

• After mating, before fertilization

• After fertilization

Geographic barriers ( allopatry)

• Gene flow ceases

• Divergence begins

Allopatry

where populations are geographically isolated and cannot interbreed due to this separation

Geographic Barriers (Allopatry)

Types of allopatry:

• Vicariance; geographic barrier divides a population

• Dispersal; individuals from one population colonize another region

Sympatry

Speciation occurs in same geographical space

• Species are more genetically different

• important barrier to gene flow is pre-zygotic isolation

Speciation in Sympatry:

Before mating barrier

Pre-zygotic barrier #1

Closely related species don’t naturally mate due to ecological or phenological barriers

• Ex: monkey flowers different pollinators ( hummingbird and bee) do not interact or transport pollen therefore no gene flow —> speciation

Is Monkey flowers two different species?

Biologically:

• Yes! in the lab they do breed and produce viable offspring

• No! they naturally do not breed

Morphological:

• Yes! Different species have different characteristics,

  Bee pollinated

  • Landing pads

  • two yellow ridges to help brush pollen onto bee

  Hummingbird pollinated:

  • more nectar (for hummingbird)

  • Lack of landing pads

  • has a longer, narrow tube

Phylogenetic:

• Yes! They form separate monophyletic groups

Speciation in Sympatry:

Post Mating, before fertilization

Closely related species can mate, but matings fail to give rise to fertilized eggs

Types:

1. Female choice:

   • Females don’t fertilize eggs after copulation

2. Gametic Incompatibility

   • Occurs when sperm or pollen from one species fails to penetrate and fertilize the eggs of another speies

Speciation in Sympatry:

Postzygotic

Bateson-Dobzhansky-Muller Incompatibilities:

• Molecular incompatibilities that arise when the genome of two species are combined in hybrid offspring

  • Hybrid can have lower fitness, or is born infertile

  • Hybrid does not persist due to being pursued by predators

Reinforcement

The evolution of stronger pre-zygotic isolation because of selection against low-fitness hybrids

• Mechanisms in place to prevent hybrids from occurring —> reinforces isolation

How does speciation happen?

1. Some sort of barrier that restricts gene flow

   • typically geographic

2. Genetic divergence between species

   • Evolution of genetic and phenotypic differences- adaptation to new ecological conditions

3. Reproductive isolation

Sexual reproduction

Reproduction where gametes (haploid sex cells) combine to form a diploid zygote

Sex

Classification based on differences in gamete size

• Male: smaller (generally more mobile) gamete

• Female: larger (more sessile) gamete

History of reproduction

Life started out reproducing asexually

• sexual reproduction is ~1 billion years old

• many reversions to asexuality have occurred

All living organisms reproduce, however not all living organisms reproduce sexually

True

Asexual reproduction

A mode of reproduction that produces offspring from a single parent, resulting in genetically identical copies of the parent

• ex: Pando, 47,000 trees in Utah are clones of one single individual

Not all sexual species have different gametes

True

Isogamy

Sexual reproduction by the fusion of similar gametes

Anisogamy

Sexual reproduction by the fusion of dissimilar gametes

• can have separate sexes ( female or male)

• can have no separate sexes (hermaphrodites)

Organisms that reproduce sexually cannot reproduce asexually

True

Not all anisogamous species have separate sexes

True

Individuals in some hermaphroditic species play equal roles in mating while individuals in other species do not

True

Not all species with separate sexes are sexually dimorphic

• Monomorphism

• Sexual dimorphism

Monomorphism

A situation in which males and females of the same species appear physically identical, with little to no sexual dimorphism

Sexual dimorphism

Refers to the differences in physical appearance between males and females of the same species

How prevalent is sexually reproduction iin animals and plants?

>90%

• Most eukaryotes reproduce sexually

Among eukaryotes, sex is common but not universal

• Asexual lineages are by large evolutionary dead ends

Cost of sexual reproduction

1. Two-fold cost of sex

   • sexual individuals produce 50% less number of offspring than asexual reproduction

2. Reduced relatedness

   • Sexual reproduction only passes down 50% of genetic material to offspring, yet sexual reproduction passes 100% of genetic material to offspring’s

3. Search Cost

   • Sexual reproduction takes time to find a suitable mate

   • Costly if population is small, it will become harder to search for a mate

4. Risk of sexually transmitted disease

   • ex: rabbits transmit syphilis

   • koala suffers with chlamydia

Benefits of Sexual Rproduction

1. Generation of novel genotypes

   • Recombination occurs and generate novel traits

2. Promotes fixation of beneficial alleles

   • By eliminating interference competition

   • By separating them from deleterious load

3. Faster evolution

   • Species must constantly adapt and evolve to survive against evolving competing species

4. Clearance of deleterious mutations

   • An important result of sexual reproduction is that deleterious alleles can be eliminated by recombination

Fisher muller effect

Sex, through recombination, eliminates competition among beneficial mutations that have arisen in different genetic backgrounds

Clonal interference

In asexual reproscution, where different beneficial mutations arise in separate lineages and compete with each other, potentially hinder the fixation of beneficial alleles

Ruby in the rubbish

beneficial mutations often appear on genetic backgrounds loaded with segregating deleterious mutations

• Shuffling genome, separates beneficial alleles from deleterious alleles

• Without recombination deleterious alleles can become linked with beneficial alleles

Muller’s ratchet

A theoretical concept in evolutionary genetics that describes how deleterious mutations can accumulate in a non-recombining asexual population over time, ultimately leading to a decline in overall fitness

What is the primary force causing disadvantages in asexual populations?

lack of recombination

Horizontal gene transfer

exchange of genetic material with one another

how do asexual species persist?

Some rotifers use gene transfer with bacteria, explaining 100 millions years of survival

• yet asexual reproduction leads to short lived lineages

Some species have both sexual and asexual reproductive strategies

1. Arrhenotoky

2. Asexual and sexual reproductive stages

Arrhenotoky

Haploid-diploid sex determination

• females: diploids

• males: haploids

Asexual and sexual reproductive stages

Transitions from asexual to sexual during lifetime