Exam 3: Biology

Species form by…

splitting off from a lineage

How can lineages split into two reproductively isolated species?

interruption of gene flow to get to a speciation event

Dobzhansky-Muller model

• population subdivided and then two groups evolve independently

• in each lineage, new alleles become fixed at different loci; the new alleles at the two loci are incompatible with one another

• genetic incompatibility between the two isolated populations will develop over time

As species pairs diverge genetically…

reproductive isolation increases

Allopatric speciation

when populations are separated by physical or geographical barriers —> they evolve through genetic drift and adaptation to different environments in the two areas —> the most common

Founder effect in allopatric speciation

some members of a population may cross an existing barrier and establish an isolated population

Dietary specialization leads to the ability to…

adaptively radiate

Adaptive radiations

single species reaching an island group and undergoing multiple speciation events

Sympatric speciation

speciation without physical isolation

Disruptive selection

type of sympatric speciation: individuals with certain genotypes prefer distinct microhabitats where mating takes place

Assortative mating

members of subgroups prefer mating within their own group

Assortative mating in sympatric speciation

helps to further differentiate groupe

Can sexual selection cause sympatric radiation?

Yes

Polyploidy can lead to…

sympatric speciation in a very short time span

Where is polyploidy most common?

plants

What must be obtained for both kinds of speciation to occur?

reproductive isolation

Incipient species

populations that are in the process of diverging to the point of speciation BUT still have the potential to interbreed —> not yet reproductively isolated

When incipient species come back into contact and hybridization…

1. if hybrids are equally fit = populations merge back into single species over time

2. if hybrids are less fit = postzygotic isolating mechanisms took place

Postzygotic mechanisms

genetic differences in diverging lineages that reduce fitness of hybrid offspring

• recued genetic compatibility

• low hybrid zygote viability

• low hybrid adult viability

• hybrid infertility

Postzygotic mechanisms result in selection ____ hybridization

AGAINST

Prezygotic mechanisms

traits that prevent hybridization from occurring in the first place

Reinforcement

individuals that do not interbreed with related species will have more offspring in the long run —> alleles that contribute to prezygotic mechanisms will spread through the population

Sympatric populations

populations that are closely related and live in the same area

Sympatric populations are expected to evolve…

more effective prezygotic barriers (have stronger reinforcement)

Prezygotic isolating

My Tint Bear Hugs Gently

1. mechanical isolation: differences in sizes and shapes of reproductive organs

2. temporal isolation: different species may breed at different times

3. behavioral isolation: individuals reject or fail to recognize mating behaviors of other species

4. habitat isolation: two closely related species evolve preferences for living or mating in different habitats

5. gametic isolation: sperm and eggs of different species will not fuse

One way to determine if sympatric species are different or not…

hybrid zones —> if reproductive isolation is incomplete, hybrid zones may form where population ranges overlap

A very hybrid zone means…

there is selection against hybrids

example: each island harbors a different species all related to a single species found on a continent

allopatric speciation by dispersion

Monophyletic

includes all descendants and common ancestor

Paraphyletic

includes common ancestor but not all descendants

Polyphyletic

includes descendants but not a common ancestor

Gonochoristic

either male or female from birth

Protogynous hermaphrodites

female —> male

Simultaneous hermaphrodites

both male and female

The Origin of Species was written by

Charles Darwin

Species

groups of organisms that mate with each other

Speciation

divergence of biological lineages; emergence of reproductive isolation between lineages

Sister species

each other’s closest relative

Morphological species concept

• introduced by Linnaeus —> also founded taxonomy and binomial nomenclature

• groups species together who look similar

• major issues include sexual dimorphism, cryptic species, regional variation, phenotypic polymorphisms (maintained by negative frequency dependent selection)

Biological species concept

• introduce by Ernest Mayr

• groups species together based on their ability to mate with each other

• some limitations: ring species, asexual species, hybridization/introgression, and extinct species

Lineage/phylogenetic species concept

• introduced by Simpson

• groups organisms that share a branch on the tree; emphasizes phylogeny

• limitations: populations can still potentially interbreed but might be classified as separate species; some divergent species may not be reproductively isolated

Ecological species concept

• introduced by Van Valen

• groups species together based on how related organisms who occupy specific ecological niches and become reproductively isolated

• limitations: could be many different ecotypes, variation in amount of divergence among ecotypes

What do all four concepts of speciation agree upon?

reproductive isolation

We want to group species into…

Monophyletic clades

Phylogenetic trees are built based on…

synapomorphies = shared, derives characters

Phylogenetics uses ____ to build the best tree

parsiomony = fewest character changes

Homoplasy

character that is not a synapomorphy; characteristic that arises randomly in different places

What causes homoplasy?

1. convergent evolution: when superficially similar traits may evolve independently in different lineages (wings in birds and bats)

2. evolutionary reversal: when a derived characteristic reverts to an ancestral trait

Homologous trait

trait shared with the common ancestor and all descendents

Morphological concept to build phylogenies

strengths

• inclusion of extinct species

• fossil evidence can order traits

weaknesses

• some taxa show morphological differences

• hard to compare distantly related species

• some variation is caused by environment

Developmental concept to build phylogenies

strengths

• clarifies deep relationships where significant divergence in form occurs in adults

• simultaneously learn about mechanisms of diversification

weaknesses

• developmental characteristics are “reused” for different functions”

Behavior concept to build phylogenies

strengths

• often as heritable as morphology

weaknesses

• trait expression often plastic

• precise measurements of comparable behavior may be difficult

Molecular concept to build phylogenies

strengths

• lots of characters

• we know a lot about trait change in DNA

• ROC vary among loci

weaknesses

• only 4 trait states per character

Mutations accumulate…

continuously

Populations accumulate neutral mutations…

at a relatively constant rate

The rate of fixation of newly-arisen neutral mutations…

EQUALS the mutation rate

If mutation rates are similar…

long-term neutral substitution rates will be too

More substitutions =

more time elapsed

Number of nucleotide changes used as a ____ to ____

Number of nucleotide changes used as a molecular clock to calculate evolutionary divergence times between species

What does a molecular clock use to gauge the time of divergence?

average rate at which a given gene or protein accumulates change

How must molecular clocks be calibrated?

using independent data— fossil record, known times of divergence, or biogeographical dates

Applications of phylogenetic studies

• relationships among organisms

• origin of characters

• sequence of character evolution

• how many times and where characters evolved independently

Phylogeny

evolutionary history of a group

Systematics

classification of living organisms

Systematics includes…

1. taxonomy- binomial nomenclature —> Linnaeus

   1. genus and species name

   2. NOT always accurate!!!

2. phylogenetics

Root of a phylogenetic tree

ancestral lineage- least common ancestor

What are most phylogenic timelines based on?

geological and molecular evidence

Branch of phylogenetic tree

lineage

Branch points of phylogenetic tree

aka nodes; speciation event

phylogenetic trees are based on…

shared characters

How are taxa sorted?

characters states

Parsimony

fewest character changes

Shared characters are either…

homologous (what we want) or analogous (not useful)

Outgroup

serves as a reference group; should be closely related but WITHOUT shared derived characters that unit the ingroup

Does genome size vary greatly among taxa?

Yes, because of difference in the amount of non-coding DNA

How are genomes measured?

in base pairs

Does genome size represent the complexity of an individual?

NO

What is most of the genome made up of?

non-coding DNA

Some non-coding DNA contains…

pseudogenes

Can non-coding DNA alter the expression of genes?

Yes, of surrounding genes; they can develop novel functions

Transposons

jumping genes = move around different areas and impact gene expression/function

The amount of noncoding DNA may be related to…

population size

What is the best way to increase fitness?

sexual reproduction- pass on genes

Two-fold cost of sex

• female only passes 50% of her genes to each offspring

• dividing offspring into gender reduces a female’s overall reproductive rate

• recombination’s can break up adaptive combinations of genes

In a sexually-reproducing population, a single ____ will have…

a single asexual mutant will have higher fitness

What a

mutations

Muller’s ratchet

deleterious mutations accumulate in asexual species causing a genetic load; only death of the lineage can eliminate them

Sexual reproduction does NOT directly influence…

frequency of alleles- it just recombines them

How do novel traits arise?

1. lateral gene transfer: individual genes, organelles, or genome fragments move horizontally from one lineage to another —> antibiotic resistance

   1. increased resistance, increased female bias, incompatible offspring

2. gene duplication: genomes gain new functions

   1. both copies keep OG function

   2. each copy may specialize

   3. one copy accumulate deleterious mutations and becomes functionless (pseudogene)

   4. one copy retains OG function, the other changes and evolves a new function

Least likely to be a source of evolutionary novelty

genetic drift

Nucleotide substitution

change in one nucleotide in a gene sequence (point mutation)

Synonymous substitution

do not affect phenotype —> syn = same

Nonsynonymous substitution

specified amino acid does change —> deleterious, selectively neutral, or advantageous —> nonsyn = not same

What is more common: synonymous substitutions or nonsynonymous

synonymous

nonsynonymous = synonymous

neutral selection —> no selective force

nonsynonymous > synonymous

positive selection: directional selection

nonsynonymous < synonymous

purifying selection: stabilizing selection

Kimura’s neutral theory

• majority of variants in most populations are neutral

• NOT saying all/most mutations are neutral\

• most genetic variability does not affect the survivability of organisms

Genetic drift

random changes in allele frequencies from one generation to the next —> more significant in small populations

Probability of allele becoming fixed =

frequency in the gene pool in a given generation