Bio 120 Test 2 (Lec 9-12)

Biological Species Concept

Species = group of org that can naturally mate w/ each other + reprodutively isolated from other groups

Cohesion species concept

Species = group that shares gene flow + shared traits from natural selection

Competition species concept

Species = org that compete w/ eachother for same mates/resources

Ecological species concept

Species = org that live + adapt to same environmental niche

Evolutionary species concept

Lineage that evolved seperately from others + distinct evolutoinary role

Genealogical species concept

Species = share close family tree + resemble eachother more than speices outside pop. 

Genetic cluster species concept

Species = org with distinct DNA with no genetic intermediate groups compared with others

Isolation species concept

Species = org with internal traits (genetics/anatomy) that naturally block them from breeding with other species aka reproductively isolated

Morphological (Phenetic) species concept 

Species = org that looks physically similar to eachother than other groups.

Phylogenetic species concept

Species = smallest group on family tree sharing unique evolutionary traits

Recongition species concept

Species = org that can recognize each other as potential mates + use specific signals/traits

Typological species concept 

Old-school view where species = fixed + unchanging "ideal" body 

Who proposed the biological species concept?

Ernest Mayr

What are the 3 qualifications for the biological species concept? 

1. Natural population- Org must be able to interbreed NATURALLY in wild (not captivity)
2. Potential inbreeding- Org has capacity to inbreed if geographic barriers = removed
3. Reproductive isolation- Org must be reproductively isolated from other species

Why is it important that biological species concept (BSC) emphaszie natural population? 

Species that interbreed in captivity ≠ interbreed in wild

What are the 3 limitations of BSC? 

1. Allopatric population- Population live in diff locations and can't meet mate (can't tell if they had potential to interbreed or not) 
2. Extinct species- Can't test whether extinct org could interbreed (only determine morphologically) 
3. Asexual org- BSC only works for sexual reproductive org. Asexual org still species

Distinguish between splitting + merging

1. Splitting: Pop become more reproductively isolated and form seperate species
2. Merging: Populations interbreed (hybrdization) + merge back together 

Define speciation continuum

Gradual stages of speciation where single population differentiates

Define pre-mating isolation

Reproductive barriers that reduces freq of success of mating BEFORE mating attempt

Post-mating, prezyotic isolation

Reproductive isolation AFTER mating occurs but BEFORE zygote is fertilized

Define prezygotic isolation

Reproductive isolation AFTER fertilization

List + define the 3 diff types of premating isolation

1. Ecological- Population live in diff habitat/niche= less likely to meet + mate
2. Behavioral- Org in diff pop do NOT recognize each other as mates
3. Mechanical- Reproductive body parts not compatible

List 2 mechanisms of ecological isolation

1. Migration (indiv move to diff habitat = lower survival rates cuz not adapted to it) 
2. Diff habitat pref (indv prefer to stay in habitat they are adapted so populations of potnetial mates = rarely meet) 

What are the 3 factors of mechanical isolation

1. Size diff: org w/ diff size ≠ mate success
2. Genital incompatability: Reproductive organs don't fit together (lock + key mechanism)
3. Structure diff (flower): Pollen can't be transferred properly between plant species

Define gametic isolation 

Type of post-mating, prezygotic isolation. Sperm + egg cells can't fuse successfully cuz surfaces of sperm/egg don't recongize eachother and thus doesn't bind 

List 2 types of post-zyogtic isolation

1. Intrinsic incompatibilities: Genetic problems reduced hybrid survival/reproduction REGARDLESS of environment
2. Extrinsic incompatibilites: Hybrids are poorly adapted to environment so environment influences difficulty of finding mates

List 2 types of intrinsic incompatibilites

1. Hybrid inviability: Hybrid CANT survive/develop 
2. Hybrid sterilty: Hybrid survive but CANT reproduce

Define mito-nuclear incompatibilities

Mitochondrial genes from one parents + nuclear genes (DNA) from another  ≠ not work properly causing cellular function problems 

What is behavioral sterility in hybrids?

Hybrids have difficulty finding mates because mating signals/behaviors are not attractive/recognizable to other indiv

Why is reproductive isolation = complex trait?

Multiple reproductive barriers work tgt to prevent gene flow and they can all work at same time

What is evolution of reproductive isolation?

Process where populations develop barriers to prevent them from successful reproduction → speciation

List 3 scenarios for evolution of reproductive isolation

1. Polyploidization: Instantly evolve reproductive isolation cuz of change in chromosome #

2. Allopatric speciation: Pop become geographicaly seperation = reproductive isoaltion

3. Ecological speciation: Pop adapt to diff enviornment = reproductive isoaltion evolve even while gene flow continues

Define unreduced gametes

Sex cells that have not reduced chromsome # during meiosis

List 2 types of polyploidization

1. Allopolyploid speciation: Chromosome sets from 2 diff species combine → new fertilie species = uneven chromosome set (unreeduced gamete)

2. Autopolyploid speciation: Chromosome sets from SAME species = duplicate entire set of chromosome

List the 3 stages of allopatric speciation

1. Geographic isolation- Barrier seperated 1 population from other

2. Population divergence- Seperated pop evolve diff

3. Secondary contact- Populations meet again + remain seperated OR merge back tgt

List 2 mechanisms of geographic isolation

1. Dispersal: Org cross an existing geographic barrier + colonize new habitat

2. Vicariance: New geographic barrier forms + seperates an exisiting population

Define population divergence

Geographically isolated pop gradually develop genetic/physical diff

Define divergent selection

Diff enviornment = favor diff traits → cause populations to become more diff

Define incipient species

Populations that have STARTED to become seperate species but not COMPLETED speciation

List the 4 diff outcomes of Secondary Contact

1. Fusion- Population interbreed + merge back into 1

2. Reinforcement- Reproductive isolation = permanent because natural selection discourages cross-breeding (too much wasted time mating for weak offspring)

3. Stable hybrid zones- Parent population still distinct but narrow zone where habitat overlap = hybrids produced. Hybrids only suitable to survive in the hybrid zone (intermediate of parents’ environment)

4. Hybrid speciation- New species of hybrids are created that are stronger than parents because unique traits = more niche

Define Dobzhansky-Muller Incompatibilities

Genetic problems that occur when genes that evolved seperately in diff populations = not work well together in hybrids

How do Dobzhansky-Muller incompatibilities develop?

Geographic isolation, genetic drift, natural selection. Can still occur without genetic incompatibilites such as other reproductive barriers (mechnical, behavioral, ecological)

Define reproductive character displacement

Related species develop BIGGER diff in mating traits/preferences in areas they live together to prevent hybridization (low fitness)

Define hybrid zones

Geographic area where 2 diff species meet + interbreed = produce hybrids

List 2 types of stable hybrid zones

1. Tension zones: Continous dispersal (parents move to diff location) + hybridization between parental species. Hybrids produced but have LOW fitness.

2. Bounded hybrid superiority zones: Hybrids have HIGH fitness than either parent in enviornment

Define introgression

Permanent transfer of genes from one species → another via hybridization/backcrossing (hyrbid repeatedly mates w/ parental species)

Define repeated backcrossing

Breeding process where hybrid offspring is repeatedly mated back w/ parent over multiple genration to transfer specific desirable trait

Define hybrid speciation

2 diff species hybridizie + produce new population that becomes reproductively isolated from both parent species

Define homoploid hybrid speciation

Hybridization creates new species WITHOUT changing # of chromosome sets. (same chromosome # as parents). Can go back to the parent species via backcrossing

Distinguish between allopatric and sympatric speciation

Allopatric: Populations are GEOGRAPHICALLY seperated
Sympatric: Populations evolve into DIFF species while living in SAME area

List 5 enviornmental differences that can cause divergent evolution

1. Diff habitat/climate

2. Diff food resources

3. Diff predators/competition

4. Diff parasites

5. Diff mating signal/preferences

Define magic traits

Traits that have 2 functions: help organism adapt to enviornment AND infleunce mate choice

Why are magic traits important in ecological speciation?

Single traits can cause both ENVIRONMENTAL adapation + ASSORTIVE MATING (pref to similar mates)

What is an example of magic trait in Darwin’s finches?

Beak size not only for adapted to eating food but also affect mating songs

List 4 criteria for adaptive radiation

1. Common ancestry: All species come from recent common ancestor

2. Phenotype-enviornment correlation: Diff phys traits = diff enviornments/niches

3. Trait utility: Trait helps org survive/reproduce better in their niche

4. Rapid speciation: Many species form in relatively short period

Distinguish between phenotype-environment correlation and trait utility

Phenotype-environment correlation: A trait is associated with a particular environment.

Trait utility: That trait actually provides a survival or reproductive advantage in that environment.

What are the 2 triggers of adaptive radiation?

1. Ecological opportunity: Many available niches that org can adapt to available

2. Key innovations: new evolutionary triats that allow org to enter/use new ecological niches

Why are African cichlid fish important examples of adaptive radiation?

They rapidly evolved into 100s of species in diff niches in Lake Victoria/Tanganyika/Malawi

List 3 main ecological axes of cichlid diversification

1. Macrohabitat: Species adapt to diff habitats

2. Trophic resource: Species specalize in eating diff foods

3. Communication: Species develop diff mating signals/pref

How does lake size affect chichilid species diversity?

Larger lakes = more ecological niches = more species evolve (generally)

What is the key innovation of chichlid fish?

2 specialized jaws:

• Oral jaws: Capture food

• Pharnyngeal jaws: Process food

Allows them to specalize in diff feeding adaption/food resources

Define transgressive segregation

When hybrid offspring develop traits that fall OUTSIDE range of both parent species. New traits for hybrids to use resources that parents can’t

Why can younger adaptive radiations have more species than older ones?

New species form rapidly early (less competiton) but over time nautral selection acts and eliminate species over time

Define microallopatry

Geographic isolation between populations over very small distances

How is there microallopatry in chichlid fish?

Cichlids live on rocky reefs w/ lots of sandy areas that act as barriers + lake level changes = repeate seperate/reconnect population → higher chance of reproductive isolation

How does sexual selection contribute to cichlid adaptive radiation?

Females prefer males with particular mating colours, reducing interbreeding between populations.

List 4 main factors that contributes to chichlid addaptive radiation

1. Ecological opporutnity + key innovation

2. Hybrdiization

3. Microallopatry + lake level fluctuations

4. Sexual selection

Define macroevolution and what it shows us

Study of evolutionary process + patterns AMONG species

Shows rise/fall of biodiveristy + rates/patterns of phenotypic evolutions across big timescales

List 2 sources of macroevolutionary insights

1. Paleontology: Direct record of past evolutionary change Most reliable evidence = fossilized species

2. Phylogenetics: Indirect record of past evolutionary change. Most reliable evidence = living species

List the 3 major eras of biologial time on Earth

1. Cambrian Explosion: Animal diversity increased dramatically over relatively short interval. 1st fossil appearance + diverse body/skeletons/organs

2. Phanerozic Eon: Complex multicellular life diversified + diff animal clades grouped into 3 faunas (Cambrian/Paleozoic/Modern)

3. Modern Era: Current state of Earth’s biosphere

Define mass extinction

Normal process over geological timescales where entire clades elimated. Mass extinctions > background rate (everyday speed where species die naturall over time via compettion/predation/enviornment w/o human interference)

List 4 triggers for mass extinction

1. Asteriod impact

2. Massive volcanic eruptions

3. Climate system change

4. Change in biological communities

Define unit of selection

Level of biological organization that nautral selection acts on (ex: genes/cells/individuals/species)

Define transposable elements (TEs)

DNA sequence that can move/copy themselves to diff locations in genome

Why are TEs called selfish DNA?

They can increase their own # of copies even if it harms organism

How do TEs cheat Mendel’s laws

By making extra copies of themselves = appear more than 50% of gametes

What are 2 methods to prevent TEs from spreading uncontrollably?

1. TE silencing: DNA/histone methylation

2. Transposition-selection balance: Balance between TE making new copies + natural selectoin removing harmful TE insertions (reduce fitness)

How is cancer an example of natural selection at cellular level?

Cancer cells evolve mutations that help them divide faster/avoid cell death = more spread. They increase their own reproduction even though it’s harmful = selfish

What does it mean when levels of selection conflict with eachother?

Trait that increases fitness can also decrease fitness at another level (ex: cancer benefit from rapid cell divison but harms individual)

What is DNA sequencing?

Method used to determine exact order of DNA bases

Define Sanger sequencing

Sequencing method that reads specific region of DNA (typically gene of interest)

Define next-generation sequencing (NGS)

Method that produces millions/billions of short DNA sequences (reads) from diff parts of genome

Define DNA sequence alignment

Arranging DNA sequneces from diff samples so matching (homologous) nucleotides = lined up.

List 2 ways to reconstruct DNA sequences from short reads

1. Reference-based assembly: Matching short reads w/known reference DNA

2. De novo assembly: Overalapping regions between reads used to reocnstruct DNA w/o reference

Define consensus sequence

Inferred DNA sequence. Made my combining info from multiple aligned reads of same sample

How are DNA sequences used to study evolution within species?

1. Genetic diff between pop

2. Migration/gene flow

3. Pop history measure

Define phylogenetics

Study of evolutionary relationships between organisms

Define phylogenetic tree

Diagram showing how organisms are evolutionarly related via common ancestors. Only HYPOTHESES

What do tips/internal nodes/nodes/branches/monophletic group (clades) of phylogenetic tree represent?

Tips: Organisms/groups being studied

Internal nodes: Inferred common ancestors where evolutionary lineage splits
Nodes: Historical lineage splitting events where lineage splits into 2

Branches: Single ancestor-descendant lineage
Monophletic group (clades): Piece of phylogeny that includes ancestor + ALL descendents

Define molecular phylogeny

Phylogenetic tree built using molecular data (DNA/amino acid sequences)

Define maximum parsimony

Method that favors evolutionary tree requiring FEWEST evolutionary changes

Define phylogenetic distance

Measure of genetic diff between 2 organisms based on DNA/amino acid sequence. Smaller distance = more similar sequence and vice versa

Define phylogenetic distance matrix

Table showing genetic distances between every pair of organisms being compared

2 important features of phylogenetic distance matrix

1. Diagonal value = zero cuz organisms has NO genetic distance from itself

2. Matrix = symmetrical because distance from A to B = B to A distance

List 5 steps to build a molecular phylogenetic tree

1. Collect DNA/amino sequence

2. Align sequence to match homologous positions

3. Calculate genetic distances between organisms

4. Create distance matrix

5. Use algorithm to construct phylogenetic tree

Define synapomorphy

Shared/derived trait for particular clade where all species in clade share + evolved from immediate ancestor of that clade

Define homoplasy

Shared phys trait/behavior/DNA sequence in 2+ diff species that did NOT come from common ancestor (analagous traits/convergent evolution)

Define neighbour-joining algorithm

Method that uses genetic distances to build phylogenetic tree

Define outgroup

Taxon outside main group being studied. Used to see where tree root belongs

List 2 major limitations of distance-based phylogenetic method

1. Convergent evolution: unrelated org can independetly evolve similar charactersitics/sequences (so not actually prove they were related)

2. Diff evolutionary rates: some lineages evolve fast than others → can lead to incorrect groupings