BIOL215 Midterm

Evidence for Evolution

Uniformity of life, common descent, fossils, and extinction

Adaptation

Fit between organism and its environment

Lack of fit → selection can improve fit
Technical Definition: heritable phenotype that increases fitness and is caused by natural selection in the current environment 

Natural Selection

One of four mechanisms for evolution

One lineage replicates faster than others

Phylogeny

Evolutionary history of a lineage or lineages (populations, genes, or species)

Phylogenetic Tree

visual representation of a phylogeny

Monophyletic Group

group of organisms that includes a single common ancestor and all of its descendants, forming an unbroken line of evolutionary descent 

Clade

monophyletic group within a phylogenetic tree
includes all species descended from a common ancestor

Paraphyletic Group

leaves out some taxa sharing a common ancestor

Polyphyletic Group

includes taxa descended from multiple common ancestors

Characters

Identifiable heritable traits

Character States

Condition of the character

Ex: Character—wings 

Character States— present, absent 

Described as ancestral and derived 

Outgroup

Species outside of the clade

Shares a common ancestor with monophyletic clade on interest 
Help identify synapomorphies 

Synapomorphy

Shared derived character state, homologous characters (inherited from common ancestor)

Homoplasy 

Character state similarity not due to common descent 

Convergent evolution: independent evolution of similar trait

Evolutionary Reversals

reversion back to an ancestral character state

ex: swimming in whales

Maximum Parsimony

fewest evolutionary steps is preferred
more than one tree is equally parsimonious → consensus tree
logistically most likely to happen 

Polytomy 

relationships between species are uncertain

Maximum likelihood

Statistical approach to deciding on a tree
Range of trees is generated → most likely tee selected based on a particular model of evolution 

Purifying Selection

selection wants to preserve function → evolve slowly

removes deleterious mutations and genetic variants from a population

ex: exons 

Maximum Parsimony in Genetics

accounts for variable rates of evolution and homoplasy → more weight to slowly changing regions and less to rapid changing regions '

depends on interest in deep time or recent time

Deep Time

slowly evolving genes

Recent time

rapidly evolving genes

Bootstrapping

Used when have multiple equally parsimonious trees

Resample and reconstruct trees → resampled tres are similar is strong support for observed tree

Value 0-1 (1 is most likely)

Distance-Matrix Methods

more genetically similar → more likely to be closely related 

branch lengths indicate number of changes 

Models of Molecular Evolution (simple & complex)

Simple: all sites equally likely to mutate
Complex: different rates for nonsynonymous v synonymous, transitions v transversions, → genes evolve at different rates

Bayesian Method

Start with model and tree, slightly change tree many times → creates probability distribution of possible trees

Phylogenetically Independent Constrasts

Series of comparisons between nodes and tips of a phylogeny 

Synonymous mutations

Don’t alter amino acid sequence, selectively neutral

Nonsynonymous mutations

Change amino acid sequence → subject to selection

Neutral Theory of Molecular Evolution

most evolution at molecular level is neutral and caused by random processes associated with genetic drift → neutral mutations become fixed in lineages at a regular rate 

Selectionist Theory

Mutations are either advantageous or deleterious, selection is what drives molecular evolution/genetic diversity

Neutralist Theory

Most mutations are neutral, and genetic drift is the main cause of evolution

Selective Sweep

a beneficial allele will fix far more quickly than a neutral allele since its selected for → dip in genetic diversity at chromosome position where it becomes fixed

Genetic Hitchhiking

Mutations linked physically (right next to) selected genes also have very high frequencies 

Eventually broken up by recombination in sexual reproduction over time 

Dispersal 

Movement of populations from one region to another 

Limited or no return

Vicariance

Formation of geographic barriers that divide a once-continuous population

Anagenesis versus Cladogenesis

Ana: Creation of new species through gradual, step-wise change
Clado: Faster, lineage splitting 

Gradualism

slow, gradual morphological changes over time → speciation through anagenesis 

Evolution by creeps 

Punctuated Equilibrium 

Long periods of stasis (no change) → brief periods of rapid morphological change → species by cladogenesis 

Evolution by jerks 

Diversity

balance between origination and extinction

Turnover

Number of species eliminated and replaced per unit of time

Standing diversity

Number of species present in an area at a given time

Adaptive Radiation

Rapid diversification of a lineage into a range of ecological niche specialists 

Origin rate > extinction rate 

Ecological Opportunity

Presence of vacant niche space → room for diversification of a lineage into a free niche (role) 
Distinct niche specialists favored in different environments → speciation 
Absence of predators → ecological opportunity for a lineage 

Key Innovation

trait that allows a lineage access to new resources

species take advantage of a resource not previously being used 

Evolution novelty 

New genetically based trait

Paradox of novelty: changing something that works → worsens life, evolution tinkers and uses old materials in new ways 

Novel Gene Generation: 
pop. in new env. using accessible enzymes and proteins → slow growth rates since limited resource → fitness improved as pop. grows → pop. large enough → opportunity for modification through selection → fitness improves

Innovation

Act of introducing a novelty

Synonym for evolutionary novelty 

Excaptation/Co-option 

An existing gene function for one purpose starts preforming a new role

Amplification

Making more of what you have, even if its not the best it possible could be

Paralog

Gene descended from duplication of same genome → have two copies of gene → choose to use one

Divergence

improves fitness through changes in gene function

Amplification and divergence can work together → amplification causes two copies → one diverges while other still keeps original function 

Background extinction 

normal rate of extinction for taxa or biota 

Mass extinctions

statistically significant increase about background extinction rates 

What’s the fuel of evolutionary change?

Mutations

Mutations → selection 

Recombination only moves things around but doesn’t create new variation 

How do mutations affect fitness?

Most are deleterious or neutral, very few are beneficial

What is Fisher’s Geometric Model?

It’s easier to make a well-adapted system worse than better 

What mutations matter for evolution?

Germ-line mutations (in gametes) are heritable
Somatic mutations (in body cells) are not heritable (ex: cancer)

Why aren’t recombination and independent assortment sources of novelty?

They mix things up and create new genetic combinations but NOT new genetic material or variation

Genotype and Environment Interaction

Phenotype = Genotype + Environment

Genotype

Genetic makeup of an individual
Combo of alleles carried by an individual at a locus of few loci

Phenotype

observable, measurable characteristic

Polyphenic Trait 

Single genotype produces multiple phenotypes 

Many genes may be involved → express modified by environment 

Phenotypic Plasticity 

Same gene having multiple phenotypes based on environment 

Ploidy

Number of copies of unique chromosomes in a cell

Pseudogenes

Non-functional genes

Types of Mutations

Point, insertion, deletion, gene duplication, inversion, chromosome fusion, genome duplication

Population 

Group of interacting and potentially interbreeding individuals of the same species

Genetic locus

Location of specific gene/sequence of DNA on a chromosome

Population Genetics

study of allele distributions and frequencies in space and time

Evolution

Change in allele frequencies form generation to the next

Null Model (in evolution)

Distribution of allele and genotype frequencies if there are no forces acting on it (no selection, drift, mutation, or migration)

Assume null model → no evolution → same frequencies in multiple generations

How do different mutations affect population?

Strongly deleterious: never establish → eliminated very quickly by selection
Beneficial mutations: if not last by chance → sweep very quickly
Mildly deleterious and neutral mutations: can be lost or increase frequency due to chance

Genetic Drift

deviations in allele frequencies caused by chance alone 

Bottleneck

Temporary reduction in population size → low genetic diversity/variation (often inbreeding) 

Founder Effect

Type of bottleneck

Small # of individuals colonizing a new isolated habitat 

Why does natural selection occur?

Replication of hereditary material is imprecise → genetic variation

Some lineages replicate faster 

Quantitative Genetics

Evolution of continuous phenotypic traits → polygenic → many genetic loci

More loci → more phenotypes → continuous distributions 

Polygenic Trait

trait influenced by many genes at many loci (epistasis) and at one locus (dominance)  

Heritability

Proportion of phenotypic variance attributable to genetic differences among individuals → property of population 

Ratio of variances 

Heritable 

Whether something can be inherited or not 

Trait can be heritable with no heritability 

Stabilizing Selection

Agents of selection oppose each other → average of the two selected for

Ex: detrimental to be too big or too small for separate reasons → average size

Disruptive Selection 

Extreme traits favored over average ones 

Opposite of stabilizing selection 

Leads to speciation 

Phylogenetic Species Concept (PSC)

Smallest possible group descending from common ancestor

Recognizable by synapomorphies (unique, derived traits)

Count the nodes

Biological Species Concept (BSC)

Species are groups of potentially interbreeding populations that are reproductively isolated from such other groups 

General Lineage Species Concept (GLSC)

Metapopulations that exchange alleles frequently enough to comprise same gene pool (spatially separated populations, any gene flow)

Allopatry

Geographic barrier, spatially separate populations evolve without gene flow between them 

Not enough alone to judge if 2 populations are separate species

Reproductive Isolation

Can maintain species barriers even species are together (in sympatry)

RI: Pre-mating

Isolation before mating even occurs

RI: Post-mating/Prezygotic (Copulatory behavioral isolation & Gametic incompatibility) 

After mating, before zygote forms

Copulatory behavioral isolation: mating results in damage to female reproductive system 

Gametic incompatibility: Sperm fails to fertilize egg

Post-mating/Postzygotic

Hybrids produced often have low fitness, can be sterile

Allopatric Speciation

Geographical isolation → no gene flow

Sympatric Speciation

No geographic isolation → complete gene flow

Ex: plants evolving different flowering times → reproductive isolation

Reinforcement

natural selection favors prezygotic isolation mechanisms → prevent formation of hybrids with reduced fitness

hybrid mating VERY RARE even in sympatry

Ecological Speciation

selection for different ecological traits in different niches → reproductive barriers → pre & post zygotic isolation 

Bateson-Dobzhansky-Muler Incompatibility

genetic incompatibility in hybrid offspring caused by epistatic interactions at two or more loci → genes that work fine separately cause problems when together

Allopolyploidy

polyploidy (different number of chromosomes) resulting from interspecific hybridization 

extremely rapid selection 

AFTER ORIGINAL POLYPLOIDY: entire genome duplication in hybrids of species with different # of chromosomes → viable offspring → often new species 

Stable Ecotype Model

Niche specific adaptations define species in microbes