BIOL215 (copy minus early price stuff)

Autotrophs

Obtain carbon from inorganic sources (CO2), self feeder like plants, phytoplankton etc

Heterotrophs

Obtain carbon from organic molecules, feed on other things like carbs proteins fats from food

• secondary production, consume primary producers

lineage

chain of ancestor-descendent connections over time

Natural Selection

- Definition: The process that results from the differential survival or reproductive success of a lineage

• causes heritable phenotypes with genetic basis that change in response to the environment

• more effective in bringing about change in large populations

• rate of this happening is an estimate of selection

• consequence of this process is an adapatation

• variable over time and can result in rapid evolutionary change

Fitness W_i

- Definition: A measure of reproductive success

- Types:

  - Relative fitness: Absolute fitness scaled by a standard (compared to others)

  - Absolute fitness: Rate of replication

adaptation

the fit between an organism and its environment

• formally the heritable phenotype that increases fitness and has arisen due to natural selection in the current environment

• a consequence of natural selection

• can occur because there is heritable variation

• xxx to one environment comes at the cost of xxx to another environment

evidence for evolution - design versus descent

• all life uses the same basic inefficient materials and processes

• this is only explained by the fact that we all descend from a common ancestor

• common descent: children resemble their parents, we are similar and we share ancestral genes

• designing an organism would make use of a wider array of processes

homologous trait

similar because of inheritance from a common ancestor. ex: human arm, seal flipper, bat wing

evidence for evolution - extinction

• majority of species are extinct, species living now only represent ~1% of total biodiversity

• fossils are abundant and diverse, more living species have gone extinct than are currently living

• species lifespan is about 5my

• ex. fossil horses first originated in asia but there were species everywhere that evolved over 55my, each species lived ~3my

evidence for evolution - adaptation

• function and ancestry contribute to the evolution of the form

  ex. large marine animals like whales, fish and sharks share a fusiform body shape that minimizes drag in the ocean

• sharks share a CA w fish but whales are mammals descended from a hippo-like terrestrial ancestor

• thus these animals share body plan through adapting to aquatic life NOT shared ancestry

Vestigial Organ

An organ or structure that has lost its original function through evolution

Adaptive Radiation

- Example: Galapagos finches from a common mainland ancestry within the last 3 my another example of their adaptations is beak length increasing after a long drought

• environment acts as a potent source of selection

- Definition: The process by which organisms/a lineage diversify rapidly into several new ecological niche specialists

• resource driven selection

Theory of Evolution

  - Composed of many hypotheses, modification with descent resulting in a change in the genetic composition of a population, contingent and only makes use of materials available to it

  - Not progressive (no species is inherently better than others)

  - Involves not just selection, but also drift, migration, and mutation

  - Undirected, with no intelligent designer

DOES NOT occur for good of the species

Topology

Definition: Alternative evolutionary histories represented in phylogenetic trees

Phylogeny

- Definition: A tree-like diagram showing evolutionary relationships, history of a lineage(s) (populations, genes or species)

- Key features:

  • Parents/species/populations are at nodes: represent common ancestors for all descendent species

  • Tips represent species

  • Branches connect species, converging at nodes, trees do not depict a hierarchy or continuum

pedigree

individuals

• in a sexual species, a node represents a recombined genome from two parents

• any number of offspring can result

clade

a common ancestor and all its descendents

Taxon

- Definition: A named group of species, genus, order, or class

- Note: Different traits define the categories

monophyletic groups

clade, represents all species descended from a common ancestor

paraphyletic group

a group that leaves out some taxa, sharing a common ancestor

polyphyletic group

a group that includes taxa descended from multiple common ancestors

Linnean classifications

• he organized species in names based on shared characters

• modern taxonomy aims to construct more accurate phylogenies in terms of evolutionary history

• his was NOT an evolutionary taxonomy

characters (character states)

identifiable, heritable traits

• states would refer to present or absent

• ancestral or derived (ex. vestigial organs appendix) NOT primitive and advanced

outgroup

species that is outside of the clade whose relationships we wish to resolve

• shares a common ancestor with the monophyletic clade of interest

• character states resemble those of the common ancestor

• allows for a direction to be set from ancestral (shared w the xxx) to derived (not shared) on an evolutionary change

synapomorphy

shared derived character state

• homologous characters because they’re inherited from a common ancestor

• including gene sequences

• has evolved independently in multiple taxa from a shared ancestor

• is only character type that can be used to resolve phylogenetic relationships because it 1) differs from the outgroup and 2) is shared by some but not ALL taxa in the clade being studied

homoplasy

character state similarity NOT due to common descent rather caused by

• convergent evolution or evolutionary reversals, or parallel evolution

• so its the same character but NOT bc of evolutionary histories

Convergent Evolution

Distantly related species evolve similar traits due to similar selective pressures.

they resemble eachother more than their ancestors did

- Examples: Bats and birds, porcupines and hedgehogs (wings and spikes)

evolutionary reversals

reversion back to an ancestral character state eg. swimming in whales

• especially common in DNA sequences because each site takes ¼ character states and mutation can access all of them

Parsimony

- Definition: The principle of choosing the simplest explanation or hypothesis, fewest evolutionary steps is preferred

- Application: In phylogenetics, favoring trees with fewer character state transitions 

Polytomy

- Definition: An unresolved branching in a phylogenetic tree

- Usage: When we can't determine exact relationships between species

Homology

- Definition: Similarity due to shared evolutionary history

- Example: coelacanth Fish fins are xxx to tetrapod limbs as theyre more lobed and stronger

another example: mammalian ear bones are xxx to bones of reptile jaws, they evolved over time to work in the inner ear of the opossum

exaptation

natural selection co-opting a trait for a new function: ex panda’s thumb

exons

protein coding genes

• under strong purifying selection because function will be preserved and tends to evolve slowly

introns

neutral in the eyes of selection and evolve faster

Parallel evolution

Similar traits evolve independently in related lineages

Bootstrapping

- Definition: A resampling technique used in phylogenetic analysis

- Process:

  - Resamples the dataset multiple times

  - Constructs trees from each resampled dataset

  - Provides support for phylogenetic inferences 

what do distance matrix methods tell us ?

lineages that are more genetically similar are more likely to be closer related

Maximum Likelihood Method

- Definition: A statistical approach for phylogenetic tree construction

- Key features:

  - Uses a molecular evolution model

  - Calculates probability of observing the data given a tree

  - Selects the tree with the highest probability (best xxx)

bayesian methods

start w a model and a tree, change the tree slightly many times

• generates probability distribution of possible trees, those with the highest probability are preferred

is HIV monophyletic?

NO! HIV evolved using convergent evolution, not a single spillover event. M,N independently evolved in chimps O,P independently evolved in gorillas, both directly from SIV. (attacks white blood cells, causing immune deficiencies)

M,N,O,P share a common mutation NOT found in SIV.

Phylogenetic Independent Contrasts

- Definition: A method for comparing traits across species while accounting for phylogenetic relationships

• looks at correlation among traits based on evolutionary independent transitions

- Application:

  - Used to test correlations between traits

  - Helps avoid false conclusions due to shared ancestry 

• take the mean of two traits branching off the same node

Synonymous Substitutions (dS)

- Definition: Mutations in DNA that don't change the amino acid sequence

- Characteristics:

  - Governed by chance alone

  - Used as a molecular clock for estimating divergence times 

• often but not always selectively neutral

non-synonymous mutations

change the AA sequence of a protein and more likely to be subject to selection

neutral theory of molecular evolution

Kimura (1968) formalized it

• most evolution at molecular level is NOT selective and is governed by processes associated with genetic drift

• neutral mutations become fixed in lineages at regular rates

• support for the theory arose from substitutions in cytochrome c gene which showed more distantly related species had more substitutions and a linear relationship

selectionists

• argued the abundant genetic variation in natural populations resulted from selection

• so if theres a bunch of diff niches in environment, selection will preserve the fittest type in each niche and maintain diversity

• preserves specialist in each niche

• sometimes called balancing selection

neutralists

believe that most genetic variation was selectively neutral, did not impact fitness

Selective Sweep

Definition: The process by which a beneficial mutation rapidly increases in frequency in a population, a beneficial allele fixes faster than a neutral allele

- Example:

  - D614G mutation in SARS-CoV-2 spike protein

genetic hitchhiking

mutations that are linked physically to the selected allele ‘hitchhike’ to high frequency

Purifying Selection

- Definition: A type of natural selection that removes harmful mutations

- Indicator:

  - dN/dS ratio less than 1 

non-synonymous substitutions (dN)

change protein, faster evolution

Tajima’s D

uses two estimates of genetic diversity to ask whether a population is evolving neutrally or not

• S = number of variable sites

• pi = mean number of differenences between a pair of sequences

these both estimate theta = the quantity of genetic diversity in a population under neutrality

D = theta_pi - theta_S

• tells us whether a population is evolving neutrally or not

D = 0 is neutral

D < 0 = directional selection( more rare alleles than expected, suggests selective sweep eliminated variation happened recently)

D > 0 = balancing selection (fewer rare alleles than expected, suggests selection favours distinct alleles in the same population)

Macroevolution:

• Starts with speciation

• Involves large-scale evolutionary changes over time

• considers broader changes in diversity at higher taxonomic levels and how this is distributed

microevolution

changes in allele and gene frequencies within populations

speciation

how genetic changes within populations lead to new evolutionary clumps

• defined in terms of reproductive isolation = will thus create a new species

biogeography

study of the distribution of species across space and time

dispersal

movement of populations from one region to another with limited or no return exchange ex. marsupial evolution : most living are found in Australia but oldest fossils were found in china and north america evolved w a mix of this and the other because the modern day marsupial has CA from N america and S america too

vicariance

formation of geographic barriers to dispersal that divide a once-continuous population. ex. if continent divides and population splits there could be more species so for marsupial their phylogenetic patterns mirror the order in which the continents broke up

anagenesis

wholesale transformation of a lineage from one form to another

• not our understood definition of evolution, things did not evolve gradually, there were species that took over eachother

punctuated equilibria

periods of stasis followed by brief periods of rapid morphological change linked to speciation

• sees speciation and morphological change happening simultaneously

ex. bryozoans diversification pattern works well with this model

gradualism

slow, gradual morphological changes over time resulting in speciation

• involves anagenesis and speciation

turnover

number of species eliminated and replaced per unit time

standing diversity

number of species present in an area at a given time

ecological opportunity

presence of vacant niche space

• absence of competitors opens this up for a lineage

• leads to adaptive radiation

key innovation

trait(s) that allows a lineage access to new resources

evolutionary novelty

new genetically based trait

• used to improve in totally new conditions, take whatever enzymes you have and grow faster

EAD model for evolution of novel gene function

Exaptation: use what you have to perform a new role

Amplification: make more of what you have (enzymes) even if its not the best

Divergence: improve fitness through changes in gene function, more copies of genes allows one copy to diverge without compromising og function

promiscuous proteins

exaptations with one main function and many side functions as well

• sloppy which makes organism get by in an environment where its not well adapted

paralogs

genes descended from duplications

evolution of novel trait in e coli example

• usually cannot metabolize citrate aerobically (diagnostic trait)

• a citrate metabolising strain emerged!

• exaptation: e. coli had the machinery to do this but it previously only worked anaerobically

• amplification: duplication of citT and linked sites inserted after the promoter allows for its expression in oxygen presence

• divergence: intitially strain could barely grow but further copies accumulated mutations that led to citrate specialist that coexisted with glucose specialist

cambrian explosion

sudden appearance of diverse animal body forms ~541 mya

• thought to have originated from early developmental mutations leading to new body plans

• caused by changing geology expanding habitats

• new ecological opportunity

background extinction

the normal rate of extinction for taxa or biota

mass extinction

a statistically significant increase above background extinction rates

origination

when the rate of new species formation exceeds the rate of extinction

leads to an increase in diversity

cladogenesis

the splitting of a lineage into 2 or more descendant lineages

mutation

any change to the genetic sequence, will be inherited by the cell’s descendants, imperfect copying procedures

Only way to introduce new variation into a population

  - Somatic ones are not passed on to offspring

  - Insertions and deletions (indels) can affect gene function

• rates for any given gene are low but per genome and population many new ones arise each generation, which will generate variation

Chromosomes

Condensed DNA strands wrapped around histones

Plasmids

Can move independently of host, potentially spreading antibiotic resistance

microRNA (miRNA)

can block translation and have major phenotypic effects, non-coding RNA that regulates gene expression

alternative splicing

RNA splicing to create multiple proteins from a single gene in eukaryotes

ploidy

number of copies of unique chromosomes in a cell

Gene Duplication

  - Can change physical appearances significantly

  - Maintains ancestral function while diverging to create novel functions

  - More genetic material provides more mutation material for natural selection 

• thought to explain lots of rapid diversification and rise of new clades

the c-value paradox

• the amount of DNA in a haploid genome does not correspond to the complexity of the organism

• rather its mostly pseudogenes and mobile genetic elements that parasitize the host’s replication machinery to make copies of themselves

somatic mutations

affect cells in the body of an organism; not heritable but they can be very damaging

germ-line mutations

affect gametes; heritable and relevant to evolution, other type isnt

Conditional Expression

Some traits (e.g., beetle horns) only appear after reaching a certain body size or nutritional threshold 

Heritability

How much of a population's variation is associated with genetics

• the proportion of the phenotypic variance that is attributable to genetic differences among individuals

• a ratio of variances

• fraction of phenotypic variation that is passed to the next generation

what does Independent Assortment (IA) do?

Determines which chromosomes go into which gamete

Recombination

Creates variation different from parents but not brand new

genotype

the genetic makeup of an individual

phenotype

an observable, measurable characteristic as the manifestation of the genotype of an organism (PHYSICAL)

• P = genotype + environment

• ex. human height depends on resources and nutrients along with internal morphogen signalling molecule gene expression exchange rate

polyphenic trait

single genotype produces multiple phenotypes depending on environment

quantitative trait locus QTL

examines known markers across the genome to identify those that are linked to high/low values of a trait

• markers closely linked to genes conferring a trait value are likely to remain linked despite recombination

• marker is not usually the gene of interest

• use log of odds (LOD) score to indicate an association between a marker and a trait value that is unlikely to have arisen from chance

population genetics

• studying the distribution and frequencies of alleles in populations and the mechanisms driving allele frequency change

• how genes move through populations

population

a group of interacting and potentially interbreeding individuals of the same species

group of organisms of the same species occupying a particular space at a particular time

• usually collections of smaller sub-xxx connected through dispersal

• extent of subdivision depends on features of landscape and motility of individuals

• if isolated it becomes genetically distinct

• drift occurs independently, different alleles will be lost and genetic divergence overtime occurs in each sub-xxx

genetic locus

location of a specific gene or sequence of DNA on a chromosome

• could be allele of gene, segment of genome, or specific nucleotide etc

• deliberately vague

haploid

individuals carrying a single copy of an allele at each locus

diploid

individuals carrying two alleles at every locus

homozygous

AA alleles are the same

heterozygous

Aa alleles are different, have greater fitness than the other only in diploids as haploids don’t have another chromosome

 Null Model

A model where no evolutionary change is expected

  - No natural selection, migration, or other drivers of evolutionary change

  - Important because it sets a baseline for comparison

• any deviation from this model tells us the population is evolving even tho we may not know the cause