BIO205 Evolution Exam 3

how are developmental biology and evolution related

• developmental bio is the study of the processes by which an organism grows from zygote to adult

• evolutionary bio is the study of changes in populations across generations

evolutionary biology

study of changes in populations across generatoins

• ecolutionary changes in forms and function are rooted in corresponding changes in development

• evolutionary bio addresses why changes occur

• developmental bio addresses how these changes happen

evolutionary developmental bio (evo devo)

• compares the developmental processes of different organisms

  • addresses the origin and evolution of embryonic development

  • how modifications of development and developmental processes lead to the production of novel features

  • role of developmental plasiticity in evolution

  • how ecology impacts development and evolution

  • the developmental basis of homoplasy and homology

homology

• traits shared bc they were inherited from a common ancestor

homoplasy

similar features in two organisms that were not present in their most recent common ancestor (convergence)

• evolved the same/similar traits separately

parallel evolution

how homoplasy results from same developmental mechanism in distinct taxa

• involves closely related species who evolve similar traits from shared ancestor

are bats and wings homologous or due to convergent evolution

• depends on where you start comparing (the farther in phylogeny one goes, a common ancestor can be found for both)

heliconius butterflies

•  example for developmental homology / homoplasy

  • Different Heliconius species have independently evolved similar / identical color patterns

    • Phenotypic homoplasy → convergent evolution

    • Developmental homology → same genetic mechanism used to produce same trait

  
  

generating diversity from a common genome

• gene regulation — the alteration of gene expression by molecular mechanisms - enables a common genome to generate a diversity of cell types

• same genes involved in development of all such features

heterochrony

change in developmental rate and timing

heterotopy

• change in spatial patterning of development

some of the same regulatory genes are implicated in the generation of hair, features, and teeth

• teeth, breasts, feathers, and hair all develop from the interactions between layers of skin

deep homology

cases where growth and differentiation processes are governed by genetic mechanisms that are homologous

• organisms that don’t have common ancestor or same structure but share same genetic mechanisms

  • same genes that control different structures in different species

• beyond ordinary homology

• leads to similar convergence on developmental pathways over deep evolutionary time

deep homology ex: FOXP2

• gene required for different organisms for different things → mutations drastically change development

• req for proper brain and lung development in mammals

• in humans causes limited speech

• in mice- less squeaks as pups

• bats can’t hear in dark — implication in echolocation

• birds — harder to learning songs

homeotic genes

• determine the identity of individual body segments

  • are transcription factors which regulate the transcription of other genes -→ important regulatory role

  • have a highly conserved homeobox DNA-binding domain that proteins recognize and bind to regulate gene expression

hox gene

• one group of homeobox genes comprises the hox genes which include the homeotic complex of drosophila

• group of transcription factor genes that regulate gene expression during development and establish body plan order

spatial colinearity

• how hox genes are arranged on a chromosome and how they are expressed in embryo

  • gene order mirrors body order

  • colinearity tends to be highly conserved among taxa but not essential

cascade of gene regulation…

a cascade of gene regulation establishes the polarity and identity of individual segments of drosophila

• in development, succesively smaller regions of the embryo are determined

hox mutants in drosophila

• loss of function → mutant has extra set of wings (4 wings) instead of balancer organs

  • then another segment could develop like a more anterior segment

• gain of function → activation of antennae growth when it shouldn’t (legs instead of antennas)

  • then a segment could appear in the wrong place if its like activation of antennae growth.

    • legs grlwing where antennae should be

cyclops

• giant with a single eye

• 3 genes that influence eye formation → mutation to Shh (signaling molecular that defines midline)

  • determines left vs right eye etc

• sheep ate wild corn lily which had cyclopamine (inhibits Shh signaling) → causing offspring to have cyclopia

hox genes in flies and mice

• same hox genes in both mammals and flies

• duplication event (4 more sets of hox genes in same sequence as flies)

• genes for each species have different expression (how much, when, etc) that make unique

how is gene regulation achieved?

• dna → transcription → RNA → translation → protein

• noncoding DNA controls what proteins activate genes

cis regulatory elements (CREs)

• are regions of non-coding DNA which regulate the transcription of nearby genes

• includes regulatory promotoers, nearby enhancers

trans-regulatory elements (TREs)

• are regions of non-coding DNA which regulate the transcription of distant genes

  • includes distant enhancers, insulators, etc

  • proteins/RNAs

transcription factor

• protein that binds to a specific DNA sequence, such as CREs, thereby controlling the transcription of genetic information from DNA to messenger RNA

stickleback example

• single nucleotide polymorphism that changes physiology of fish

• SNP causes Wnt to not send a signal to EDA, the gene that codes for such trait

• EDA is not turned since no signal from Wnt → no plat

voles

• prairie voles are highly social and monogamous which montane voles

• corresponds to much more expression of vasopressin receptor (V1a) in prairie

  • repeat expansion of enhancer of receptor associated with broad expression of V1a

• adding this expansion to mice leads to broad V1a in mice

• and much higher social interest

simple vs complex regulation

• rhodospin vs Pax-6/eyeless

• rhodospin: has much less regulation (fewer regulatory elements)

• Pax-6/eyeless: several different regulatory regions though all on the same DNA strand

hairy gene example

• many transcription factors are at play for this gene’s expression

synonymous substitution

• does not change amino acid

  • less subject to selective forces, pften considered ‘neutral’

nonsynonymous substitution

• changes amino acid

• subject to selective forces

nonsense mutation

• change to stop codon

are evolutionary changes to protein sequences (such as TFs) or DNA regulatory sequence (CREs) more important to morphological evolution?

genetic theory of morphological evolution

1. form evolves largely by altering the expression of functionally conserved proteins

2. such changes largely occur through mutations in the cis-regulatory regions of mosaically pleiotropic developmental regulatory genes and of target genes within the vast regulatory networks they control

the idea that evolutionary changes in bodyforms happen through changes in gene regulation specifically by mutations in CREs like promoters, enhancers, and nearby DNA change — CREs of mosaically pleiotropic dev regulatory genes

evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution

• proteins that serve multiple roles or have multiple effects are called pleiotropic

• most proteins that regulate development exhibit what is termed mosaic pleiotropy in that they function distinctly in different cell types, germ layers, body parts, and developmental stages

• this extend of pleiotropy was a surprise as there was no particular reason to expect that the formation and patterning of such different structures would or oculd involve the same protein

pleiotropy: yellow monkeyflower

• the yellow monkeyflowers lives in alpine ranges where growing season is limited

• many plants fail to flower before dying

• a single locus control days to flower and fecundity (seeds produced)

  • shorter DTF flowers have lower fecundity

  • but more flowers before death

• this pleiotropic constraint limits shortness of flowering

  • homozygotes produce almost no seeds (even if quicker)

• one gene affecting multiple traits with a single locus controlling fecundity (seeds produced) and days-to-flower (how long it takes for flower to flower)

  • Really short growing season

  • Trade-off!

    • Flower before they die → no seeds

    • Produce lots of seeds → don’t flower before die

Mosaic pleiotropy:

distinct function in different cell types, germ layers, body parts and developmental stages

Pleiotropic constraint:

hindering the evolution of certain traits since they are linked with another trait

pleiotropy: lectin-like low-density lipoprotein receptor

• lox-1 impacts immune function and LDL binding

  • early in life some alleles can enhance immune function

  • later in life these same alleles increase risk of cardiovascular disease

• androgen receptor (AR)

  • some alleles can confer lower risk of breast cancer

  • while increasing the risk of ovarian cancer

ancestral genetic complexity

• morphologically disparate and long-diverged animal taxa share similar toolkits of body-building and body-patterning genes

functional equivalence of distant orthologs and paralogs

• many animal toolkit proteins, despite over 1 billion years of independent evolution in different lineages, often exhibit functionally equivalent activities in vivo when substituted for one another. these observations indicate that the biochemical properties of these proteins and their interactions iwth receptors, cofactors etc, have diverged little over vast expanses of time

• : substituting different genetic toolkits for distantly related species can still allow them to function the same

deep homology

The formation and differentiation of many structures such as eyes, limbs, and hearts—so morphologically divergent among different phyla that they were long thought to have evolved completely independently—are governed by similar sets of genes and some deeply conserved genetic regulatory circuits.

infrequent toolkit gene duplication

Duplications within several prominent toolkit gene families have
been surprisingly rare in the course of animal diversification relative
to duplications of other gene families. These observations indicate
that gene duplication is not a necessary ingredient for
morphological novelty, as once assumed, and there is evidence
that duplications of some toolkit genes are actually selected
against because of their effects on gene dosage-sensitive
developmental processes

heterotropy

Changes in the spatial regulation of toolkit genes and the genes
they regulate are associated with morphological divergence.

modularity of cis-regulatory elements

Large, complex, and modular cis-regulatory regions are a distinctive feature of pleiotropic toolkit loci.

vast regulatory networks

Individual regulatory proteins control scores to hundreds of target
gene CREs

1. a single transcription factor regulate a variety of genes, not just one

Sickle cell anemia example:

one gene affects many functions (one mutation leads to multiple phenotypes)

• SNP causes polymerization of hemoglobin → blood clots, stroke, etc.

• Heterozygotes are resistant to malaria!

• Homozygotes getting sickle cell anemia :(

Antagonistic pleiotropy:

pleiotropy resulting in mutations that have beneficial and harmful effects

8 principles of the genetic theory of morphological evolution:

1. Mosaic pleiotropy: most proteins regulate multiple developmental processes

2. Ancestral genetic complexity: though several morphological differences, we all use same genetic toolkits

3. Functional equivalence of distant orthologs and paralogs: substituting different genetic toolkits for distantly related species can still allow them to function the same

4. Deep homology: same genetic mechanisms across species

5. Infrequent toolkit gene duplication: not much gene duplication events (very rare)

6. Heterotopy: changes where the gene is expressed

7. Modularity of cis-regulatory elements: each enhancer controls gene expression at a specific place and time

8. Vast regulatory networks: a single transcription factor regulate a variety of genes, not just one

developmental hourglass

every species starts developmental very differently → converge to look very similar during mid-development → they diverge as they develop into different adult forms 

a brief history of (early) life

• earth formed 4.5 billion years ago

  • oldest known rocks are 4Gy old (limits out resolution)

• earliest definitive evidence of life is 3Gy old

  • but life existed before this

• cyanobacteria likely radiated around 2.8Gya

  • led to great oxygenation event

• multicellular life about 1Gy ago

“hadean” period (4.5-4.0 Gya)

• mostly molten rock

• giant impact around 4.3 gya thought to have given rise to moon

• oceans cool and atmosphere forms (mainly N2, Co2, no O2)

evidence for life: chemical traces and microfossils

•  C12 was found in larger concentrations than C13 → sign for life

  • Multicellular life in rocks and fossils dating 3.26 billion years

3 Gya

• evidence of life before 3 Gya is rare and often difficult to interpret

• Could be earlier

• More evidence but lots to still find out (ie. cyanobacteria (2gya), multicellular eukaryotes (1gya))

properties of life

1. homeostasis: ability to adjust the internal environment to maintain equilibrium

2. structural organization: ability to maintain distinct parts and connections between them

3. metabolism: control of chemical reactions

4. growth and reproduction

5. response to environmental conditions and stimuli

how could the chemical building blocks of life have arisen?

• miller-urey experiment

• murchison meteorite

• phylogenetics

how could they have gotten assembled into something iwth the minimal requirements of life?

• philosophical views on origin of life

• conceptual requirements

• top down vs bottom up

• centrality of RNA

• how did pre-RNA arise?

Origin of Life

• complicated by difficulty of fossil evidence

• hard to see through fossil evidence and phylogenetic trees (can’t see past LUCA)

the miller-urey

• foundational experiment in 1950s demonstrative that complex organic molecules could arise in conditions similar to abiotic earth

• with electricity and all compounds known to have existed at time of life’s origin, 5 amino acids were found to exist

  • Simple molecules in right conditions can form complex, life-related molecules

  • H₂, CH₄, NH₃ → assumptions

    • Now, we know its CO₂, N₂, H₂O

  
  

murchison meteorite

• meteorite that fell in australia in 1969

  • carbonaceous chondrite (high carbon)

  • fell from Australia in 1969 and had amino acids, complex hydrocarbons and nucleobases

    • Supports claim that organic compounds could have abiotic origins → could have come from space or non-living things

    
    

3 philosophical positions on the origins of life

1. miracle

2. it was an enormously improbable accident

3. it was an inevitable consequence of the laws of chemistry and physics, given the right conditions

requirements of life

• energy source

• ability to produce more complex molecules from simple building blocks in environment (catalysis)

• boundary from external environment (concentration, protection)

• reproduction, mutation, heredity

top-down hypothesis

• start with properties of known organisms and work backward to reconstruct properties of early life

• assumes first life is RNA-based

• currently: nucleic acids encode proteins —> proteins required to replicate nucleic acid polymers

  • neither can be produced without the other

  • chicken meet egg

top down approach - ribonucleotides

• stores genetic information and can carry out basic functions

• carry energy (ATP, GTP)

• are key cofactors in electron transfer (NAD, FAD) fundamental to life

• are the precursors to deoxyribonucleotides

top down approach — RNA

• carries information (mRNA, ncRNA, RNA viruses)

• catalyzes peptide bodes (ribosomal RNA does this)

• RNA using ribonucleotides

  • one RNA replicase, several nucleotides, and primer led to self-replication

• RNA can act as an enzyme (ribozyme)

  • RNA and ribonucleotides play roles in many fundamental enzymes in extant life today (eg ribosomes)

  • RNA can form ribozymes that cleave, replicate RNA oligos, and bind cofactors regulating their own expression

    • focuses on reproduction, mutation, and heredity

ribozymes

• all complex eukaryotes share enzymes with RNA as the catalytic units

  • suggests conserved feature in LUCA

• early experiment showed ribozyme can catalyze joining of two fragments to form copies of itself

• but requires A + B present (did not polymerize rNTPs)

  • so it links amino acids together and are important to the function of RNA — alows for self replication

RNA world difficulties

• ribonucleotides are quite complicated (phosphate + sugar + base)

hypercycle model

• model of self replicating molecules connected in a cyclic, autocatalytic manner

• each member boosts replication of another

• molecules won’t be supported if it doesn’t contribute to the group

• division of labor

evolution of cell

• separation of ‘inside’ and ‘outside’ is a fundamental component of cells

• initial membranes are simple

• simple fatty acids with polar heads —> bcame micelles (amphipathic, spherical structures)

• simple fatty acids can flip back and forth → due to presence of water

• can lead to bilayer extrusion → when many micelles are added into a membrane, it will split up after incorporation

  • shows how simple molecules were used/combined together to make more complicated molecules

bottom up hypothesis

• redo conditions on life and see how life could have been achieved

• life originated in bottom of sea (more suited for this hypothesis)

• question: do we really need a self-replicating molecule to start evolution by natural selection?

  • no, with the hypercycle model, we can develop a network of replicators through natural selection

bottom up hypothesis: alkaline deep sea vents

• satisfies conditions ofr origin of life

• natural production of all kinds of molecules needed for origin of life

• naturally established proton gradient by environment: water coming out of vents (less acidic) and surrounding water with dissolved Co2 (more acidic) -→ such mixing allows for proton gradient

• proton gradients used by almost all organisms

  • atp synthesis during respiration

  • photosynthesis

  • molecular transport

bottom up approaches focus on 1-3 , top down (esp rna world) approaches focus on 4

1. energy source

2. catalysis

3. boundary from external environment

4. reproduction, mutation, and heredity

a brief history of life

a history of life - dinosaurs and creatures

extinction paves the way

• many large radiation events are preceded by large extinction events

  • the five best known include K-T (dinosaur killer)

  • almost all major geological periods have a nearby extinction evetn

• humans are currently causing one of the worst (biodiversity wise)

tree of life

• traditional view: most clades eukaryotic

• modern view: enormous diversity, most of it outside of the big 3 (plands animals fungi)

  

early evolution

• once life began, evolution quickly started

  • modern DNA has enzymes that can reduce mutations but RNA does not have such correction enzymes

    • higher mutation rate in early evolution → since life likely started with RNA, it was fast and messy due to high mutation rate of RNA

rise of o2

• first organisms had simple metabolism since atmosphere was O2 free → anaerobic

• all were prob chemoheterotrophs

  • got nutrients from organic and inorganic material

    • modern archaea resembles earliest life

      • obtaining energy from chemical reactions involving hydrogen, sulfur, and iron compounds (all abundant on early Earth)

photosynthesis

• most important new metabolic process evolved gradually

• organisms that lived close to ocean surface prob developed means of absorbing sunlight (UV)

• once absorbed, developed methods of turning it into energy

• initially used H2S as electron donor

• first oxygenic photosynthesis appearing in cyanobacteria (blue-green algae)

  • emitted O2 and how it started using H2O instead of H2S

rise of O2

• highly reactive

• all initial O2 would react with rock and minerals in water

• O2 would not accumulate in atmosphere until surface rock was saturated

• Rocks formed banded iron formations: layers of iron rich rock that indicate that oxygen was present

• rise of O2 would have created a crisis for life- O2 reacts with bonds of organic materials

  • surviving species avoided effects of O2 bc they lived or migrated to underground locations

    • many anaerobic microbes found in such locales today

    • around 2.4Gya “great oxygenation event”

      

ediacaran biota

• the ediacaran period saw large diversification event

• large radiation of diverse organisms mostly now extinct

• vast array of body plans

• organisms were replaced by modern animals during cambrian explosion

  • animals that dig into microbial mats may have disrupted ediacaran habitats

  • changes in environmental conditions

  • cambrian animals outcompeted them

  • evidence states that cambrian explosion filled niches emptied out by Ediacaran extinctions

cambrian explosion

• most major animal body plans appeared very rapidly

• animals with complex, distinct body plans

before most organisms were simple single or assembles of multiple cells

ordovician

• life still essentially entirely aquatic for early ordovician

• cooling event ended this period → drop in Co2

  

silurian

• when life started to conquer land

• vertebrate evolved first bony fishes

• ended through Silurian-Devonian Terrestrial Revolution: transition of life from water to land

devonian

• first major diversification of life on land

  • strong establishment of arthropods on land -→ insects and spiders

  • evidence of earliest tetrapods → major step toward land dwelling vertebrates

  • ended through series of extinction events due to land plants removing Co2, mountain building increasing rock weathering, which reduces Co2 as well

    • lot of reduction of Co2

carboniferous

• coal bearing

•  huge deposits of coal that formed massive forests

  • Diversification of amphibians as dominant land vertebrates

  • First massive forests

  • Ended through climate shift and collapse of vast rainforests

  • CO₂ level drops sharply → emergence of massive rain forests that sucked CO₂ out

    • Cooling and drying due to CO₂ drop → large change in climate

permian

cool dry climate favored radiation of amniotes (vs amphibians)

avoring of egg-laying vertebrates with the cool dryclimate

• Permian-Triassic extinction event: triggered by massive volcanic eruptions, leading to CO₂ levels skyrocketing

  • Ocean acidification, severe global warming, ecosystem collapse

mesozoic

• dinosaur time

•  reptile dominance but also emergence of birds, flowering plants and early mammals

  • Triassic: allowed for dinosaurs to dominate

  • Jurassic: earliest birds and modern sharks appear

  • Cretaceous: flowering plants and bees radiate

Brief history of life:

 simple plants → invertebrates → vertebrates

1. Earth formed 4.5 billion years ago

2. Definitive evidence of life is 3 Gy old

3. Cyanobacteria likely diversified 2.8 gya

   1. Led to great oxygenation event

4. Multicellular appeared 1 gya

5. 540 mya → all major animal phyla appear

6. 460 mya → plants colonize land

7. 360 mya → forests

8. 350 mya → tetrapods (four limbs)

9. Earliest dinosaurs to humans is from 230 mya to 1 mya

extinction paves the way

• many large radiation events are preceded by large extinction events

  • almost all major geological periods have a nearby extinction event

• humans are currently causing on the worst (biodiversity wise)

• Mass extinctions are always followed by major evolutionary radiations

  • Extinction clear out many niches

  • Almost every major geological boundary is near a mass extinction

  
  

extinction

• all individuals in a given species have died out with no living descendants

• mass extinction: widespread and rapid decrease in the biodiversity on Earth

• 5-20 have occurred

  • Initial event leads to chain of events that lead to severe environmental catastrophe

extinction events: the big 5

• Late Ordovician: caused by global cooling, possibly due to volcanic ash

• Late devonian: no single cause pinpointed

• Permian triassic: massive volcanic eruptions in Siberia

  • Volcanic emissions released caused global cooling, acid rain and global warming → loss of ocean life, ecosystem damage, fungal blooming, etc

• Triassic-jurassic: likely caused by another major volcanic event

  • 70-75% of species lost

• Cretaceous-paleogene: asteroid impact

Extinction events cause massive losses in biodiversity and are detectable in fossil records

pleistocene megafauna extinction

• as humans evolved globally, large animals soon started to disappear

  • Long before modern civilization, humans had major ecological impact

  • How?

    • Hunting: hunted meat into extinction

      • some argue early hunter gatherer societies would not have consumed this much meat

      • other counter that slow generation time of large megafauna would still allow this collapse over time

    • Second-order predation: humans killed predators → increase in herbivores → no plants because nothing to regulate herbivores

      • Disruption of ecosystems by killing predators

• extinction of the earth’s megafauna, unique bc of its extreme size bias toward large animals

what predicts species extinction?

• geographic range

  • species with wider geographic range tend to have eggs in more baskets

  • others include species in climate extremes and specialization in habitat

• Geographic range: spread out in more environments → less likely to go extinct

• Climate extremes and specialization → broadly distributed, adaptable species survive better

are all extinctions bad?

• Can lead to evolutionary opportunity

• Major groups did not succeed because they were superior

• Adaptive radiation: a process whereby an ancestral species diversifies rapidly into multiple new species/forms

• End of triassic killed all dinosaurs → K-Pg (cretaceous-paleogene) blossomed with radiation of mammals

trends

how evolution is occurring

cladogenesis: a species branches into two new species

anagenesis: changes to a species over time without branching, resulting in appearance of a new species

trends: phyletic gradualism

• species change historically viewed as gradual process occuring at a relatively fixed rate over time

trends: punctuated equilibrium

• newer view tends to view species as keeping ‘status' quo’ until rapid evolutionary change occurs often resulting in speciation

diversity of life (metazoa)

• two groups within eukaryota have produced complex multicellular organisms

  • archaeplastida - gave rise to plants

  • opisthokonta - gave rise to fungi and animals

    • all have a single posterior flagellum in flagellated cells

features of metazoa

• multicellular

• heterotrophics

  • obtain energy and organic molecules by ingesting other organisms

• active movement

• complex tissue structure

  • differentiated and specialized tissues

• diplontic life cycle

  • diploid state is multicellular whereas the haploid state is (typically) gametic