Biology

How old is the earth? how old is life? how old is animal life? whats the evidence for earliest animal life?

Earth is 4.5 billion yo, life on earth is 3.8 billion yo, animal life is 560 million yo.

Cambrian explosion

a rapid evolutionary event starting about 560myo when most major animal groups suddenly appeared in the fossil record. the geologically rapid evolution of diverse animal body plans.

the genetic revolution: prob not an ecological revolution leading to an evolutionary arms race, it would be too localized how’d we get so many “new” body plans so quickly?

they are not new genes

instead, they are a change in location and timing of hox gene expression and hox duplications in one obscure subphylum of chordates

what factor could change on a global scalre to trigger an evolutionary arms race that continues today?

oxygen

oxygen levels rose from less than 0.1% to perhaps 1-2%

why did oxygen levels increase?

a failure of earth’s magnetic field:

• reduced strength of earth’s magnetic field

• loss of hydrogen gas through the weakened magnetosphere

  • relative increase in oxygen in earth’s atmosphere allowing animal life to diversity

diurnal vertical migration

by the cambro-ordovician period, the daily movement of trillions of marine organisms between the ocean's surface and deep layers. It is the largest animal migration on Earth by biomass

evolution before darwin

lots of research before darwin and wallace’s joint book

the broad and biological defs of evolution

broad: evolution is the theory that the universe is not constant but instead changing over the course of time

biological: a change in the frequencies of genes found in the natural populations over generations

Darwin’s 5pt Theory

1. organisms are transformed over time

2. every group of organisms descended from a common ancestor

3. species have multiplied over time

4. evolutionary change takes place through gradual changes in populations rather than the sudden production of new types

5. heritable variation leads to differential survival of individuals who will then give rise to subsequent generations (natural selection)

4pts of Natural Selection

1. individuals w/in pops are variable

2. some of the variation among individuals is heritable

3. an excess of offspring are produced

4. survival and reproduction of these offspring is nonrandom

4 forces of darwinian evolution (3 of which he was unaware)

1. natural selection

2. genetic drift

3. gene flow

4. mutation

genetic drift

random change in allele frq across generations

gene flow

exchange of genetic material between populations

mutation

random, heritable change in a gene/chromosome

the modern synthesis

the mainstream scientific theory of biological evolution that unites darwin’s theory of natural selection with gregor mendel’s rule of genetics

• mutation isn’t an alternative to natural selection but instead provides raw material (variation)

• mutations of small effect, over time, can lead to speciation

geneticists

understand population genetics thanks to rediscovery of mendel’s work and through the formulations of fisher, haldane, wright

naturalists

understand species concepts and speciation, but ignorant of advances in genetics

Theodosius Dobzhansky

• russian born geneticist

• pioneered genetic studies in natural pops of fruit flies

• showed that natural pops aren’t unuform

• conveyed mathematical pop gen to broader audience of biologists

george gaylord simpson

• vertebrate paleontologist

• showed that paleontological data are consisten w pop genetics and natural selections

• proposed notion of “quantum evolution”

quantum evolution

a small pop shifting drastically into a new adaptive zone where transitional forms are unstable and quickly perish

ernst mayr

• naturalist/systematist described a mechanisms for speciation (the origin of species)

• consistent with natural selection and pop genetics

Proximate v ultimate causes

• proximate: “how” eg. biochemical mechanism of translating genetic program into a phenotype

• ultimate: “why?” eg. historical reasons responsible for a particular genetic program or phenotype

punctuated equilibrium

the idea developed by stephen jay gould, niles eldredge that the history of a lineage is full of long periods of stasis (equilibrium) that are interrupted (puncutated) by rapid bursts of morphological change

phyletic evolution: anagenesis and cladogenesis

anagenesis: the transformation of a lineage over time (a to b)

cladogenesis: the splitting of one lineage into two or more lineages (A to B and C)

Sexual Selection, theory extended by Robert Trivers

1. The sex making the greater investment in the offspring (usually female) will be choosier

   1. the remaining sex (usually male) will compete for matings and females preferences can lead to runaway sexual selection

runaway sexual selection

an evolutionary process where a physical trait in one sex and a mate preference for that trait in the other sex become linked together in a self-reinforcing positive feedback loop

naked mole rats and inbreeding

high levels of inbreeding lead to high genetic relatedness among colony mates

hamiltons rule

if genetic relatedness is high, and benefits are great, then genes can increase in frq despite costs to the altruist

hamilton’s formal rule

an organism may benefit from altruistic acts when rB - C > 0

where:

r = genetic relatedness of the recipient to the actor

B = the reproductive benefit that acrues to the recipient

C = the reproductive cost to the actor

Selfish gene theory

Richard Dawkins:

• organisms are vechicles for replicators (genes)

• adaptations are for replicators, not vehicles

  • inclusive fitness (individual reproductive success + effects on success of relatives) is how to determine fitness (at gene level, not individual level)

neutral evolution

most genetic changes at the molecular level don’t affect an organism’s survival/reproduction, changes are from random mutation instead of natural selection because these genetic changes do not affect an organism's survival or reproductive success

honeybee example of hamiltons rule

honeybees sacrifice their own reproduction in order to protect the queen because she is the main reproductive female of the colony. By helping the queen raise more sisters and brothers rather than reproducing themselves, worker bees pass on more of their genetic material to the next generation than they could on their own

naked mole rat example of hamiltons rule

naked mole rats live underground and are thus super inbred. if genetic relatedness is high, and benefits are great then genes can increase in frequency despite costs to the altruist. naked mole rats sacrifice their own potential in order to protect the queen and others.

prairie dog example of altruism

Prairie dogs show altruism by barking whenever there is something dangerous approaching, in order to alert their relatives, even though it puts them in danger by alerting the predator that they are there. it does this because it increases the chances that their shared family genes will be passed on to the next generation

inclusive fitness

measures an organism's total genetic success through both its own offspring and the reproductive success of its genetic relatives

according to williamson, insects w/ caterpillar larvae should express which typs of genes?

express onychophoran and adult insect genes

the reason that williamson believes insects w/ caterpillar larvae should express both genes is:

hybridogenesis fuses genomes from multiple lineages

Williamson’s hypothesis for larval evolution:

completely unsupported

Williamson hypothesized that onychophorans are:

the direct ancestors to caterpillars

holometabolous

insects that metamorphasize

williamson’s ideas and their tests:

rhizocephalans will have a bigger genome size b/c they inherited two → they actually have hte smallest genome size of all barnacles

insects with larvae have bigger genomes than those w/o → they actually have smaller genomes

insects with larvae will be more similar to onychophorans → phylogenetic analysis shows insects w/ and w/o larvae are much more similar than either is to onychophorans

onychophoran genomes are smaller than those for insects with larvae → onychophoran genomes are larger than those for insects with larvae

tunicates (sea squirts) have bigger genome sizes than larvaceans b/c they “hybridized” while larvaceans are entirely independent group that lived as free-swimming tadpole-like adults → tunicates actually have comparable/smaller genome sizes than larvaceans

homology

equivalence of parts among different organisms due to descent from a common ancestor

examples:

• the forelimbs of humans, cats, whales, and eats are homologous b/c the bones are the same pattern and orientation but w/ different functions

morphogen

gradient of diffusable gene products

developmental process: what cells can do

cells divide

cells differentiate: endogenously via differential gene expression or exogenously via induction

cells orient

cells move: via cytoskeletal elements like actin/myosin and tubuin

cells stop: via adhesion proteins

cells die: via programmed cells death aka apoptosis

what are major diffs between protosomes and deuterostomes

1. spiral vs. radial cleavage

2. determinate vs. indeterminate cleavage

3. opening of the mouth

4. type of coelom formation

Spiral vs. radial cleavage

spiral cleavage is found in protostomes

• cells divide at an oblique angle, creating a twisted misaligned pattern of cells

• determinate cleavage, each cell’s future job is fixed very early and cells differentiate

radial cleavage is found in deuterostomes

• cells divide parallel/perpendicular to the polar axis, creating stacked, symmetrical tiers of aligned cells

• indeterminate cleavage, meaning early cells can each still form a complete organism

determinate vs. indeterminate cleavage

determinate (protostomes) cleavage:

• the cells are fixed and assigned very early in development

• each cell doesn’t have the capacity to develop into a complete organism

indeterminate (deuterostomes) cleavage:

• flexible and not predetermineds during early divisions

• each early cell can develop into a complete separate organism if isolated

opening of the mouth

protostome = mouth first

deuterostome = mouth second, anus first

blastopore

the first opening that forms during early animal development, connects the inside cavity of a developing embryo to the outside

proto: mouth

deutero: anus

what is phenotypic plasticity

organismal behavior, morphology or physiology change in response to the environment

which genetic feature is required for the PFE (plasticity first hypothesis)

cryptic genetic variation is uncovered in a novel environment

what is the role of the environment in pfe?

the environment induces changes in gene expression, endocrine signaling etc. that result in a novel phenotype

is the plasticity first hypothesis an example of adaptive evolution

Yes

What organisms have the strongest level of support for PFE

spadefoot toads and cavefish

homeotic genes

genes which control the overall body plan and tell cells what specific body parts to form during embryonic development

homeotic mutants

a body part appears in a place where it normally should not be

hox genes

a group of related genes that control the basic body plan and the head to tail organization of developing embryos in animals

hox genes are a subset of the broader family of homeobox genes

all hox genes are homeobox genes, but not all homeobox genes are Hox

mutations in Hox genes are responsible for homeotic mutant phenotypes. all hox genes share ~homeobox sequence, which codes for 60 amino acids

remarkable conservation of Hox genes in animals

• 59/60 amino acids are identical btwn frogs/mice/flies

• spatial and temporal colinearity of expression btwn chromosome and embryo

Explain plasticity first evolution: the tadpole model

1. the different tadpole colors represent different genotypes

2. then, the environment changes, shown by the difference in background color. the solid lines become dashed lines, which represents a change in phenotype (the genotype has not changed). important to note that not all of the tadpoles change, some of them may have the same phenotype. all of the tadpoles may have some sort of cryptic genetic variation, but this specific environment change may not have revealed it for them all.

3. selection will happen, and the tadpoles that have the certain cryptic genetic mutation that helps them in the new environment will be selected

4. after multiple generations, the tadpole that was selected became bigger and better and survived after the trait is refined over and over

5. genetic accommodation:

   1. Polyphenism- single genotype makes two or more distinct, discrete phenotypes in response to different environmental cues

   2. Genetic assimilation- trait becomes hardwired

are there limits to plasticity

Yes

e.g., humans holding breath

canalized phenotype

a trait that remains constant despite minor changes in the organisms environment

Spadefoot toad populations

some tadpoles are carnivores and some people are omnivores

some become cannibals when they eat brine shrimps when they are young

the difference btwn the omni and carnivores is a case of plasticity driven by polyphenism

kins selection role: it would benefit them to not eat their cousins/siblings so their traits can be passed, so they have a way to tell up to 2nd cousins

What are the 3 types of animals tissues and how are they related in embryos?

1. endoderm- inner layer, lines the internal structures

2. ectoderm- outer layer, forms the outer covering of the body and the nervous system

3. mesoderm- middle layer, develops into muscles, bones, connective tissues etc

What is a coelom and how is it related to animal tissue types?

a coelom is a fluid-filled body cavity that sits btwn animals gut and outer body wall, and lined with the mesoderm

Proto/deutero distinctions: enterocoely vs schizocoely

Protostome w/ schizocoely: organisms whose coelom develops from the splitting of the solid embryonic mesoderm layer (Mullusca, Annelida, Arthropoda)

Deuterostome w/ entercoely: organisms whose coelom develops from pouches that pinch off from the primitive gut

how conserved is development at the gene level?

very conserved, its the same hox genes in the same order from simple worms to humans (the difference is when they are expressed and which ones)

how conserved is development at the phenotypic level?

less conserved, even among close relatives w/ the same body plan, you can get lots of variance

other homeobox gene complexes

• pax 6 and the evolution of vision

• distal-less and the evolution of appendages

• tinman and the evolution of the heart

pax 6 genes

pax genes likely arose in last common ancestor of all metazoans

they were independently recruited multiple times to construct morphologically distinct eyes from

distal-less

The Biological Species Concept

defines a species as a group of individual organisms that can interbreed in nature and produce healthy offspring

goal of phylogenetics

to infer evolutionary relationships among living organisms

a phylogeny is simple a branching digram or tree thats a visual rep of hypothesized evolutionary relationships

ancestral character state vs derived character states

ancestral character state is a trait inherited from a common ancestor, while a derived character state is a novel trait that evolved later and distinguishes a smaller group from than ancestor

outgroup

a more distantly related group of organisms used as a reference point to determine the evolutionary relationships of an ingroup

character polarity

the direction of evolutionary change for a specific trait w/in a lineage, identifying which condition is ancestral and which is newly evolved

synapomorphy vs symplesiomorphy

a synapomorphy is a shared derived trait that defines a specific clade (derived)

a symplesiomorphy is a shared primitive trait inherited from a distant common ancestor (ancestral)

scale of comparison matters: symplesiomorphy at one level may be synapomorphy at another