Biology Notes

Origin of Species

Biological Barriers that Lead to Reproductive Isolation
- Prezygotic: Impede mating or prevent fertilization.
  - Habitat isolation: Species in the same area but different habitats (e.g., ground vs. trees).
    - Example: One group lives on the ground, another in trees; they never meet.
  - Behavioral isolation: Unique mating signals and rituals.
    - Example: Firefly blinking patterns, bird courtship displays.
  - Temporal isolation: Different mating times.
    - Example: Orchid species flowering on different days.
  - Mechanical isolation: Incompatible reproductive mechanisms/anatomy.
    - Example: Differences in mammal penis shape, animal pollinators, and flower structures.
  - Gametic isolation: No fusion of gametes.
    - Example: Sperm cannot survive or fuse with the egg.
- Postzygotic: Prevent hybrid zygotes from developing or being fertile.
  - Reduced hybrid viability: Spontaneous abortions are common.
  - Reduced hybrid fertility: Hybrid offspring are often sterile.
    - Example: Mule (donkey + horse) cannot halve chromosome number correctly.
  - Hybrid breakdown: Fertile F1 hybrids produce weak or infertile F2 offspring.

Two Modes of Speciation

Allopatric Speciation: Geographic barrier blocks gene flow.
- Allo = other, patric = fatherland.
- Geologic processes causing isolation:
  - Volcanic eruptions, earthquakes.
  - Cliff formations.
  - Human activities.
  - Land bridges covered with water.
  - Large lake drying into small ponds.
- Most likely when peripheral organisms are separated from the parent population.
  - Peripheral organisms often have extreme phenotypes → founder effect (genetic drift) → natural selection in new environments.
  - Speciation occurs quickly, or localized extinctions are possible.
  - Adaptive radiation (Darwin's finches): divergent evolution of diversely adapted species from a common ancestor.
    - Example: Cretaceous extinction and mammal adaptive radiation.
Sympatric Speciation: Reproductive barrier blocks gene flow, not geographic.
- Sym = same, patric = fatherland.
- More typical in plants.
  - Accidents during cell division cause polyploidy; asexual reproduction perpetuates new chromosome number.
- In animals, diversifying selection is the most common way sympatric speciation might occur.
  - Organisms with extreme phenotypes mate with each other, leading to speciation over time.
  - Reproductive isolation based on behavioral choices, often due to food specializations.

Tempo of Speciation

Gradualism: Evolution occurs slowly over time, with constant small changes.
Punctuated Equilibrium: Long periods of no change interspersed with rapid speciation.
- Allopatric: Harsh new environments drive rapid speciation.
- Sympatric: Genome change immediately stops interbreeding.
- Stabilizing selection explains periods of little change in stable environments.
Evolution likely occurs at a pace somewhere in the middle, and the pace might not be constant.
Molecular Clock: Gradual accumulation of DNA sequences differences estimates when clades diverge from common ancestors.
- Mutation rates affected by
  - Generation time of species
  - Size of population
  - Intensity of selective pressures
- Sharks have low molecular clocks.

Origin of Life

Cyanobacteria (blue-green algae) evidence that life is older than 3.5 billion years old.
Photosynthesis probably took 0.5 billion years to evolve; life is about $∼4$ billion years old.
Spontaneous Generation: Formation of life from non-living materials.
- Requires metabolism + replication.
- Early Earth conditions promoted this:
  - Little oxygen, lots of UV radiation, high volcanic activity and emissions, frequent lightning, meteorites.
Hypothesis: 4 Stages of Chemical Evolution
1. Formation of small organic molecules.
2. Bonding of monomers into polymers.
3. Aggregation of polymers into protobionts.
4. Formation of hereditary system & metabolism.
Testing the Hypothesis
- Oparin + Haldane's proposal: Early Earth conditions (shallow oceans, reducing atmosphere).
  - Reducing atmosphere: $H<em>2$ , $CH</em>4$ , $H<em>2O$ (g), $NH</em>3$
- Miller + Urey Experiment: Primitive Earth model.
  - Simulated early Earth conditions- spark, gases etc…
  - Produced:
    - 20 amino acids monomers to proteins
    - Monosaccharides monomers to polysaccharides
    - Small lipids
    - Nucleotides
    - ATP
- Polymers can also form when water with monomers dripped onto hot sand/clay/metal surfaces.

Heterozygote Advantage

If evolution's "job" is to select for the fittest, why does the recessive allele (aa) still exist?
- Environment changes - what is bad now might be desirable later.
- Recessive alleles hide in the heterozygote.
- Sometimes being heterozygous is the most fit.

What is a Species?

Can organisms breed together?
Do they have similar physical traits, diet, or behavior?
Do they live in similar places?
Is their DNA similar?
Biological Species Concept: Population of organisms that can potentially interbreed and produce viable, fertile offspring.
- Doesn't apply in all cases:
  1. Hybrids?
  2. Asexual organisms?
  3. Extinct fossilized species?
  4. Geographically isolated groups?
Circles are gene pools: populations sharing genes with others.

Origin of Life

First form of life: Bacteria.
Oldest fossils are 3.5 billion years old.
- Stromatolites: Fossilized mats of bacteria (cyano?).
Fossil: Impression, cast, or original material of any animal or plant preserved in rock.
- Bones, teeth, shells.
- Can also be an impression of the material (molds, cast).
Conditions that promote fossilization
- Hard parts: skeletal bones or exoskeletons.
- Rapid burial & lack of oxygen
Types of Fossils
- Body Fossil: Trace of the actual organism, unaltered- bones, skeleton
- Trace Fossils: Trace of the animal left behind- cast, molds

Protobionts

"First" "life-like"
Aggregates of polymers Coacervates are an example
Carbohydrates + proteins

Diversity of Life

Mitochondria+ endosymbiotic exist today!
- e.g. coral tissues + zooxanthellae
The Origin of Eukaryotic Cells
- descended from Prokaryotic ancestors nucleus evolved ~2.1 bya (but maybe as early as the advent of an oxygen atmosphere)
- endosymbiont theory more than I
- addition of mitochondria and plastids probably derived from prokaryotes living within a larger eukaryote (as undigested prey or parasites)
- suggests that the cytoskeleton and endomembrane system came first.
- evidence: similar enzymes and ETC; replication; circular DNA; can transcribe and translate Free lining organism small prokaryote ate by big prokaryote binary fusion eventual mutualism cell membrane Com part men- tilization.
The Origin of Multicellularity
- not all protists are unicellular multicellularity evolved ~1.5 bya colonies developed first (there are colonial bacteria as well) each cell replicates on its own, but they all live together different cells have different jobs specialization Led to evolution of tissues, organs, systems
"Kingdom" Protista Has a Problem…
- it is paraphyletic…
- so we break this group of organisms into several different kingdoms (not all scientists agree with all the groupings)
- "protist" is a general term for things that are not plants, animals, or fungi Share few common characteristics, other than the fact that they are eukaryotic
- 3 Basic Groups (Based on Convergence) algae photosynthetic "plant-like" protozoans eats stuff heterotrophic "animal-like" absorptive protists "fungi-like"
Tentative Phylogeny-6 Major Branches Calderians Molluscs Flatworms Annelids Arthropods Echinoderms Chordates where humans belong.
Phylum Porifera Sac with holes No real tissues cells cats by themselves gateway animal.
Phylum Cnidaria Sac with stomach 2 body plans Can be dimorphic Cnidae with nematocysts hydra anemone No true muscle Nerve net
evolution of cephalization head Phylum Platyhelminthes Real muscles Acoelomate Flame cells Osmotic balance worm round worm Phylum Nematoda Pseudocoelomate Have both mouth and
anus Blood vascular system Free-living and parasites Stiff cuticles - parante -Pinworms!
Phylum Mollusca 3 main parts Foot Visceral mass Mantle Often have shells Cephalopods have closed circulation, large brains, and advanced senses gastropods (foot stomain) snail clam octopus bipods cephalopat head foot
Phylum Annelida Segmented coelom Closed circulation Metanephridia Excretory tubes Mostly burrowers, some parasites e.g: Earthworms, leeches.
Phylum Arthropoda Largest # of species General characteristics Specialized segments Exoskeleton ++ and -Cephalization and good sense organs Open circulation true hard skeleton I-attached muscles.
Types of Arthropods Trilobites Spider is Arachnids mites 8 legs, fangs, webs Insects Flight Malpighian tubules Tracheal system Complex behavior butterfly spider Crustaceans 2 pairs of antennae carapace lobster exoskeleton
Phylum Echinodermata Radial symmetry, but bilateral larvae Spiny skin Water vascular system (5 part) Brittle star Sea star Sea lily Sea cucumber Sand dollar e.g. Seastar Spiny Skinsa
Chordate Phylogenetic Tree-Derived Characteristics? (unicates) Cephalochordate (ancelets) Hag Fish -Jawless Chondric Mhyes (sharks and rays) Fishes Pharyngeal slits = gills Bony fishes are the most abundant and diverse vertebrates tetrapods.
1. Notochord Nerve first Toy at a backbone. 2. Dorso, Hollow chord 3. Pharnygeal. Gil Hits 4. Musular Post; Anal. Tail. spinal cord vertebrate In embryos Chordate Phylogenetic Tree - Derived Characteristics? tail bone.
tetrapods. Bony fish Class Amphibia Evolved from fish First vertebrates on land Both aquatic and terrestrial phases. hagfish salamander shark frog
The Movement Away From Water Amniotic egg →whole life cycle can be accomplished on land -Shell - Amnion amniotic fluid - baby wants to come out of shell
snake
What classes are comprised of amniotes? Chordate Phylogenetic Tree - Derived Characteristics? halochordata (ancelets) Agnathans (sharks and rays) Ost sichthyes (bony Rapillarepiles) Mammala (mammals)
Class Reptilia Breathe using lungs "Classic" reptiles are ectotherms Behavior Energy conservation lizard turtle crocodile vertebrae cranlum jaws amnlotlc
Order Dinosauria (formerly Class Aves) Most closely related to dinosaurs Flight Endotherms Insulation (feathers) Cardiovascular Complex behaviors Archaeopteryx Vanous reptiles classes.
Class Mammalia Cretaceous extinctions adaptive radiation Characteristics Hair Endothermy Milk Large brains Differentiation of teeth Modified jaws
Chordate Phylogenetic Tree-Derived Characteristics? Urochordata (unicates) Cephalochordata (lancolata) Hag Flah ool eyes (by ahea freaded milk, fur Campion tetrapods Vertebrate cranium, jaws
Monotremes Mammals that lay eggs Have hair and produce milk Marsupials Mammals that complete embryonic development in a pouch Mostly in Australia Convergent evolution
Eutherians Placentals Mammals that complete development within the uterus Uterine wall Placenta Bleeding Joined to mother by a placenta Umbilical Cervis Walking is what made us diff.
Evolutionary Trends in Hominins Bigger leg and butt muscles More downward facing foramen magnum More curvature of the spine Lower and broader pelvis Arms shorten while legs lengthen Flatter faces Larger cranial capacity and brain volume Smaller teeth and jaws Less body hair Primate Evolution First primates were small arboreal mammals Limber shoulder joints Dexterous hands with opposable thumbs Close-set forward-facing eyes Good eye-hand coordination Parental care
Evolution of Populations (Microevolution) Hardy-Weinberg Theorem states that the frequency of alleles and genotypes in a population's gene pool remain constant over the generations (NO EVOLUTION OCCURS) UNLESS acted upon by agents other than sexual recombination in other words, evolution won't occur in a population as long as: 1. the population is large 2. the population is isolated from other populations 3. the population doesn't experience any net mutations 4. the organisms in the population mate randomly no change o = H. W
equilibrium 5. no natural selection takes place in the population OF COURSE, it's hard for all these conditions to be met, so H-W equilibrium often does NOT. occur and microevolution occurs! 1. small populations are subject to genetic drift (evolution through chance due to fewer alleles being available for recombination) 2. populations often experience gene flow when individuals from nearby populations migrate 3. mutations happen! 4. organisms typically demonstrate at least some pickiness when it comes to who they mate with (mates are chosen based on certain criteria about fitness) 5. natural selection OCCURS because some organisms are more fit than others and/or the environment changes evolution can be measured as changes in allele frequencies using the following two equations:

p + q = 1 \
p^2 + 2pq + q^2 = 1 \
Example: An allele W, for white wool, is dominant over allele w, for black wool. In a sample of 900 sheep, 891 are white and 9 are black. Calculate the allelic frequencies (i.e., p and q) within this population, assuming that the population is in H-W equilibrium.
The allelic frequency of w is represented by the $q$ term and the allelic frequency W is represented by the $p$ term. Always start with your recessive individuals because you can't tell the difference between homozygous dominants and heterozygotes. To calculate the value of $q$ , realize that $qq$ or $q^2$ represents the homozygous recessive individuals (or the black sheep in this case). Since there are 9 black sheep:

q^2 = \frac{9}{900} = 0.01 \Rightarrow q = \sqrt{0.01} = 0.1 \
Additionally, $p+q=1$ , thus $p = 1-q$ or $p = 1 -0.1 = 0.9$
Stabilizing Selection (Balancing Selection): When inter-mediate forms of a trait are favored & move extreme phenotypes are selected against a to vot Selection against both extremes Population after Selection Original ВоршалD
Sickie cell have AAYAN AND IN have -Human Birth Weight Percentage of Infant mortality malana. → Birth weight in mind get stuck in get infections, mothers pens not fully developed Clock WC-sections Yose heat
Disruptive Selection (Diversifying Selection): When extremes forms end of a trait ave favored over the intermediate phenotype -For both extremes, against moderate traits tuning Selection against the mean - Extreme population after election If selection + original Population+ Extreme + Extreme happens for long enough, them and the Two pops no longer overlap on X-axis -- 2- new species!
Ch. 19 Phylogeny and Systematics
features unique to a clave (group of related organism) How Do the Novel Features of Major Taxonomic Groups Evolve? Mechanisms of macroevolution may include: (Speciation) preadaptation (modifications of older structures) gradualism each step had to have a function. dinosaur limbs → bird wing. gliding? defense? Some thing else? changes in genes that control development of zygotes into adults, such as heterochrony (when the sequence and timing of development are slightly different between two types of organisms) human VS.
Chimp Is slightly longer in utero. brain development of humans bigger brains -homeosis (placement of body parts) →e.g. tetrapods this can include paedomorphosis (when the mature adult form retains juvenile features of ancestors due to a small genetic change) e.g. axolotl Many different clades (or groups) have evolved over time. cladogenesis: the initial evolution of a new group due to divergence from an ancestral group evolution does NOT move in a straight line with a "goal" in mind → evolution creates many branches,
Study Evolutionary Relationships? Homology vs. Analogy have to weed out which similarities are due to homology or analogy Jimilar Coug Tm cture = relationship divergunt evolution You want it to be ba want it to be based on Homology not Analogy Biologically bad. Jurface level resemblances & relationship. * Convergent revolution Two species evolved similar adaptation to deal w/ Similar ennroment (diff. evolutionary events) We study phylogeny (the development of a group through evolution) and systematics (the arrangement of groups based on their genetic relationships so we can classify them correctly) scientists create phylogenetic trees based on the number of genetic similarities (cladistics is the science of measuring these similarities) the goal of systematics is to match the classifications with the evolutionary histories as measured by DNA amino similarities and distinguish between homology/analogy to construct phylogenetic trees (more homologies acids means a higher likelihood of relationship)
When a taxon Includes I ancestor and all its decendants + a group Taxon= a Phylogenetlc tree = *Monophyletic Tree Clade false grouping Polyphyletic Tree When a taxon Includes members that DONT have a Close common ancestor. based on convergence. Willful ianorance - basil taxon -terminal -terminal Taxan - nodes (most recent -ancestor evolving Species) - basil taxon Paraphyletic Tree When a taxon