Biology 114 Exam 2

extinction vortex

 point of no return, if they continue like how they are now, pop will start process of going extinct in our lifetimes

Hardy Weinberg Equilibrium

p^2 + 2pq + q^2 = 1.0

Allele vs genotypic frequency

the proportion of one allele’s occurrence in the population (p or q) vs the proportion of a particular genotype in the population, ex AA, Aa, aa (p2, 2pq, q2)

Assumptions of the HW model (5)

• random mating

• no mutations

• no migrations into

• no natural selection

• infinite/large population size

Bottleneck

certain amount of diversity in population, then something happens to reduce the amount of genetic diversity

Examples of cheetah bottlenecking

2 bottlenecks:

1. Ice age 10k years ago → habitat receded, glaciers moved, big bottleneck

2. Poaching, habitat loss (humans killed food that cheetahs want to eat) 100 years ago

Violations of the Hardy Weinberg:

1. Non random mating (they mate within their sub populations/locations)

2. Small population size

People used to collect the kids to raise them as pets

1. They can be docile, tend not to hunt people

4 ways a population can change

genetic drift, gene flow, natural selection, mutation

genetic drift

the effect of a founder event, fluctuation in allele frequencies due to randomness in reproduction within a population, this is most influential in small populations.

1. Within a population

2. Due to random events (change in allele frequencies due to random events)

3. Evolutionarily neutral, does not violate HW

Founder events

 when you have a small group of individuals separating themselves from a large population, whatever caused them to go there/the act of them going there is a founder event

gene flow

movement of genes from one population to another, Effects the population that the genes are leaving, and the population they are going to

example: Example: Mount St Helen volcano erupted, one year later, Lupine flower colonized a new site and formed a population. The oldest member of the new population is the most genetically diverse. Over the course of time, the new generation starts to look like the source generation. Time equilibrates. Tjis is the only way to get both increase and decrease in genetic diversity

Between 2 populations, Movement of genetic material from one population to another due to migration, affects HW

Mutation

 occurs from DNA replication error/environmental stressor and change in nucleotide sequence, random with respect to fitness (most lower it)

increases genetic variation/diversity by creating new alleles

Most mutations are in junk DNA so they don’t show up in trait genes, but they cause genetic diversity and it’s possible to find unique differences in their junk dna (ex used when identifying someone by DNA)

Natural selection

causes a decrease in genetic diversity because traits are being selected against

assortative mating

1.  the tendency for individuals to mate with others with similar phenotypes to themselves (who look like them, behave like them, etc)

   1. Ex: Blister beetles: mate with those of similar size

      1. There is a reduction in fitness if the female chooses a male with difference in body size

   2. Increases in genetic similarity (can keep genes in the family/keep it going)

Disassortative mating

1. choosing individuals to mate with who are different

   1. Ex: Gray wolves: choose mates that differ in color

   2. Increases genetic diversity, so more likely to be able to accumulate good genes overall

      1. Tendency on dogs is to outbreed

Inbreeding

the tendency to mate with someone with similar genetics/genotypes, mating with an individual who has a fairly recent common ancestor

1. All of the chromosomes are affected because share common ancestors

2. It increases in homozygosity, decreases in heterozygosity, but does not cause a change in evolution because allele frequencies are the same/don’t change

3. causes inbreeding depression

Increases homozygosity without changing allele frequencies

inbreeding depression

1.  loss of fitness because of the increase in homozygosity

   1. The presence of more homozygous recessive traits can make individuals lose fitness

      1. That’s why recessive alleles is called “loss of function”

      2. A lot of reactions that happen in your body are caused by a dominant allele

   2. Heterozygosity is also good for disease resistance

      1. Ex: homozygous recessive are more likely to get malaria, and homozygous dominant allele that fights malaria are more likely to have sickle cell anemia (red blood cell have sickle shape)

         1. Heterozygous is the best

   3. In humans, first cousin is the usual limit for not causing inbreeding depression

      1. children of first cousins have greater mortality rate

      2. some states it’s illegal

Inbreeding is common in plants

1. A lot of plants can self fertilize/pollinate

2. Cardinal flower: lower fitness for those that self fertilize

3. Alternatives are wind/animal carrier pollinators, but that doesn’t always happen, so self pollination happens too, but gives lower fitness

sexual selection

specialized form of natural selection

the selection of traits that a person possesses that enables their ability to get partners

female selection

acts on males more than females, because females can be more choosy about who to mate with, since they put more effort in the reproduction/invest more, Females select traits that they find attractive in males

Ex: peacocks. Can be competing selective pressure because brighter blue ones might attract more females, but also might be bigger of a target for predators. Also, blue is difficult to make in nature, so brighter blue says positive things about his other traits

male male competition

Two male competing to get more matings. Ex: male deer can fight/spar with their antlers. Sexual selection pressure = more muscular necks for better sparring

Sexual dimorphism

 this sexual selective pressure makes male and female traits be different within a certain population

• ex: male guppies have more spots, or birds that females are grey/brown and males stand out because of sexually selected traits

• Golden winged warbler- Male has a bright yellow cap, yellow arm bars, dark eye circle, Female has a more subtle cap and not as extreme colors

• deer- male has antlers

Sexual dimorphism can also happen because it makes certain competition less, so it makes things better for the species. Ie- males go after one thing, females after another, so they have different traits for that

taxonomic hierarchy (DKPCOFGS)

1. Species

2. Genus/genera

3. Family

4. Order

5. Class

6. Phylum/phyla

7. Kingdom

8. Domain

Carolus Linnaeus

Given credit for using this binomial nomenclature (using 3 names- species and genus) → wanted to standardize scientific terms for plants

• he didn’t develop the hierarchy himself, but used it frequently

• he was a swedish botanist

• Felt that the more you could classify the natural world, the closer you are to understanding religion

• classified into 2 kingdoms: plantae, can’t move, vs animalia, can move

3 kingdoms

1. Plantae (were green, photosynthesized)

2. Fungi (didn’t photosynthesize, not green)

3. Animalia

3 domains

Bacteria, Archaea, Eukarya

Bacteria

1. Not, became:

   1. Archaea (prokarya)

   2. Eukarya

Now, there are 5 kingdoms

1. Monera, bacteria single cell organism

2. Protista, non bacteria, mostly single celled organism

3. Plantae

4. Fungi

5. Animalia

White tailed deer

1. Eukarya domain

2. Animalia kingdom (animal)

3. Phylum chordata = have spinal chord

4. Class mammalia = hair, mammary glands (are mammals)

5. Order artriodactyla = even number of toes

6. Family cervidae = bony antlers

7. Genus odocoileus = live in small groups, have white hair under their tail

8. Genus then species name: Odocoileus virginianus = all antler points extend from single main beam of antler

   1. Capitalized genus name and no capitalized for species name

   2. Shorten genus name if you’re reusing it, because you might have to pay per page to publish a scientific paper

Species

Evolutionarily independent groups, ie Group of individuals who are independent in terms of their accumulation of mutations, genetic drift, or naturally selected traits

How do we distinguish between species?

1. Biological species concept

2. Morphospecies concept

3. Phylogenetic species concept

Biological species concept and why doesn’t it work completely

Reproductive isolation = if two individuals can create viable offspring together/interbreed, then they are the same species

1. This concept doesn’t work if:

   1. the animals are extinct

   2. tthere are two animals of the same sex

   3. they would never overlap in the wild (live in different places)

   4. Asexual reproduction → doesn’t require 2 individuals

Prezygotic isolation mechanisms

1. Ex: fireflies can create light flash patterns, different ones make different patterns, female firefly will watch for a male doing her flash pattern because that means they are the same species

2. This is all happening before zygote is formed, isolation mechanism happens before they get together to form zygotes

3. Temporal: if humans are not ready to mate at the same time of day or year, there won’t be a zygote

Postzygotic isolation

Something happening after zygotes are formed to keep species separate

1. Hybrid viability = an embryo mixed from two species may die before becoming fully formed

2. Hybrid sterility = the hybrid individual is born and is viable but cannot reproduce. This keeps the two sexual lines separate because there won’t be another individual like that one

   1. Ex: mules, mix between horse and donkey, they cannot reproduce

Morphospecies concept and problems with it

1. If they look different or behave differently, they are different

   1. Different in size, shape, or morphological features, they must have been separated for a long time

2. Problems:

   1. Sexual dimorphism (females look one way and males look another)

   2. Variation within a species population

      1. So you have to choose your traits carefully

      2. Ex: easy with two things like butterfly and elephant, they are very different, but what about two different types of hawks (cooper and shark shin hawk have different kinds of tails)

Phylogenetic species concept

The more recent common ancestor, the more likely it is that they are related

Relates to phylogenetics: the study of an evolutionary history of an individual to determine how closely related they are

Terminal node = the end of phylogenetic branches

Phenetics vs Cladistics

Phenetics = studying evolutionary past/relationships by considering all traits equally

Cladistics = only studying recently evolved traits

• Less likely to assume that convergent evolution occurred among a group of closely related organisms

• “phenetics groups organisms by overall, observable physical similarity (morphology) regardless of evolutionary history, while cladistics groups them based on shared derived characteristics”

Parsimony

 the idea that the simplest answer is usually the correct one, ie homology is more likely than homoplasy

Golden wing warbler x blue winged warbler

1. Acc to biological species concept, they would be the same, but they are different

   1. They breed to form the lawrence’s warbler and brewster’s warbler

2. Morphological species concept, they are different, because they all look the different

3. Phylogenetic concept shows that there is enough genetic separation that they would all be four separate species

4. The more stable our communities = more diversity of genetics, the more stable our ecosystem = it’s good to increase diversity so it stabilizes them all

   1. This is important for conservation (we should conserve all of them separately to increase stability)

Dusky seaside sparrow

1. 6 sparrows around North America

2. Dusky is along the Atlantic coast in marshy areas, birds ate mosquitoes, the population started to decline because of mosquito insecticides that people were spraying, then people flooded the area to build a highway

   1. 1979, only 6 dusky seaside sparrows left, and they were all male

   2. Scientists brought in Scott’s seaside sparrows to mate with them

   3. Phylogenetic analysis with cladistics found that dusky and Scotts were different, they were from Atlantic and gulf coast

   4. They ended up diluting the gene flow/hurting diversity

Allopatric speciation

two different groups that are in two different spatial areas. Often this happens after dispersal = a group that migrates away intentionally. If there is no gene flow between the two groups, they will remain isolated, and accumulate differences, eventually they will be considered different species. Vicariance = dispersal but by chance, ex: a big fire goes through a group of insects, rips them into two, then they never meet again

How do we get new species?

Requires physical/temporal isolation and genetic divergence

Allopatric speciation or sympatric speciation

sympatric speciation

Caused by preferences for different habitats or different food

Ex: the apple maggot fly. They will go into hawthorn apples as their mating sites. egg will hatch and then larvae will emerge as an adult. They are philopatric = they will return to where they were born to reproduce. Those that mate in hawthorn apples and domestic apples have become different species.

What happens when species come back in contact?

1. If it hasn’t been so long, they intermingle, there is gene flow, and they are returned together 

2. reinforcement, hybrid zones, new species through hybridization

Reinforcement

If they interbreed, and there is lower fitness to those who are interbred, then there is reinforcement of the fact that they are separate species

Hybrid zones & new species through hybridizations

an area between with hybrid populations, maybe making new species, this is what happened with brewster and lawrence warblers

Speciation event

when one common ancestor’s descendants branch into two

• This happens through isolation and divergence

• Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages

Things all plants have in common

• have chlorophyll, use to photosynthesize

• cellulose that makes up cell membranes/walls, acts as deterrent to predators because it’s hard to digest

• produce starch

• have thylakoid condition

Thylakoid condition

 within chloroplasts, the stacks of thylakoid and gaps between them provides for maximum amount of surface area for sunlight absorption

Conditions favoring the evolution of land plants

• wavelength/light resource limitation

  • Quality of light under water, especially deeper, loses red part of the spectrum of colors, so sunlight penetrates with less quality

  • The plants grow more and more in the shallow water, allowing even less to get through

  • Bodies had to be really long to attach to ocean floor and be extended to top of water

• CO2 =  limited in water, have to wait for it to diffuse in water from the atmosphere (which it does slower in water than in air)

• New niche space available for plants that could tolerate out of the water living

  • On land, there was better sunlight, more CO2 available, and no heterotrophs

• evolutionary pressure/competition

new ways to move material from bottom to top:

• Elongated cells = cells were elongated

• Contractile fibers = linear intracellular organization

• Cytoplasmic streaming = cytoplasm is continuously moving within cell which makes transport of organelles nutrients faster/easier

• Cellulose = plants that live in tidal water have more cellulose because it is needed to keep plant together/stable

heterotrophs

competing consumers

Changes to life on land

1. Dehydration (aquatic plants didn’t worry about this)

   1. Transportation of water → need to bring water from roots to leaves, or top to base

2. Support

   1. Plants in water can float upright, but plants on land need to stay upright, so they evolved to get more cellulose

3. Transportation of sugar after photosynthesis

4. Reproduction

   1. In aquatic plants, gametes swim around in water until they find each other

   2. Plants evolved ways to get gametes around

5. Too much sunlight

   1. UV radiation can affect DNA of plants

   2. Dry them out

Chlorophyta

Non-vascular plants without cuticles

• green plants that cover lakes

• ex: stoneworts, order: charales

• freshwater green algae

• no vascular

• no cuticles needed bc surrounded by water

bryophyta

Non- vascular plants with cuticle

• mosses

• liverwort is example

• reproduce through sporophied stalks/spores

• grow in damp, cool areas

• land plants

• no vascular tissue, but have trachea (simple tube to transport resources around plant)

• cuticle prevents them from drying out

• was the first to have stomata

Pteridophyta

• ferns

• vascular, seedless plants

• Evolved vascular tissue → arranged in vascular bundles phloem and xylem

• some of the oldest plants with seeds

• reproduce by spores, need standing water

phloem

Used to move sugar, which is dissolved in water

Cells are alive

Xylem

Used to move strictly water

Cells are dead

Gymnosperms

Vascular plants with naked seeds

• example: coniferophyta, ginkgos, gnetophytes

• seed coat allows seeds to not dry out, slows down seed predators

• evolved pollen

  • sperm is made in pollen grain, allows long term viability

• evolution of needles —> surface area to volume ratio, minimize water loss, have thick waxy cuticle

angiosperms, anthyophyta (= large division)

Vascular plants with fruit/flower covered seeds

• flowers, fruits

• fruits are used to attract animals to spread the seeds

• Colorful vs grey flowers ← color and smell attract pollinators

  1. Pollen grain may be too heavy to be picked up by breeze

  2. So pollen allergies are caused by the nondescript flowers, because they are light pollen grained ones and are blowing in the wind (ex grass, ragweed)

• Monocots vs dicots

Monocots vs dicots

1. Monocots:

   1. Has one leaf in the beginning when a plant starts sprouting out of the seed

   2. Monocot leaves have horizontal lines/parallel veins, ex grass

   3. Vascular bundles are randomly arranged

   4. Number of petals is divisible by 3

2. Dicots:

   1. Has two leaves when a plant starts sprouting from a seed

   2. Can split the seeds to two equal halves (ex peanuts)

   3. Vascular bundles are arranged around the periphery

   4. Veins are arranged in a branching pattern

   5. Number of petals is divisible by 4 or 5

Two ways of thinking about evolutionary processes

Phyletic gradualism vs Punctuated equilibrium

Phyletic gradualism

1. slow changes happening in a population over a lot of time

   1. Ex: variation in a trait being spread if it’s an increased fitness trait

   2. Change is very gradual, almost y=x slope of change vs time

   3. Accumulation of change happens slowly

   4. Does not explain the complete diversity of species that we have today (life has not been around long enough for phyletic gradualism to account for everything → phyletic gradualism is too slow to be the lone paradigm)

   5. Analogy: more triangular kind of phylogenetic tree → represents slow change

Punctuated equilibrium

1. long periods of time that very little happens

   1. For the majority of species, they go without changing (in equilibrium states/stasis), then are “punctuated” when there is an increase in evolutionary divergence, mainly due to an environmental change

      1. Evolutionary radiation = the creation of a large number of species at one time because of exogenous shock

         1. Species will evolve to fit empty niche spaces (ie available resources, because then there is minimized competition for used resources)

         2. When new resources become available, species will evolve to fit the new resources

   2. Staircase type of graph of time vs change

   3. Analogy: more “block” style phylogenetic tree

Endosymbiosis theory

Theory that organelles came from bacteria

1. Hunting eukaryotes sent membranes around cyanobacteria and enclosed them, sending into it digestive enzymes

   1. If there is a cyanobacteria that is hard to digest, or if the hunting eukaryotes delay digestion, it can use energy product that the bacteria is releasing → this is an advantage for fitness

   2. This continues until eventually, cyanobacteria starts living inside the eukaryotic cells

   3. Cyanobacteria became mitochondria and chloroplast

Evidence for the theory of endosymbiosis

Both mitochondria and chloroplasts have:

• multiple membranes that surround them

• their own genetic material

• Replicate in nontypical ways

  • Have independent gametes

  • Replicate by fission

Roots

Below “crown”

Provides moisture and nutrients

needs both water and oxygen /co2

where we don’t have nodes or leaves sprouting

5 types of roots

Tap roots

Fibrous roots

Tuber

Prop roots

Pneumatophores aka Snorkel roots

Tap roots

1. roots of plants that are relatively few, but they are very long and deep

   1. In shallow soils, plants with tap roots won’t access nutrients well

   2. In deeper soil they grow very well

   3. Hardpan substrate = substrate of mostly clay, under soil, very hard/impenetrable, that plants can dig through

      1. Some tap roots can go through, ex sunflowers are good at going through hardpan substrate

   4. These are harder to get rid of because roots will remain

      1. Ex: dandelion root- goes very far down, so if you pick it off, it will regrow

Fibrous roots

1. roots branch into a “mass” of root structures, can get a lot of moisture out of shallow soil

   1. Also good for plants in areas with brief rainfall because rain would only soak the upper layer of the soil (this was question on the video)

Tuber

Large lumps in roots that store carbohydrates from photosynthesis

Sweet potato vs yam

Sweet potato is part of root system

Yam is part of shoot system, just grows underground. Is not as sweet and more starchy, can grow to a couple feet long

Prop roots

Grows above ground that helps stabilize, ex in corn plants

Pneumatophores aka snorkel roots

for plants evolved to live in standing water

main roots are underwater, but pores stick up out of water that allows oxygen to get down into it, like snorkel tubes

Axial shoots

1. there is a central “spine” that connects every part of the tree, like a christmas tree shape or palm tree with central/main trunk

   1. Triangular shape is because it grew from the top, which just kept lifting, and making smaller and smaller branches

      1. Also a good “design” for snowy areas (evergreens) because the snow can fall down onto the ground without damaging the branches

      2. Also it helps with bearing wind (for palm trees)

   2. Mostly evergreens

Dendritic

1. main trunk comes up and splits, then each branch continues having branches

   1. Can spread out leaves more

   2. Allows for maximum exposure of sunlight for leaves

   3. However, branches can break more easily during snow or rain storms because it’ll build up on the leaves and weigh them down

   4. Mostly deciduous trees = lose their leaves every year

Buttress roots

1. very large tree that needs supportive structure, buttress roots are part of the shoot system but they help keep the tree from falling over

   1. Also it helps tree get taller to get more sunlight

Simple leaf

1. single blade structure attached to a twig

   1. Connected to an axillary bud at the base of the leaf

Compound leaf

1. a leaf that’s made up of a lot of leaflets

   1. Axillary bud at bottom of all of them, so you know it’s all one leaf

Double compound leaf

1.  leaflets on leaflets on a leaf, only one axillary bud all the way at bottom

   1. This is good for a lot of rain environments or very windy places, rain can flow through all of the leaflets with minimal damage

Needles

each needle is its own leaf (don’t ask him why)

Secondary cell wall

Waxy cuticle that only some cells have, cells have flexible membrane, and are also surrounded by secondary and primary cell wall that is stiffer

Meristematic cells

undifferentiated

1. These are all the young cells that don’t have a finalized form yet

2. Differentiation = maturation

3. Ie stem cells of plants

4. Occur usually in the growing tips and vascular areas

5. Located where rapid cell division is taking place

Parenchyma cells

1.  slightly differentiated, can be dermal tissue or ground tissue, or can revert back

   1. This makes up spongy mesophyll and phloem

Cortex – parenchyma food-storage cells in the “ground” tissue of the root

Collenchyme cells

Mostly differentiated, but stretching

1. Not very common

2. Their job is support

3. They form long, stringy tissue that keeps plants from falling over

4. Ex: fibrous stalks in celery

Sclerenchyma cells

1.  fully differentiated, occur in non growth areas

   1. Are only fully functional when they’re dead → becomes a hollow tube through which water can move

      1. Ex: xylem cells

   2. Have secondary cell wall 

      1. Lignan is produced by it, a rigid structure in plants

Trichomes

1. Grown by secondary cell wall, through primary cell wall

2. Used to prevent small herbivores (like caterpillars) from eating the leaf, also can have chemical waste on it

Upper epidermis

 needs to keep water in it, waxy cuticle is there

Palisade layer

chlorophyll/ majority of photosynthesis happens here, not tightly packed together so sunlight can penetrate from all sides

Spongy mesophyll

gaps are more amorphous between these cells

Lower epidermis

 has a thinner waxy cuticle on it with openings so water can escape to the rest of the plant, covering the stoma, and CO2 can come in to help with photosynthesis

Stomata

guard cells + pores, the kidney bean shape guard cells take in water and become turgid (rigid) when moisture is present, opening a pore between them, but close the pore during dry conditions. The stomata regulate water vapor (transpiration) and gas passage into and out of the leaf

Cork cambium

produces cork cells, often with lignin, to outside the cork cambium layer

Secondary vascular cambium

produces secondary phloem cells to the outside, secondary xylem cells to the inside, and parenchyma cells horizontally (rays) that transport fluids/nutrients between inner and outer cells of the trunk

Hartwood vs sapwood

1. Sapwood is on the outside, lighter color

   1. light-colored xylem layer active in water transport

2. Hartwood is darker color and stores more materials, is a bit harder/more stiff

   1. dark-colored xylem in core of a tree that no longer transports water, but serves as a depot for resin (anti microbial and anti fungal)

Spokes aka Rays

 allow fluids to travel in and out from center of truck outward, intersect the rings

Apical meristem

1. When tip moves away from roots, there is the zone of cellular maturation (bc those cells are maturing over time), and near the zone of cellular elongation

2. Damage to this can lead to the end of it → it’ll stop growing there

   1. Ex: Europeans brought to the US a fungus and a beetle called the weevil that eats the apical meristem of white pines, so trunks became less straight

Root cap

Grows cells very quickly and covers the apical meristem to protect it, by using the chemical mucigel (a kind of lubricant to protect the apical meristem)

Male flowers

Anther, filament = stame

This is where sperm, pollen grain is produced

Female flowers

Stigma + ovary = carpel

Where pollen grain lands

Sepal

Green covering over flowers until they are old enough to let petals be exposed

Some colorful “petals” are a part of the sepal

Evapotranspiration

 movement of water through the plant

1. Xylem- moves water from root to leaves (only one direction)

2. Phloem- moves sugar (dissolved in water) mostly from leaf to root, but also some from root to leaf (can be both directions)

   1. In the beginning of spring, sugar is in soil, so sugar goes up

   2. Or if there is high damage of leaves, sugar has to go up

Endodermis

single cell (endodermal) layer cylinder that protects, inside of root

Material can’t go in and out because of casparian strip, which is waterproof bc its waxy