Foundations of Biology 2 (biosc 0160) final (outdated)

Created by taylorlazzari. Dr. West - University of Pittsburgh - Spring 2020

Evolution

change in genetic composition of populations over time.

Evolutionary change

is observed in lab experiments, natural populations, and the fossil record.
- These genetic changes drive the origin and extinction of species and the diversification of life.

reproduce, reproduces

Darwin's Observation:
1. If every individual born was to successfully __, populations would grow exponentially
- Not every individual __the same amount of offspring

size

Darwin's Observation:
2. Populations tend to remain the same stable \__ over time

differential

Based on Darwin's Observation 1 and 2...
Therefore, not every individual in a population can be reproducing at the same rate: there must be \__ reproductive success

Resources

Darwin's Observation:
3. \__ are present in constant amounts in a stable environment

Variation

Darwin's Observation:
4. \__ between individuals is present in populations

survive, reproduce

Based on Darwin's Observations 3 and 4
Therefore, some variations may help individuals \__ and \__ more successfully, particularly in the face of limited resources.

heritable

Darwin's Observation
5. Some types of variation are __

increasing

Based on ALL of Darwin's observations...
Therefore, successive generations, as long as the availability of resources remains constant, will contain an \___ proportion of individuals descended from parents with those helpful variations. Thus, the frequency of a helpful trait in a population will increase over time.

Environmental/habitat

\__ pressures are responsible for driving evolutionary change by natural selection

variety, heritable, successfully, help

Darwin's principals of Natural Selection:
1. In every population, there is \__ in traits
2. Some of that variety is __: it is passed on to offspring
3. Not all individuals \___ reproduce
4. So, over time, individuals with traits that \__ them survive and reproduce will become more frequent in the population

pattern, process

Darwin's idea of natural selection was a hypothesis about __, not process. Factors not included are:
o What causes differential reproductive success?
o What is the mechanism for inheritance?

Natural Selection

a mechanism of Evolution:
a. Existing variation is selected on via differential reproductive success
b. Environment selects
c. Mechanism: differential reproductive success (external)
d. What it acts on: existing variation in phenotype in the population

Sexual selection

Mechanisms of Evolution
a. Existing variation is selected on via nonrandom mating
b. Choosing a mate - individuals choose
c. Mechanism: nonrandom mating (internal)
d. What it acts on: Existing variation in phenotype in the population

Genetic drift

Mechanisms of Evolution
a. Random processes are especially impactful over time in small population
b. Mechanism: random events are impactful at small population sizes
c. What it acts on: existing variation in phenotype in the population

Mutation

Mechanisms of Evolution
a. Results in new alleles with potential new function (gene duplication, lecture 11)
b. Mechanism: introduced by mutation
c. What it acts on: new variation in genotype

Migration

Mechanisms of Evolution
a. Change allele frequency, introduce new alleles
b. Mechanism: introduced by new individuals
c. What is acts on: new variation in genotype

Hardy Weinberg

No mechanisms of evolution are present in a \__ \__ equilibrium (which means this equilibrium is rare)

Hardy Weinberg equations, two

- a way to test whether evolution is taking place in a population
o If a gene pool contains \__ alleles for a given locus, and the relative frequencies of those alleles is unchanging then the number of individuals with each genotype (AA, Aa, aa) can be predicted by these equations

1. A large breeding population → no genetic drift
2. Random mating → no sexual selection
3. No change in allelic frequency due to mutation → no mutation
4. No change in allelic frequency due to immigration or emigration → no migration
5. No natural selection

For frequency predictions of Hardy Weinberg equations to come true:

frequency of A

p

frequency of a

q

frequency of AA

p^2

frequency of Aa

2pq

frequency of aa

q^2

1

p2+2pq+q2 \=?

directional selection

two different species form overtime

disruptive selection

results in two different species

stabilizing selection

middle phenotypes are favored with extremes are unfavored

allele frequencies

Natural selection acts at the level of \__ \__ (phenotype)
ex: Females Cichlids (fish) select the most brightly colored male to mate with.
•Since the females select mates based on color, male fish pick in a environment where their color shows best

islands

Adaptive radiation is often found on __

o Niche specialization drives adaptive radiation
o Each of these finches has a beak specialized to a specific type of food.
o This allows many species to coexist without competing for resources

Darwin's Finches

Microevolution

Hardy Weinberg equations, mechanisms of evolution

Macroevolution

constraint - evolution is constrained by trade-offs and history.
-Biogeography
-Sexual selection
-Adaptive radiation

Ring species

· belong to the same species but are a different subspecies, they are reproductively isolated and morphologically distinct. Ex: California salamanders from class
· a window into the process of speciation

Biogeographic barrier

separates a species from mating

-Subspecies of Cali salamander that are next to eachother in the "circle" that surrounds the valley can interbreed while those across from each other over the barrier cannot
- The farther south you go along each side of the valley, the more different each subspecies is from its relative across the valley - even if geographically, it is very close.

give an example of how biogeographic patterns may be reflected by phylogenetic patterns

pattern of relatedness + pattern of geography

\__ + \__ \= biogeography

Adaptive radiation

· a pattern of speciation, and occurs when one species undergoes rapid speciation, resulting in many closely related species arising over a short amount of time.
-May be due to invasion of a new habitat, ex: an island
-Or to the appearance of a new phenotypic trait

· Adaptive Radiation on Islands, island, adaptive radiation

• New \__ forms \= species that inhabit it have no competition for resources
• Since many niches are occupied by descendants of a single common ancestor, their relatedness is an example of \__ __

Diversifying selection

genetic variation in ancestral population is supported and allowed to increase by the ability of varying habitats in the new location ~ original ancestral trait is diversified to fit new environments/niches

limited space

Diversifying selection is further driven by \__ \__ - for so many individuals to coexist without competing, they will do better if they are able to exploit different niches within the habitat

unrelated species,

o Similar branching patterns in the family trees of \__ \__ are evidence for adaptive radiation
- Genetic differences between Galapagos snakes shows a history of arrival on each new island followed by adaptive radiation once arrived.

looking, less

· One result of adaptive radiation is similar \__ species are \__ closely related than geographically proximal species

morphology, external forces, ancestral*

· Adaptive radiation can be spurred by __
• Arrival on a new island/in a new lake, or the extinction of a major competitor - habitats becoming available through \__ __
• Some adaptive radiations may be due to changes in the \__ species morphology

larger, longer

Adaptive radiation can also take place at \__ geographic scale and \__ timeline
- Ex: mammals after extinction of dinosaurs, now had access to a great variety of habitats

pseudogenes, pseudogenes, molecular fossil

Chitinase \__ show that mammal diets diversified after dinosaurs went extinct
-Mammals that eat insect have five copies of chitinase are now _ in placental mammals
-These are \__ \__ evidence for adaptive radiation

gene expression

Modularity allows formed differences in the patterns of \__ __

Genetic switches

govern how the genetic toolkit is used

Developmental

\__ genes in distantly related organisms are similar

phenotype

Changes in developmental patterning & timing lead to __changes

similar effects

Differential expression levels, times, and locations can have \__ __

cDNA

\__ is used to measure expression

1. Determination - set the fate of the cell
2. Differentiation - process by which different types of cells arise
3. Morphogenesis - organization and spacial distribution of differentiated cells (shape formation)
4. Growth - increase in body side by cell division and cell expansion
(muscle cell example)

Process of Development*

Cell fate, region

-can be mapped experimentally
-is usually determined in early development
-The exact timing can be figured out by transplanting cells from one embryo to a different \__ in a different embryo.*

modular

· Animal development is __
-Common developmental pathways are involved in embryonic development of many animals, such as the formation of eyes in both insects and vertebraes

DNA sequences, regulatory proteins,

\__ and \__ \__ common in developmental pathways comprise a toolkit. Genetic switches control how the toolkit is expressed.

Heterotopy, Heterochrony, Heterometry

Mutations to regulatory regions

Heterotopy

change in location of gene expression

Heterochrony

change in timing of gene expression/when expression happens

Heterometry

change in level of gene expression, based on controlling transcription + translation

Heterotypy

Mutations to coding regions

Heterotypy def

change in gene product

regulatory region

Mutation that changes \__ \__ can change phenotype significantly

In anthropods - upregulates DII expression like millipedes
In insects - a mutation in Ubx gene causes it to downregulate DII expression
So, difference in legs is due to mutation in regulatory gene UBX that turned it from a cis-regulator to a trans-regulator

regulatory region mutation example:
o Gene Distalless (Dll), which controls leg development
o The Hox gene Ubx is expressed in abdominal segments but has different effects on Dll in different species.

switches
-the eyeless gene is the switch that coordinates expression of all the genes needed to build an eye. Ex; can put eyeless gene on leg and it will make ectopic eyes develop
-Pax6 encodes a cis transcription factor for the eye module in mammals. Two genes - good eyes develop, one gene - okay eye develops, netierh gene - no either develops

Complex modules, like the eye, are controlled by __
- In Drosophila, the eyeless gene
- Pax6 switches eyes on/off in mouse

convergent evolution

Independent evolution of similar features from different ancestral traits. The toolkit of genes that builds eyes is different in mice than in flies. Insect eyes and vertebrate eyes are analogous.

Ancestrally homologous

derived from similar gene in common ancestor. Ex: the switch that turns this toolkit on, named eyeless in flies and Pax6 in mice, both derive from a similar gene in a common ancestor

Derived homology

- inherited trait from common ancestor. Ex: The eyes of all vertebrates are inherited from the eye of a vertebrate common ancestor. The eyes of all insects are inherited from the eyes of an insect common ancestor.

Conserved

- transcription factor in one speices can be used by a toolkit in another species. Ex: The eyeless and Pax6 genes contain sequences that are highly conserved, meaning that although Pax6 is a mammal transcription factor, the fruit fly's eye toolkit could be up-regulated by it.

developmental,

Highly conserved \__ genes make it likely that similar traits will evolve in the same ways in isolated populations of a species.

parallel

· Phenotypes with the same genetic basis sometimes appear in separate populations, in \__ *

Heterotopy example*, different

-One gene, Pitx1, is not expressed in the pelvic region of freshwater sticklebacks, and spines do not develop
-A deletion in the enhancer causes the spine gene to not be expressed in the pelvic region, resulting in the freshwater phenotype.
-The specific deletion is \__ in each population but has the same outcome.

Heterochrony example

In giraffes this signal is delayed in the neck vertebrae, so they grow for a longer time during an individual's development.
-The neck-building toolkit is the same in both these mammals

Heterotopy example

-The webbing between toes that is present in limb buds disappears (apoptosis) by the time a chick hatches.
-In ducks and other web-footed animals, the genetic signal responsible for apoptosis is not expressed between the toes.

Heterometry example

Different expression levels of Bmp4 cause different beak width and depth

Structural gene has deeper homology than switch gene*

• Species concept

Morphology

structure/phenotype

Morphological species concept

concept that groups species by structural appearance (Linnaeus taxonomy). The only species concept that is applicable to (most) extinct organisms. Can be used in the absence of behavioral or population genetic data

Evolutionary species concept

a concept where a species is a "separately evolving lineage". This is based on the BSC, but with the inclusion of an explicit historical component.

Biological species concept

• concept where a species is reproductively isolated population. Note the use of "population" here implies something slightly different if we try to scale it up... a species may be made up of several populations, not necessarily in contact with one another...

Cryptic species

species that look morphologically alike, and occupy the same range, but do not interbreed. Evidence for this is in the form of genetic data, showing several distinct clusters of populations that are reproductively isolated.

unknown

• The mechanism by which this isolation of cryptic species is maintained is as yet __: possibilities include different song patterns, different breeding seasons or times of day, different niche occupation (eg: living at different heights in the trees), different number of chromosomes (polyploidy)

Speciation

becoming two different species

Allopatric speciation

occurs in the presence of a geographic barrier, preventing gene flow between parts of what was initially a single population.

dispersal & vicariance

Types of allopatric speciation

Sympatric speciation

can be caused by specialization into different niches or differences in timing of life events or activities (different active times/mating times in a species) - not divided by barrier but some other factor

Niche

different activity or trait that makes them unique

Dispersal

movement of a species, may also occur across an existing barrier, in an unlikely but still theoretically possible event. This followed by the formation of a barrier preventing their return can result in allopatric speciation

Sweepstakes

when dispersal occurs across an existing barrier, in an unlikely but still theoretically possible event (eg: rodents originated in Eurasia but are found in South America starting about 40 million years ago, when the Atlantic was already quite large).

Vicariance

• Appearance of a new barrier within the existing range of a population, causing it to be divided & resulting in allopatric speciation. (type of allopatric speciation). Ex: cichlids of Lake Malawi: a population ranging across the entire lake was divided into several parts when water level fell

Lineage

species through time

Endemic species

• a species found only in one area, for instance a single island or a single lake. Ex: dispersal to new islands caused penguin diversity.

Phylogenic species concept

• The Chatham Islands (3 million y/o). Many geologically young islands have endemic penguin species, including for instance the Galápagos. Today, different (but closely related) species of crested penguins are found on islands all around the Antarctic. *A combination of DNA & morphology showed that the fossil represents a now-extinct species, endemic to the Chatham Islands.*

Sister species

• directly branch off of the same node

Phylogeny

Evolutionary history of a species

Most recent common ancestor in a phylogenic tree

• first node where a species meet in a phylogenic tree

Common ancestor

• shared ancestor (node) between species