Biology-Evolution Unit

allele

one or two or more DNA sequences occurring at a particular gene locus

gene pool

is the set of all genes, or genetic info, in any population usually of a certain species

genotype

refers to the genetic makeup of an organism; in other words, it describes an organism’s complete set of genes

* ec: BB, Bb, bb

phenotype

the set of observable physical traits

* ex: BB gives the color blue

heterozygote fitness

higher relative fitness than either the homozygous dominant or homozygous recessive genotype

Evolution

is the change in genetic composition of populations over time

Darwin’s observations

1. If every individual born were to reproduce successfully, populations would grow exponentially.
2. Populations tend to remain stable in size


1. therefore, not every individual in a population can be reproducing at the same rate: there must be a differential reproductive success: some individuals leave more offspring in the next generation than others do, often due to traits that confer advantages in survival and/or reproduction
3. Resources are present in constant amounts in a stable environment
4. Variation between individuals is present in populations


1. Examples of phenotypic variation:


1. color, size, shape, life history, behavior, and more
2. Therefore, some variations may help individuals survive and reproduce more successfully, particularly in the face of limited resources
5. Some types of variation are heritable


1. passed on from parent to offspring


1. Therefore, as long as the availability of resources remains constant, successful generations will contain an increasing proportion of individuals descended from parents with those helpful variations. Thus, the frequency of a helpful trait in a population will increase over time

Fitness

the ability of an organism to pass on its genetic material to its offspring

* Being able to live long enough to reproduce and keep the population or species alive

Mechanisms of evolution

Natural selection- existing varitation is selected on via differential reproductive success

Sexual selection- existing variation is selected on via nonrandom mating

Genetic drift- random processes are especially impactful over time in small populations

Mutation- results in new alleles with potential new functions

Migration- change allele frequency, introduce new alleles

Null conditions =

hardy weinberg equilibrium

What conditions are required for the predictions of HWE to come true?

1. 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 = no migration
5. no natural selection

qualitative traits

influenced by alleles at only one locus

* e.g., smooth vs wrinkled pea seeds

quantitative traits

show continuous variation; influenced by alleles at more than 1 locus

* ex: distribution of body size in a population resembles a bell shaped curve

Natural selection can act on quantitative traits in 3 ways:

Stabilizing selection, directional selection, and disruptive selection

stabilizing selection

preserves the average phenotype- favors the trait mean

directional selection

favors one trait extreme

* if directional selection operates over many generations, an evolutionary trend occurs

disruptive selection

favors 2 trait extremes

* individuals at either extreme are more successful average individuals

Selection can maintain allelic variation in a population:

1. both alleles can be maintained when fitness depends on an allele’s frequency in the population: frequency dependent selection
2. different alleles of a gene may be advantageous under different enviornmental conditions, so both may persist in a population that experiences a varying enviornment: heterozygous have an advantage at both enviornmental extremes
3. a broadly distributed population may experience different selective pressures in different parts of its geographic range, leading to clinal variation

Lineage

a series of populations, species or genes descended from a single ancestor over evolutionary time, which we can depict as a line drawn on a time axis

Node

a split in a phylogenetic tree when one lineage diverges into 2

Root

represents the common ancestor of all the organisms in the tree

Taxon

a group of species we designate with a name

* ex: humans, primates, mammals

Clade

any taxon that consists of all the evolutionary descendants of a common ancestor

Homologous

any 2 features shared by 2 or more species that have been inherited from a common ancestor

* may be any hertitable traits
* ex: the supporting bones in bats and bird wings

Convergent evolution

superficially similar traits may evolve independently in different lineages through this phenomenon

Evolutionary reversal

a character may revert from a derived state back to an ancestral state through this process

ancestral trait

an evolutionary trait that is homologous within groups of organisms that are descended from a common ancestor in which the trait first evolved

derived trait

are those that appeared (by mutation) in the most recent ancestor- the one that gave rise to a newly formed branch

convergent trait

analogous structures arise; they can arise from convergent evolution, which occurs when species occupy similar ecological niches and adapt in similar ways in response to similar selective pressures

* ex: wings in bats and weirds evolved convergently

Parsimony principle

simplest explanation of observed data is the preferred explanation, it minimizes the number of character changes in a phylogenetic tree

* it is a specific case of occam’s razor: the best explanation is the one that best fits the data with fewest assumptions

Paleontology

can provide info about morphology and biogeography

* fossils provide information about morphology of past organisms and where and when they lives
* fossils help determine derived and ancestral traits and when lineages diverged
* Limitations: fossil record is fragmentary and missing for some groups

Genetically determined behaviors

* behavior can be inherited or culturally transmitted
* bird songs are often learned and may not be a useful trait for phylogenies
* frog calls are genetically determined and can be used in phylogenetic trees

Molecular clock

the average rate at which a gene or protein accumulates changes to gauge the time of divergence for a particular split in the phylogeny.

* tells us when speciation events took place

Morphological species concept

How to look different in some way- phenotypes, the only species concept that is applicable to (most) extinct organisms,

* can be used in the absence of behavioral or population genetic data
* ex: Biologists take multiple measurements of traits in grasshoppers. they find distinct differences among different populations and reclassify what had been populations of the same species as several different species

Biological species concept

Biological species are **reproductively isolated**: individuals in a species can only reproduce with individuals of the same species

ex: In the western U.S., populations of an annual plant can be found almost continuously from San Diego to Seattle. Even though individuals from the San Diego and Seattle populations never come into contact, they can still be considered part of the same species under this concept because they can potentially interbreed.

Evolutionary species concept

an evolutionary species is a separately evolving lineage

* idea of time is implemented
* based on the BSC, but with the inclusion of an explicit historical component: a species is a “separately evolving lineage”
* incorporates info from phylogenies
* most widely applicable

speciation

natural consequence of population subdivision

* as pairs of species diverge genetically, they become increasingly reproductively isolated
* reproductive incompatibility develops gradually in many groups, reflecting the slow pace at which incompatible genes accumulate in each lineage

dispersal

the movement of individuals to a new area

* type of allopatric speciation
* dispersal moves individuals across a barrier over which they cannot return: the population is split into 2 parts with no gene flow between them

Vicariance

occurs when a barrier forms, dividing a population

* the appearance of a new barrier within the existing range of a population, causing it to be divided and resulting in allopatric speciation
* nobody ever crosses the barrier
* a barrier appears suddenly; nobody moved, and as a result, subsequent differentiation of populations

Dobzhansky-Muller model

An ancestral population is divided by a barrier to gene flow, and the two groups evolve independently.

* In each lineage, new alleles become fixed at different loci. the new alleles at the two loci are incompatible with one another
* the reason for fixation could be natural selection
* it could also be randomness (genetic drift)

allopatric speciation

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

* This can occur if some individuals cross a barrier to forming a new, geographically isolated population

sympatric speciation

occurs in the absence of a geographic barrier

* speciation does not require physical isolation: it can be caused by reproductive isolation between parts of a population that live in the same place
* can occur with disruptive selection if certain genotypes have a preference for distinct microhabitats where mating takes place

Example of sympatric speciation

Apple maggot flies in eastern north america:

* the flies previously deposited eggs only on hawthorn fruits
* when apple trees were brought by European immigrants, some began laying eggs on apples
* the incipient species are partially isolated because they mate primarily with individuals raised on the same fruit
* they also emerge from their pupae at different times- apple-feeding flies develop faster

Sympatric speciation most commonly occurs by

polyploidy= duplication of whole sets of chromosomes

Mechanisms that reinforce speciation

prezygotic isolating mechanisms prevent hybridization from occuring

postzygotic isolating mechanisms reduce the fitness of hybrid offspring and they result in selection against hybridization, which in turn reinforces prezygotic mechanisms

prezygotic mechanisms

* mechanical isolation
* temporal isolation
* behavioral isolation
* habitat isolation
* gametic isolation

mechanical isolation

differences in size and shape of reproductive organs makes mating impossible

* in plants such as orchids, mechanical isolation may involve pollinators

temporal isolation

mating periods don’t overlap

behavioral isolation

individuals reject or fail to recognize potential mating partners

* breeding calls of male frogs quickly diverge between related species. female frogs ignore calls from other species

habitat isolation

when two closely related species evolve preferences for living or mating in different habitats, they may never come into contact during mating periods

gametic isolation

extremely important for aquatic species that spawn

* ex: eggs of one species don’t have appropriate chemical signals for sperm of another species; or sperm can’t attach to and penetrate the egg

postzygotic isolating mechanisms

* low hybrid zygote viability-zygotes fail to mature or have severe abnormalities
* low hybrid adult viability- offspring have lower survival rates
* hybrid infertility-offspring are infertile
* if hybrid offspring have low fitness, natural selection may favor prezygotic barriers
* individuals that can avoid mating with members of another species would have a selective advantage

Sponges are sessile_________

filter feeders

* sessile: does not move voluntarily around its environment
* they do not have muscles, a nervous system, or a gut, and are asymmetrical
* sponges use cilia to move water through their bodies and filter out particles of food: they are filter feeders

placozoans

* the adults of most species are sessile, sticking to rocks and other surfaces
* they do not have muscles, a nervous system, or a gut and are asymmetrical
* they eat by secreting digestive enzymes and absorbing whatever algae gets digested by them

ctenophores

* swim using cilia
* many live in the deep sea and can emit light
* commonly known as comb jellies because of their rows of cilia
* they are predators, using sticky tentacles to capture small prey to eat
* they have muscles and a nerve net that lets them sense light and touch and coordinate their movements
* they have radial symmetry
* they are motile
* they can move voluntarily
* can coordinate movements to respond to environments

cnidaria

* includes jellyfish, sea anemones, and corals
* a gut with a single opening
* move using hydrostatic skeleton: muscles pull and push against the fluid-filled body
* have muscles, a nerve net, radial symmetry, and capture prey with stinging tentacles
* all have a medusa stage (swimming) and many have a polyp stage (sessile)
* have radial symmetry

all animals are

* multicellular
* heterotrophs- obtain energy from eating other organisms by breaking down the food they eat, rather than synthesizing energy directly from sunlight or heat

predators

eat other animals

parasites live on or inside

the animal they are eating

herbivores eat

plants

detritivores eat the

remains of other organisms and waste material

most animals undergo _______ during development

metamorphosis- usually one stage more able to disperse

* sessile animals usually have a swimming larval stage, to ensure dispersal can take place
* many animals have larvae that occupy a different niche to the adult form to avoid competition for space and food

acoelomate and pseudocoelomate animals move using

a single layer of muscle around the outside of their body

coelomates have muscles lining their digestive systems as well as

around the outside of their bodies

Organs are held inside the

coelom (body cavity) and surrounded by fluid

synapomorphy

a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants.

sponges and placozoans lack a

nervous system

ctenophores and cnidarians have

convergently evolved nerve nets

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nerve nets

are a network of neurons that doesnt have a particular concentration in any part of the body

protostomes and deuterostomes are the

two clades of bilaterians

* they are named after how their gut develops in the early embryo

triplobastic

three layers of cells form in the early embryo, leading to more complex systems of organs and tissues

during early development the embryo forms a

gastrula

gastrulations results in a

hollow ball one cell thick, with an indent that becomes the blastopore

protostomes

“mouth first”- blastopore develops into the mouth

deuterostomes

“mouth second”- blastopore develops into the anus; mouth develops later

bilaterians have a

* central nervous system


* CNS- has one or more dense regions of neurons (brain or ganglia) that work together to do more information processing and coordiant signlas around the network
* bilateral symmetry one plane of symmetry (front and back)
* also allows for the development of a head, with a concentrated region of the CNS and sensory organs like eyes and nose

hox genes

are switches that help organize the animal body plan

* hox gene products act as transcription factors to induce expression of the sets of genes that build body parts

Hox genes in bilaterians

an anteroposterior gradient of hox expression helps organize the developing body

* many hox gene copies with different jobs are present in bilaterians

a hox gene expressed in the wrong location can cause

a body part to grow in the wrong place

arrow worms are

an early-diverging clade of bilaterians

* embrologically they resemble deuterostomes
* genomic phylogenies put them closer to protostomes

Lophotrochozoa includes

annelids and mollusks

* mollusca is a very large group of animals including gastropods (snails and slugs), cephalopods (squid and octopus), and bivalves (clams, oysters, etc.)
* a quarter of all known marine animal species are mollusks
* annelids are segmented worms, such as earthworms and leeches. there are many marine species of annelids, too, such as tube worms

Ecdysozoans

shed their skins

* ex: insects
* the largest clade of ecdysozoans is Anthropoda which includes insects, spiders, scorpions, millipedes, centipedes, horseshoe crabs, isopods (pill bugs and their relatives), shrimp, crabs, barnacles, lobsters

trilobites

are extinct marine anthropods and are among the oldest animals

deuterostomata echinoderms

are secondarily radially symmetrical

* we can tell that echinoderms are bilaterians because they have a coelom, CNS, share hox gene copies with other bilaterians, and have a deuterostome pattern during development
* echinodermata includes sea stars, sea urchins,and sand dollars

hemichordates

are a group of marine worms

* this clade contains relatively few species

chordata includes vertebrata

animals with a spinal cord and an internal skeleton are vertebrates

Umwelt

is the point of view of a particular animal; each animal senses the enviornment: the organism’s subjective world

* the idea of umwelt is needed to study any animal’s behavior

Ethology

the study of an animal behavior in natural environments

* behavior is viewed as inextricable from physiology, morphology, and habitat

salvation

in response to the sight, smell or taste of food is a natural reflex response to a simulus, but salvation in response to sound was a learned response

Knockout experiment

one of an organism’s genes is made nonfunctional (“knocked out”) to see what effect its elimination has on the organism’s phenotype.

* knocking out genes involved in sensory pathways can have pronounced effects on behavior

Deprivation experiments

used to demonstrate the genetic determination of a behavior

* Ex; fixed action patterns

Fixed action patterns

are performed the same way without learning, are stereotypic (performed the same way each time), and cannot be modified by learning

* ex: the greylag goose rolling an egg back into its nest
* the rolling behavior is stereotyped: this means that the goose completes the action regardless of what may change.

Stereotyped behaviors are a

response to a releaser

* in the goose example, the releaser is the presence of an egg (or egg like object) outside of the nest

proximiate cause

why, in an immediate, individual sense, an animal decides to do a thing

ultimate cause

why, in a macroevolutionary sense, a behavior persists in a population

Pheromones

are chemical cues, sensed by organs like antennae and the vomeronasal organ

Snakes

pick up chemicals from the air and surrounding surfaces with their tongue, and transfer it to the vomeronasal organ

* it is positioned in a pit at the front of the roof of the snake’s mouth
* it is not well developed or used in some mammals (humans) because they prioritize other senses (in our case; vision)

Mechanoreceptors

sense touch, electricity, and sound

* sharks pick up currents in jelly-filled pits on their face and body called ampullae of lorenzi
* platypus have a different type of electroreceptor pits, covering their bill

touch based communication

many animals allogroom or allopreen to form or reinforce social connections

* grooming of other species may be a symbiotic relationship benefited both species

snakes see warm-blooded prey with

heat-sensing pits on their face