Organic Evolution Exam 2

systematics

the field of biology that comparatively studies features of organisms and the relationship among themselves

tries to organize groups and establish relationships

phylogenetics vs taxonomy

phylogenetics: to reconstruct the pattern of ancestor to descendant species through time , establish evolutionary relationships

taxonomy: the naming and classifying organisms

Haeckel

divided the scientific community into Darwinians (progressives) and traditionalists (conservatives)

coined the term phylogeny to describe the scheme of genealogical relationships

evolutionary versus numerical taxonomy

evolutionary→ Evolutionary taxonomy aimed to look at how species came from a common ancestor and also how they have changed over time to become who they are now but Scientists could disagree about how much evolutionary difference was enough to put organisms into separate groups.

numerical: Phenetics aimed to be more objective by actually measuring how similar an organism was by comparing many traits and then determining a numerical relationship of similarity. A phenogram is different from a phylogenetic tree because it shows only how similar organisms are, not their actual evolutionary history

saint-hilaire

argued that the environment not the species are the driving force for transmutation (different from linnaean), believed that all life originated from a single fundamental unit (LUCA)

LUCA and evidence for LUCA

• LUCA needed to be a single-cell free living organism, able to metabolize oxygen, and extremophile

evidence:

1. all organisms that we know use RNA and DNA

2. use the same 20 amino acids and sugars

3. have ribosomes

4. have lipid bilayer and ATP synthase

character and sources

an observable property or attribute of a given organism, which can be divided into character states (versions of that character)

character= the question

character state= the answer

1. anatomy

2. ontogeny (development)

3. fossil records (one of the most important features)

4. innate behaviors

5. molecular information (sequences of amino acids, proteins, or gene organization

character matrix and scoring characters

• summations of all observations made in an orderly fashion to facilitate comparisons among organisms

• scoring characters : the act of assigning a character state to a particular organism in the matrix

HOMOLOGY criteria

1. morphology: similar in appearance

2. topology : in similar location to neighboring structures or organs

3. ontogenetic: similarity in embryological development

4. congruence : all the characters are in agreement

Two kinds of homology

can describe if a character is from an ancestor or is it a new derived trait

1. apomorphy-→ a new derived trait that recently arised

2. plesiomorphy→ the character arises from a common ancestor, an old trait

optimality criteria (what is it and the two kinds)

the quality based on what we evaluate a phylogenetic process

1. parsimony: the hypothesis that makes the less assumptions from one character state to the next

2. statistical methods

polarization and the outgroup comparison

polarization: uses the outgroup comparison to determine if a character is plesiomorphic or apomorphic

outgroup comparison: is a taxa that is related to but not in the group that we are studying (known as the ingroup). if the character state is shared with the outgroup, then it can be said that the shared character state is pleomorphic, and any adaptation towards it is apomorphic

synapomorphy

a shared derived character that two organisms share from a common ancestor

monophyletic, paraphyletic, and polyphyletic groups

monophyletic: also known as a natural group or clade, a group of taxa that encompasses all the derivatives from the same node

paraphyletic: a group of taxa that includes only some derivatives of the same node

polyphyletic: group of taxa that encompasses derivatives from multiple nodes

linneaus naming system

• created a binomial nomenclature, a system of two part names in which each species is referred to by its genus and species name

hierarchical versus natural classifications

hierarchical: some groups contain a large number of organisms that share very fundamental characteristics, these categories are mutually exclusive meaning you one genus cannot belong to more than one order

natural: the ones based on phylogenetic hypotheses and reflect natural or monophyletic groups

monophyletic groups are defined by an apomorphy

non-monophiletic groups are a result of..

• a misinterpretation or lack of data, we group organisms together in the wrong ways!!

Paraphyletic: mistake an apomorphy for an old feature plesiomorphy . Some of the descendants from a common ancestor are left out

polyphyletic: mistake a homologous feature with a convergent feature and misgroup organisms together based on shared features but they may have different environmental pressures

typification

When a scientist discovers and names a new species, they keep a specific specimen as a permanent reference so other scientists can check what that species actually is.

The type specimen is the particular specimen that is the main reference for a species name . It can help us with falsifiability and repeatability

ghost lineages

• is a line of descent that has left no traces in the fossil record. with sister group relationships, we can deduct that the species has existed at the same time, even if we have an absence of a fossil record

  • sister groups diverge at the same time, so you can backtrack for the group that lacks fossils and create a ghost lineage even if you have no concrete evidence of the emergence of the one needing the ghost lineage

lazarus taxon

• the discovery of a living population of a believed extinct taxa can extend the timespan of its lineage

  • can be a younger fossil that is discovered and fills in the gap of time

  • can also be that the species is literally rediscovered to be alive

how systematics can help limit zoonotic diseases

• a zoonotic disease is one in which a host can jump species, it is important that we identify the infection source to contaminate. see the evolution of a disease!!

  • to determine the most likely source, we can compare genomic regions, and create a phylogeny

  • whichever is most similar to the version that has adapted and is able to infect humans is most likely the carrier source for infection

  • example: human SARS-coV which was most similar to the SARS in bats

optimization

• the process of finding the best explanation or arrangement of character changes on an evolutionary tree. Where on the evolutionary tree did this change occur

  • we want the explanation that is the most parsimonious, meaning it makes the minimal amount of assumptions

example: swim bladder which is homologous to the lungs of land vertebrates, people hypothesized that the swim bladder evolved into the lung

Two techniques for optimizing a phylogenetic tree

• upper pass: start at the taxa and work at the root

  • if two sister taxa have the same state, mark that state in their common ancestor

    • if the sister taxa have different states, put both states in their common ancestor

    • if one of the nodes has both states, and the other just one, mark the ancestral node with the state in common

    • if two nodes have different states, but poth at their common ancestor

• Lower pass: start at the root and work back towards the taxa

  • if a node below and above have the same state, but the node in between the two has both, put the shared state on the middle ambiguous node

  • if a node below and one of the taxa have the same state, but the node between has both, put the state shared on the middle node

adaptations

attributes that evolved through natural selection and increases an organisms reproductive success, directly or indirectly

• can be morphological, physiological, or behavioral

adaptationism

• the assumption that every feature of an organism results from an evolutionary adaptation to a given function, while ignoring all other possible explanations

  • we don’t want to always invoke adaptationism when simpler explanations exist, a feature is a byproduct of another adaptation, when a feature is an outcome of a historical process (phylogenetic legacy)

constraints for adaptations

1. formal

   1. adaptations must conform to the natural laws of physics and chemistry

2. historical

   1. evolution doesn’t make things from scratch, it can only adapt with what it has already

3. developmental constraints

   1. if a potential adaptation cannot be formed during development to work with other parts of the organism, it will not exist

4. trade-off

   1. selection that makes one feature better may make another worse

5. plasticity

   1. the capacity for bodies to adjust their observable characteristics in response to environmental cues, its not genetic or passed down

adaptive shift (exaptation)

the shift in the function of a feature from the role it was designed for by generations of natural selection to get a new function

• because it evolved under past natural selection conditions, it can be hard to evaluate why it evolved

Example: feathers originally adapted to insulate dinosaurs and other organisms, so they were selected for. Over time they became able to help with flight by creating lift

adaptation for insulation, exaptation for flight

adaptive radiation and causes

• an event that causes a lineage to rapidly diversify and speciate to produce a large variety of new species with different adaptations

1. geographic colonization→ species migrates to a new habitat with new resources to be explored

2. mass extinction gets rid of groups and opens new niches

3. new resources based on geographic changes of the earth

4. key innovation: critical new adaptations (apomorphies) that allow a group to enter a new environment and take advantage of previously unused resources

optimality method and problems

optimality method- based on the assumption that adaptations maximize an animals fitness, allows us to determine why a particular feature evolved

1. identify problem an organism must solve

2. hypothesize how the problem might be solve

3. test the hypothesis

problems: adaptationist prone, assumes similarity by adaptation and ignores shared common ancestry

• species differences: limit our understanding

• preconceived notions or expectations might influence our hypotheses

• testing hypotheses might be impossible in a lab

  • example of giraffe neck, if they evolved to reach other food niches, we expect them to eat only at higher levels when other herbivores are present, but they eat at shoulder height, so we realize long necks are sexually selected for

comparative method and problem

characters are observed and compared in related species that live in different ecosystems, with the expectation that differences are to be the result of different environments pressures

problem: correlation does not mean causation, need to prove that the morpholoigcal character evolved after the ecological change

the optimality method develops a prediction based on a model, while the comparative method examines patterns in real organisms.

extreme sexual size dimorphism

• one sex (usually the female) is at least twice as big as the other

Tree thinking comparative phylogenetic approach

• the inheritance of traits should be considered as the null evolutionary hypothesis, and only traits that demonstrate to be derived in the phylogeny should be chosen as candidates for explanations that invoke actual environmental conditions

fossil

any preserved remains or trace of life from the ecological past
paleontology: the science that finds and studies fossils

Body Vs Trace Fossil

Body fossil: includes actual remains of the organism (hard body tissues, egg shells, bones)

trace: includes hint or inclination that the species was once there (nests, footprints)

fossilization process

1. death

2. decomposition

3. rapid burial (the remains of the organism are protected by mud or sand sediments

4. sediment buildup: the sediments begin to build ontop of the organism and create pressure and more layers

5. fossilization: mineral rich groundwater goes into the pores and creates inorganic material where organic once was (permineralization)

   1. this is a form of altered preservation: where organic is replaced

unaltered preservation and how it occurs

when the organic material is chemically still the same as before

1. mummification

2. entrapment: inert material isolates the rest of the organism from air

3. freezing: extremely cold temperatures preserve

fossil dating techniques

1. relative dating: compare the age of the rock layer its in with the known age of something else (stratigraphy)

2. absolute dating: using radioisotopes of the rocks to determine a more specific range

what can fossils tell us?

• biodiversity: lagerstatte, a ton of fossils can tell us about the biodiversity of an area

• Evolution: how organisms have changed over time

• behavior: how things could have possibly behaved in the past

• physiology

fossil bias

• patterns in records may be false due to biased phenomena in how fossils are made and how we study them

  • environments

  • abundance

  • organisms: some are better at fossilizing

ecological biogeography, phylogeography, and island biogeography

• study of how the current distribution of organisms is shaped by ecological factors, characterized by a smaller time scale

• phylogeography: study of the geographic distribution of evolutionary lineages , , strong emphasis on population genetics and genomic data

• island biogeography: study of species richness and diversity across islands and other isolated habitats

historical biogeography

• study of the geographic distribution of organisms over geological time, characterized by a larger time scale

distributional data

1. scientific records

2. historical records

3. digital records

4. fossil records

describing distribution

1. endemic( defined to one unique environment) vs cosmopolitan(ranges extending all around the world)

2. narrow( species found in limited areas) versus widespread (species found across large geographic areas)

3. disjunct (has gaps) vs continuous (no gaps in ranges)

dispersal

• movement of organisms away from their ancestral range into a new area

  • sweepstakes (rare event that moves them)

  • phoresis: organisms attaches to another just for movement

vicariance

species range is split into separate areas due to a physical barrier, common mechanism of allopatric speciation

biomes definition and type
climate definition

a distinct geographic region with an associated climate, ecosystem, fauna, and flora

• tundra

• savanna

• tropical rainforest

• desert

climate: long-term period of weather patterns in a region

factors impacting shaping climate

• solar irradiance: the amount of solar radiation from the sun a piece of land gets, more land over surface area gets less radiation (earths tilt makes equator get a lot)

  • latitudinal diversity gradient: gradual increase in species richness from the poles toward the tropics

• wind and ocean currents

  • move water and energy around the planet

  • convection cell: circulating fluid motion patterns resulting from density differences

• landforms: can alter wind, water, and heat patterns like rain shadows: side of the mountain with reduced rainfall and away from winds

• plate tectonics: movements of earths continents over geological time

• co2 concentration: co2 traps heat

molecular dating

• some components of DNA accumulate changes over time with predictable rates that vary between lineages (molecular clock)

• timing estimates generated from phylogenetic analysis of molecular data with statistical models

• if cladogenesis coincides with geographic separation, thought to be vicariance

• if cladogenesis happens before or after separation, it is inconsistent with vicariance and favors dispersal

Wallace line

a division between islands that showed they have different fauna (asian or australian like)

the biogeographic realms

1. nearctic

2. neotropical

3. palearctic

4. afrotropical

5. indomalayan

6. australasian

how the earths continents split apart

1. pangea becomes Laurasia and Gondwana

2. Laurasia splits into Nearctic and palearctic (Bering strait land bridge forms and connects asia and north america)

3. India smashes into asian contintent and forms himalayas

4. isthmus of panama forms filter for land animals and barrier for marine life

Ecology

the branch of biology that studies the interactions between individuals and the environment that they live in

ecological niche

encompasses all the abiotic and biotic factors that compose an environment an organism is able to persist and maintain stable population sizes in

abiotic vs biotic factors

abiotic: the physical and chemical components of an ecosystem

biotic: all living things in that given area

specialists vs generalists

specialists: one specific or narrow niche

generalists: use a wide range of niches

fundamental versus realized niche

fundamental: the theoretical range of area that a species can occupy

realized: the actual range or area they occupy considering interacts with other species

ecosystem

a system comprising all organisms living in a geographically specified area, along with the biotic and abiotic factors they interact with

producers, primary consumers, predators, scavengers , decomposers

producers: make their own energy from the sun

primary consumers: get their energy from producers

predators: get their energy by eating other consumers

scavengers: find but don’t kill other consumers to get energy

decomposers: turn organic material back into inorganic and recycle the food chain

tropic levels

the position each organism occupies in the food chain or web, these chains are depictions of energy flow through the ecosystem

carrying capacity

• maximum population size of the species that the environment can sustain indefinitely given the resources

tropic efficency

• the amount of energy that can be successfully transferred through each trophic level , energy is always lost

competitive exclusion or gause principle

If two species use the same resource, one will outcompete the other, and the other will go extinct

niche differentiation

when two species compete in the same niche, they will divide the niche for optimal conditions

character displacement

if two species are using the same resource, one will win, and the other will evolve the characteristics that will allow it to switch niches and use another resource

extreme character displacement: leads to adaptive radiation

frequency independent

Not dependent on the number of individuals in a population; caused by an environmental change solely based on characteristics of the individual, not how many exist

frequency dependent

depends on how many individuals are in the population

can be positive or negative

positive: the fitness of a phenotype increases as it becomes more common, selecting for common phenotypes and decrease population variability

• mullerian mimicry, all toxic species adapt same colors

negative: the fitness of the common phenotype decreases, thus selecting for more rare phenotypes and increase variability in the population

• batesian mimicry: one species fakes being toxic, mimicking the others which is rare but helps them avoid predator search image

actor versus recipient

• actor: the one performing the behavior

• recipient: the one receiving the behavior or the one in which the behavior is directed towards

nash equilibrium

• players (organisms or species) pick a strategy, and will not change that strategy as long as it continues to work and everyone else in the game is also keeping that same strategy

  • the current set of choices is optimal and their payoffs are best in this strategy

types of interactions between actor and recipient

1. spiteful: both are harmed and no one benefits (removed by natural selection)

2. selfish: the recipient is harmed but the actor benefits

both of these are cooperation

1. altruistic: the actor is harmed but the recipient benefits (warning calls)

2. mutualistic : both’s fitness increase

   1. can be nutritional, protective, transport

zero-sum game

one wins everything, and someone loses everything, there is no in between state

evolutionary stable strategies

• explains mutualisms, if both species continue to benefit from an interaction then it will continue indefinitely because natural selection favors it

reciprocal alturism

• a behavior in which an organism temporarily reduces the fitness of the organism but helping another increase with the expectation that they will pay it forward at a later time

kin selection

• strategies in evolution that favor the reproductive success of an organisms relatives, even at the cost of the organisms own survival

direct versus indirect selection and inclusive fitness theory

direct: traits that seem altruistic but actually promote success in individual selection

indirect: traits that promote success of non-offspring relatives

inclusive fitness theory: fitness is still achieved through kin reproductive success, survival of a relative or other individual theoretically enhances genetic fitness of both

sex

the process of genetic exchange or recombination amongst individuals in a population

(the exchange of genetic material between two organisms)

aexual vs sexual reproduction

asexual: reproduction in which offspring are genetically identical to its parent, includes cell division, parthenogenesis, regeneration

sexual: the combination of haploid gamete cells to form a zygote, not genetically identical to their parents

benefits of sexual and asexual reproduction

asexual: less time consuming, independent of finding a mate, less energy output, can produce many offspring quickly

sexual: genetic recombination, mutations are be counteracted by non mutated DNA in the other partner, DNA recombination (variability), allows for DNA repair,

disadvantages of sexual reproduction

1. mixes DNA, could disrupt favorable genetic combinations and produce offspring less fit than parents

2. mating can be risky, venereal diseases, damage from competitors, risk of predation

3. low levels of sexual partners make reproduction almost impossible

mullers ratchet

sexual populations can purge themselves of harmful mutations because recombinations can generate allele combinations that exclude those mutations. can go forward but not backwards

types of sexual interactions

• nonreproductive

  • rare in eukaryotes, no new individuals are formed

  • Horizontal gene transfer

• reproductive

  • 
    

types of horizontal gene transfer

• transformation

  • get genetic information from the surrounding environment, open cell wall and collect DNA plasmid then close wall, requires competency, ability to get extracellular material

• transduction

  • genetic transmission is mediated by viruses or phages, a virus infects a bacterium, the virus picks up some of that bacterium’s DNA then transfer it when it attacks another bacterium

• conjugation

  • DNA is transferred from same species via a sex pilus

ciliate nuclei

• have micronucleus: diploid, reserved for genetic recombination

• macronucleus: polyploid and runs cell

conjugation: two ciliate connect and exchange genetic material and then the pairs disconnect and have new combinations

types of gametic reproduction

1. isogamous genetic reproduction: two same sized gametes come together to fuse

2. anisogamy : the gametes are different sizes, one large one small

male vs female gamete strategy

male gamete strategy: small, motile optimized gametes, sperm

female gamete strategy: larger, more energetically rich stationary gametes, ovum (egg)

sex determination systems

• chromosomal

• environmental

why anisogamy and what kind of selection is it

• zygote survival theory: large zygotes produced large offspring, which were more likely to survive and thus became advantageous

• large zygote can provide more resources , also easier for a small sperm to hit a large target

it is disruptive selection, both extremes are favored but no intermediates

hermaphroditism

• being both male or female

sequential: begin as one and end as the other

simultaneous hermaphroditism: being both at the same time

bateman’s principle

because sperm are easy to produce and ovums take more energy input and are more costly to produce, women are the choosier sex

sexual selection forms from and results in

• female choice: features females prefer will be selected for

• male competition: males compete with each other for female attention and develop features to help to win

Results in: sexual dimorphism, where the females and males of a species look incredibly different from each other

secondary sexual traits: traits evolved from sexual selection

evolutionary models of female mate choice

• direct benefits: protection, resources, help in raising young, territory, reduced risk

• good genes: females will choose males that exhibit good genes to pass on to their offspring

  • honest indictors, proxy measure (one trait overall exhibits good health), symmetry and good genes

sensory exploitation or sensory bias

if females prefer some trait that is linked to a survival trait, males will exhibit the trait to exploit the females natural inclination towards it and attract the female

sperm competition and sexual antagonism

the direct competition of sperm for eggs can occur after a female has mated with several males

competition between males and females leads to sexual antagonism, everyone is fighting for fatherhood , leads to arms race

cryptic female choice and modes

• females by using chemical or physical mechanisms can select which males actually fertilize their eggs

pre-copulatory mechanisms: morphological , chemical, altering the time frame, sperm destruction

males: mate-guarding, copulatory plugs, sperm cooperation