Evolution 2600 Quiz 2

What are properties associated with living things?

\-Homeostasis(maintaining a stable equilibrium)

\-Structural Organization(maintain distinct parts + connections between them)

\-Metabolism(control of chem rxns)

\-Growth + replication

\-response to environmental conditions or stimuli

What was earth like when life originated?

\-atmosphere 3-4 billion years ago was similar to today but lacked oxygen

\-ocean temperatures were high

What is the last universal common ancestor

\-LUCA

\-not the first living thing

What are some energy sources capable of making prebiotics?

\-lightning

\-cosmic rays

\-volcanic eruptions

\-Earth’s internal heat

What does prebiotic soup refer to?

\-the pool of organic molecules suspended in water before life arose, would have grown richer in complexity over time

What was Stanley Miller’s and Harold Urey’s experiment?

\-recreating conditions on earth and plausibility of prebiotic soup theory

\-produced numerous amino acids

\-analysis done later found that they produced over 4 amino acids

What are some other sources of prebiotic molecules?

\-carbon-rich meteorites

\-comets

\-interstellar ices

\-hydrothermal vents

\-alkaline vents

What is Murchison Meteorite?

\-a meteorite that is rich in molecular diversity

\-has tens of thousands of different organic compounds

\-has at least 70 amino acids

Explain how lipid membrane would have began?

\-started with simple amphipathic fatty acids

\-then the molecules spontaneously reassemble in lipid bilayers and incorporate micelles

\-lipid molecules trafficked other molecules in and out of the cell

\-Growth: vesicle tail is elongated, as it grows a long filament is formed, filament is broken into daughter vesicles that grow and repeat cycle

\-simple vesicles tend to shrink in size and those with phospholipids grow

What is RNA World and what supports it?

\-the idea that in the past RNA played both roles as n info carrier and enzymatic molecule

\-many present-day protein-based enzymes have RNA cofactors

\-DNA is constructed first with OH group and then converted to H

\-The catalytic site of ribosome (RNA→Protein) is formed entirely from RNA

Why is DNA favoured as a transmission system more than RNA?

\-DNA is more stable

\-double-strands reduce the potential for outside molecules to interact with and disrupt the coding nitrogenous bases

\-DNA replication systems also have “proofreading” capabilities

\-DNA has repair mechanisms that don’t exist for RNA

\-”proofreading” lowers mutation rate and allows longer genes and more info to be stored in genome

What is Mycoplasma genitalium?

\-a bacterial parasite of the human urogenital system - has one of the smallest genomes of any organism that can be grown in the lab.

\-has only 43 RNA-coding genes and 482 protein-coding genes

What did Pal et al(2006) do?

\-used randomized gene deletion process

\-if deletion didn’t effect fitness, left out

\-if deletion had effect, it was put back

\-using this reductive process, scientists have given us insights into what sorts of genes may be essential for basic cellular life, and hence early evolution on Earth

What did Maynard Smith and Szathmary hypothesize?

1)Individuals give up the ability to reproduce independently, and they join together to form a larger grouping that shares reproduction(eq. self-replicating molecules merged with lipid vesicles and created protocells)

2)Once individuals aggregate into higher-level groupings, they can take advantage of economies of scale and efficiencies of specialization(eg ants attacking a caterpillar together)

3)Aggregation and specialization facilitate changes in information technologies. Organisms develop new and increasingly efficient ways to acquire, process, transmit, and store information(eg. within a cell there’s different organelles, RNA to DNA)

When did Prokaryotes and Eukaryotes evolve?

\-Prokaryotic cells are ancient, having evolved approximately 3 billion years ago

\-Eukaryotic cells evolved between 1-2 billion years later

What is Endosymbiosis?

\-symbiosis within a cell

\-proposed by Lynn Margulis as the origin of chloroplasts and mitochondria

\-Independent bacterial species capable of energy production and photosynthesis began to reside within the cells of other species

\-mutualistic relationship becomes obligatory(can’t reside outside host)

More info on Chloroplasts and Mitochondria

\-both have own genomes

\-genomes are circular like bacteria

\-Chloroplast RNA is more closely related to cyanobacteria than eukaryotes

\-Mitochondria genes more closely resemble Alphaproteobacteria

What are Information genes and Operation genes more closely related to?

\-informational(transcription + translation) genes are most closely related to archaeal genes

\-operational(metabolic processes, cell membrane formation etc.) are most closely related to bacterial genes

Where does evidence suggest that the nucleus and other organelles may have evolved from?

\-nucleus from archaeal ancestors

\-organelles may have evolved from bacterial ancestors

What does gene migration refer to?

\-once endosymbiosis happened genes were either transferred to the nuclear DNA, maintained in the organelles, or both

What are the different routes of Multicellularity?

\-staying together(more common): cells in ancestral lineage remained together after cell replication

\-coming together: formerly free-living cells joining together during the early stages of the evolution of multicellularity

How is slime mold connected to multicellularity?

\-individual slime molds come together to form a slug

What is the evolutionary definition of Individual?

\-integrated and indivisible wholes that can reproduce and pass on their heritable variations

\-germ cells and somatic cells are important for individuality because of differentiation (not possible in singe celled organisms)

\-volvocine algae show that the cells evolved on 3 separate occasions

What is the Evolutionary Definition of a Group?

\-a set of conspecific individuals who affect each other’s fitness

What are benefits to Group living?

\-forage in groups(eg. fish driving their prey out of vegetation, or honeybee waggle dances)

\-increased protection from predators(many eyes hypothesis)

What are the costs of Group Living?

\-competition(compete for limited respurces)

\-cheaters(attempts to usurp resources from others)

\-parasites/diseases(spread more easily)

What are Homeotic genes?

\-genes that determine the identity and positioning of anatomical structures

\-critical for organism’s phenotype

What are Segmentation genes

\-genes that are associated with patterning of body segments

What is a Brief history of Evolution Development?

\-scala naturae: species ranked from lowest to highest with humans at top

\-ontogeny: the development of an individual over its lifetime

What is Meckel-Serres’ Law and Von Baer’s Law?

-Meckel-Serres Law: developmental stages of the individual paralleled the evolutionary history of that species

\- Von Baer Law: general traits develop before the specialized traits that allows us to distinguish species from each other(resistant to change + mutations in early stages have big consequences)

What is Heterochrony?

\-study of the time in the developmental process at which a developmental trait is first expressed in a species, compared to other species

\-two categories: reproductive and somatic traits

What is neoteny?

\-the later/stalled development of somatic traits

eg. gills in axolotl are only shown in adulthood

What are two facts about multicellular creatures?

\-every multicellular creature develops from a single cell

\-Except for gametes, every cell in the body contains the same set of genes

What is meant by Totipotent, Enhancers and Silencers

\-Totipotent: a state of cells, that have the potential to develop into any of the cell types that make up the adult organism(stem cells)

\-Enhancers + silencers: DNA sequences that turn on or off expression of particular genes

What are Hox genes?

\-Encode for transcription factors, proteins that bind to DNA and thus influence gene expression

\-involved in determining which cells become: carpels, petals etc.

\-position on a chromosome corresponds to relative position on body

What are homeobox genes?

\-180 base-pair sequence found in all homeotic genes in a wide array of animal species

\-suggests deep homologies

What are paralogs?

\-Duplicate genes that continue to be expressed

\-involved in developmental pathways can create new developmental pathways

What are the three reasons paralogs are maintained in a population?

1)may influence gene expression levels by increasing production of histones, ribosomal RNA, and other products

2)Subfunctionalization: After duplication, paralogs may diverge because they divide the work initially undertaken by the original gene before duplication

3)Neofunctionalization: Duplicated genes may diverge, with one of them taking on a new, but related, function

What are the two problems when it comes to species?

1)How to define a species?

2)How to identify species in nature and delineate boundaries between them?

What are the 5 species concepts?

1)Evolutionary

2)Phenetic

3)Biological

4)Ecological

5)Phylogenetic

Describe Evolutionary Species Concept

\-Species are “a lineage of populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate”

\-puts evolution front and center

\-based on phylogenies

\-doesn’t help with identifying and drawing species boundaries

Describe Phenetic Species Concept

\-delineates species based on phenotypic similarity

\-commonly used today with plants and microorganisms + fossil data

\-can be used on extinct species + use genetic data in same way

\-doesn’t include evolutionary history(could be convergent evolution + not shared evolutionary history)

\-Fails when within-species variation is high or between-species variation is low

Describe Biological Species Concept

\-Delineates species based on reproductive isolation

\-a species is composed of “groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups”

\-gene flow is main determining factor

\-this concept can’t be applied to extinct species, asexual species and hybridization events(says two different species would technically be one)

Describe Ecological Species Concept

\-a species is defined as a cluster of individuals that occupy the same niche

\-focuses on ecological processes that allow two populations to coexist

\-Can be used for asexual species, possibly for extinct species

\-this doesn’t work on species with different morphs

\-another con is what is the definition of niche?

Describe the Phylogenetic Species Concept

\-Based on shared evolutionary history

\-Members of species share common evolutionary history and common fate, distinct from those of other species

\-“the smallest monophyletic group distinguished by a shared derived character”

\-one critique is the shared derived traits it uses to distinguish among species can be of minimal significance with respect to natural selection

\-can’t account for polymorphic traits(they won’t form a clade)

What are three modes of speciation?

1)Allopatric

2)Parapatric

3)Sympatric

What is Allopatric speciation and give an example

\-speciation in different places – geographically isolated

\-Alpheus shrimp

What are the two models of Allopatric Speciation?

1)Vicariance Model: one very large population

subdivided into two large populations, drift is unlikely, eg. Alpheus shrimp

2)Peripheral Isolate Model: Division of populations that are different sizes –one large and one or more small

What is parapatric speciation and give an example

\-speciation in populations that are adjacent to each other, no geographic barrier

\-diverging populations form a cline(

spatial gradient in the frequency of phenotypes or genotypes)

\-gene flow causes hybrid zone + hybrids are selected against

\-eg. pasture grown sweet vernal grass(outcrosses more + flower earlier) and mine grown sweet vernal grass(highly selfing) : leads to interbreeding isolation

What is Sympatric speciation and give an example

\-speciation in the same place, geographic overlap and no geographic boundary

\-eg. cichlids lake apoyo, Midas are bottom feeders and arrow are open water forager

What is the resource competition model?

\-Competition for resources plays role in sympatric speciation

\-scenario 1: beak size and seed size have same distribution so no competition

\-scenario 2: they dont follow same distribution so medium beak sizes are competing for medium seeds

What is secondary reinforcement?

\-when a barrier disappears before speciation and the population begin producing hybrids, lower fitness reinforces reproductive isolation

What are the two reproductive isolating mechanisms

1) Prezygotic

2)Postzygotic

Give ways of prezygotic isolation

\-deters or prevents mating

\-prevents fertilization

\-can be mechanical, temporal, behavioural and habitual

\-eg. plants species and special pollinators

Give ways of postzygotic isolation

\-deter or prevent viable offspring

\-lack of hybrid viability

\-infertile offspring

What is isolation through changes in chromosome number

\-polyploidy, common in plants

\-error in meisosis

\-hybrids are sterile

\-Plants can self-fertilize to ‘wait’ for viable mates

What is isolation with chromosomal rearrangement?

\-may be initiated when genes or clusters of genes become rearranged on a chromosome

\-hybrids formed by individuals with different chromosome arrangements will often produce dysfunctional gametes, and, as such, these hybrids will have reduced rates of genetic recombination and fewer or no offspring

\-the reduced rates of genetic recombination found in hybrids will lead to an increase in linkage disequilibrium in their descendants

What is isolation with Dobzhansky-Muller Incompatibility?

\-result of negative interactions between alleles that arose in different genetic backgrounds

\-hybrids selected against

\-maintains the isolation btwn parent species(or population)

\-hybrids with both mutations have reduced fitness, having only one is fine

What is isolation with Haldane’s Rule

\-Among hybrid offspring, if one sex is rare

or sterile it is the heterogametic sex

\-they’re at a fitness disadvantage

What is extinction, extant and extirpated?

\-extinction: all individuals of a species (or taxa) have died out leaving no living descendants.

\-extant: a species that is still in alive someplace in the wild

\-extirpated: A species that no longer exists in the wild in a specific area, but occurs elsewhere

Why would it be bad to lose the Tuatara?

\-considered a living fossil

\-great loss of phylogenetic diversity

\-part of a distinct lineage

What is the definition of a fossil and the process of fossilization?

\-fossil: the remains or traces of a past-living organism usually reserved for specimens older than 10,000 years old

\-process: organism dies(usually in sedimentary rocks, when water levels rise, sediments settle on remains, and then remains are transformed into rock

What is Lagerstatten and give an example.

\-Lagerstatten: huge concentrations of fossils

\-eg. Burgess Shale in the Canadian Rockies of British Columbia

How do Paleontologists choose sites?

\-sites that best match the geological and abiotic conditions

\-researchers often begin at or near sites where others

\-Predictions derived from phylogenetic reconstruction, biogeography, and/or molecular genetics might guide paleontologists to a particular area

What are ways to age fossils?

\-law of superposition: fossils found lower in the strata are older than fossils closer to the surface

\-radiometric dating( carbon-14, uranium-235 and potassium-40)

\-Paleomagnetic Dating: as sediments settle, they align with the earth’s magnetic field which has changed polarity numerous times

What is a Mass Extinction and Background Extinction?

\-Mass extinction: a series of events that causes large-scale loss of all species in many taxa over a broad geographic range(a loss of >50% to >75% of all species in many major taxa)

\-background extinction: extinction occurs outside a period of mass extinction(90% of extinctions are just background extinction)

What is Endemic?

\-when a species is only found in one specific area

What is the Coevolutionary arms race and give examples.

\-Coevolutionary arms race: predator and prey evolving to catch prey and avoid predation, respectively

\-if predator evolves fast or new predator is introduced, prey can go extinct

\-eg. inoceramid clams or pigs, eagles and foxes of Santa Cruz Island

\-eg. Knoll found that as a dominant species declines, a new one follows

What contributes to background extinctions?

\-Disease(eg. fungal disease killing amphibians at alarming rates)

\-human colonization(eg. bird species on Hawaiian Islands by disease, predation by humans, invasive species, competition and destruction)

When were the 5 major extinctions?

\-The end of the Ordovician

\-In the late Devonian

\-The late Permian

\-The end of the Triassic

\-At the Cretaceous-Paleogene boundary

What is significant about the K-Pg Mass Extinction?

\-Iridium was found in the K-Pg Layer(rare element on earth but abundant in space matter)

\-asteroid impact site is called Chicxulub Crater

\-asteroid cases worldwide calamity

What’s significant about the Permian Mass Extinction?

\-90% of all life on earth went extinct(90% aquatic and 70% of terrestrial)

\-combination of increased temperature, global hypoxia, massive amounts of acid rain, and the release of methane gas may have contributed

\-species with the ability to survive anoxia were able to survive

\-species that hibernated or burrowed were at lower risk

What are the effects of species longevity and geographic range on Extinction Probability?

\-there is not correlation with species longevity and extinction probability

\-broader geographic range makes species less likely to be extirpated(species is either planktrophic or nonplanktrophic )

What is Cladogenesis, Anagenesis and Pseudoextinction?

\-Cladogenesis: speciation occurs through branching events

\-Anagenesis: speciation occurs through gradual modification of form without branching(basically replacing itself)

\-Pseudoextinction: the result of anagenesis (the ancestral species appears to be extinct)

What is the punctuated equilibrium model?

\-evolutionary changes do not occur through a slow, gradual process

\-Instead, while some minor degree of change is always occurring within lineages

\-When evolutionary change does occur in lineages, it is not only rapid but also typically results in branching speciation; that is, cladogenesis(eg. Cambrian explosion)

What is the Enviromental Unpredictability Model, the Multiple Niche Model and Red Queen Hypothesis?

\-environmental unpredictability model: suggests sexual reproduction is favoured in unpredictable environments, but not predictable

\-multiple niche model: suggests sexual reproduction is favoured where there’s large number of different niches but not a few

\-Red Queen hypothesis: suggests sexual reproduction is favoured when parasite load is high but not low

What is Asexual Reproduction?

\-production of offspring from unfertilized gametes

\-Apomixis and Automixis?

What is Sexual reproduction?

\-offspring have genetic material from two parents. Characterized by amphimixis

\-recombination → Gamete production → Gamete Fusion

What is the Two-Fold Cost of Sex?

\-In a population with asexual and sexual individuals, the number of asexuals should increase at twice the rate of sexuals

\-also arises in anisogamy: production of two kinds of gametes (egg and sperm)

What are some other costs of sex?

\-can break up favourable gene combinations

\-time and energy to search for mate and courtship

\-more susceptible to predator by doing so

\-infection with parasites and diseases during sex

What are benefits of sexual reproduction?

\-Sex purges deleterious alleles by reversing Muller’s Ratchet(irreversible buildup of deleterious alleles)

\-Increases genetic variation – Fisher-Muller Hypothesis( acceleration of adaptive evolution due to increased genetic variation and breakdown of linkage disequilibrium)

\-Sex and the Red Queen hypothesis(helps host continually chnage theor genotype, parasite-host evolutionary arms race etc.)

\-Benefits in unpredictable environments(increases variability of traits, natural selection favours sexual reproduction, can increase fitness of offspring, can create niche specialization)

How does Sexcal Preproduction Lead to Sexual Selection?

\-Proto-eggs that fuse with proto-sperm are selected for

\-Intrasexual competition is usually much stronger in males than females AND females often choosier about their mates than are males

What is Intersexual selection and the four models with it?

\-Competition between sexes - competition for mates

\-Direct benefits model(choose mates that provide something to increase their chance of mating success)

\-Good genes model(Selection will favour females who can pick males with good genes)

\-Fisherian model(Females select based on preference for a trait that has no fitness benefit, positive feedback loop)

\-Sensory bias model, or sensory exploitation model(Females choose a mate based on some sensory bias that may or may not have any genetic benefit but is simply “wired” into the female’s choice, eg female frogs prefer “chuck” sound because they like low frequency sounds)

What is Intrasexual Selection and Sexual Conflict?

\-Competition between members of the same sex for the opportunity to mate with the opposite sex

\-ranges from subtle to brutal, most common in males

\-sperm competition: Sperm from more than one male compete to fertilize eggs

\-sexual conflict: Traits that evolve in one sex are detrimental to individuals of the other sex

What is social behaviour and the evolutionary context of it?

\-Social behaviour – interactions that organisms have with others

\-evolutionary context: individual’s actions may affect their own AND others fitness

What is Cooperation and the Potential Problems

\-Cooperation: an outcome of some interaction where two or more individuals receive a net benefit from their joint actions

\-problems: altruism(why would natural selection favour an individual that improves another’s fitness and not their own?) and Free-rider(why would natural selection NOT favour individuals that “free-ride”receive public benefit with no input?)

What are the 3 pathways of cooperation?

\-Kinship

\-Reciprocity

\-Group Selection

Explain the Pathway Kinship

\-2 ways to get alleles to next gen.: Direct fitness(produce offspring yourself) and Indirect Fitness(help relatives produce/care for offspring)

\-inclusive fitness: direct fitness + indirect fitness

\-coefficient of relatedness(r):the probability that an allele in one individual has a copy that is identical by descent in the other individual

\-inclusive fitness theory also helps explain eusociality(division of reproductive labour, cooperative rearing of young, overlapping generation)

Explain the Pathway Reciprocity

\-Reciprocal altruism: exchanging acts of altruism; Individual A helps B at cost to A; B helps later at cost to themselves

\-most likely occur in stable groups

\-eg. Small birds more likely to drive away predator by mobbing it since all prey birds benefit from predator leaving

Explain the Pathway Group Selection

\-Traits/actions that benefit the group, often impose cost on individual

\-Trait-group: set of individuals that affect each other’s fitness

\-two levels natural selection operates: Within-group and Between-Group

What are some conflicts with Sociality?

\-makes resources limited

\-conflict among non-kin(can lead to lethal fighting)

\-conflict over parent investment(selection should favour whoever hand off most care, siblings fight over access to resources)

\-parent-offspring conflict(selection favours selfish offspring)

What is Communication with Sociality?

\-Sharing information has either no cost or less cost than most other forms of sharing

\-if two have same interests, they can do honest signaling

\-signals can emerge through antagonistic coevolution

\-signals can be costly(costly signaling theory dishonest or eg. loud squawks)

\-coventional signals aren’t costly(honest)

What is Coevolution and the 2 types of interactions?

\-Coevolution: Process where changes in heritable traits in species 1 drive changes in heritable traits of species 2, which feed back to affect traits in species 1, and so on(eg. Lichens- fungus and algae)

\-Mutualistic interactions – interactions driving coevolution increase the fitness of both species +/+

\-Antagonistic coevolution – interactions driving coevolution decrease the fitness of both species -/-

\-often involves more than two species

What are the 4 ways mutualism could have happened?

Initially neutral interaction

\-Initially commensalism (one benefits and other no benefit or harm)

\-Initially parasitic relationship

\-Mutualistic from the start

What is cospeciation and give examples of Mutualism

\-Cospeciation – speciation in one partner in a coevolutionary relationship leads to speciation in the other

Examples of Mutualism: Ant-Fungus, Glochidion trees and Epicephala moths

What are the two main types of antagonistic coevolution? Also give examples

\-Predator-prey coevolution(evolutionary “arms race)

eg. predatory whelk and bivalve prey

\-Host parasite coevolution(there’s cospeciation, specition of one drives the other, possibel due to issolation on new species)

eg. Pigeons + doves and ecoparasitic feather lice

What is Mullerian and Batesian Mimicry?

\-Mullerian mimicry – multiple unpalatable species evolve similar phenotypes – reinforces signal(Heliconius species are all distasteful)

\-Batesian mimicry – one species is palatable and the other is not(non-toxic and toxic salamander)

What is Mosaic Coevolution?

\-natural selection can result in mutualism between a pair of species in some communities but antagonistic interactions between the same pair of species in other communities

\-context-dependent

What is Gene-Culture Coevolution?

\-the coevolutionary dynamics between genetic and cultural traits, both within and between species

\-Cultural transmission: transfer of info btwn individuals through social interactions( influences phenotype)

\-Cultural evolution: When cultural transmission leads to increased frequency of trait / behaviour within or between generations

What are examples with Gene-Culture Coevolution?

eg. Darwin’s finches- bird song was passes via cultural transmission

eg. lactose tolerance is cultural evolution?