Evolution Exam 3

Natural selection states that increases in ___ and ____ _____, which is key, can be small.

Survival

Reproductive success

Natural selection states that ___ in a trait cannot be easily detected by humans.

Variations

Natural selection states that ____ ____ is really key.

Reproductive success

Individuals in a population are different

Variation

The differences in a population are heritable.

Inheritance

The differences in individuals in populations increase fitness.

Reproductive success

The ability to survive and reproduce in a given environment.

Fitness

The study of the branching relationships of populations as they give rise to multiple descendent populations over evolutionary time.

Phylogenetics

Historical/evolutionary relationships between all living organisms

Tree of life

Taxon related to the others but branched off earlier in evolutionary history

Outgroup

Theory of evolution by ___ ___ does not try to explain how life on earth began, but does offer a tested theory of how subsequent life developed.

Natural selection

Last universal common ancestor. Was likely a population of organisms, not a single organism.

LUCA

What are the properties of life?

Homeostasis

Structural organization

Metabolism

Growth & reproduction

Response to environmental conditions

___ is the ability to adjust internal environment to maintain a stable equilibrium.

Homeostasis

___ is the ability to maintain distinct parts of their connections.

Structural organization

__ is the ability to control internal chemical reactions.

Metabolism

All life is subject to and has evolved by the process of ___ ___.

Natural Selection

Prebiotic Earth was likely __ than current earth by as much as 30 degrees celsius.

The ___ was different: Reducing (CH4 + N2, NH3 + H2O, or CO2 + H2 + N2) to neutral (CO2 + N2 + H2O), but no O2.

___ relations were different, like bombardment by asteroids.

Warmer

Atmosphere

Space

What was one primary theory Oparin and Haldane made?

Prebiotic soup hypothesis

Who came up with the prebiotic soup hypothesis?

Oparin and Haldane

In absence of oxygen, UV light and lightning were energy sources that converted atmospheric gases into molecules. (Energy + pre-biotic chemicals = earliest life forms).

This is what theory?

Prebiotic soup hypothesis

What are other energy sources that could have converted atmospheric gases into molecules?

Cosmic rays, volcanoes (sea & land), hydrothermal vents, earth’s internal heat

Molecular “soup” may have been enriched by extraterrestrial matter like ___ and ___ which harbor __ , ___ , and ___.

Meteorites and comets

Amino acids, purines, pyrimidines

Who did the “synthetic ocean” experiment called “Organic Compound Synthesis on the Primitive Earth” ? Electric source + gases = amino acids: glycine, alanine, valine.

Miller & Urey 1959

Who did the experiment “Thermal Synthesis of Natural Amino Acids from a Postulated Primitive Terrestrial Atmosphere.”

Methane + NH4OH + Sand at 1000 degrees C = 12 amino acids.

Also, what is NH4OH?

Harada and Fox 1964

NH4OH Is ammonium hydroxide.

Who first answered Can amino acids join into chains? with the paper titled “A theory of Macromolecular and Cellular Origins?”

Combined amino acids at high temp (120 dg C) and placed mixture into water = peptide chain (weak)

Fox in 1965, then with a later paper Fox and Dose in 1977

Another to answer the question can amino acids join into chains was ___ by writing the article “ A Possible Primordial Peptide Cycle.”

Combined amino acids at high temp (120 dg C) in presence of CO2 and placed mixture into water = stable peptide bonds.

(CO was thought to exist in prebiotic atmosphere).

Huber et al. 2003

The breakdown of HCN to the next member of the series is called ___ ___ of hydrogen cyanide and its derivatives?

It showed that precursors of amino acids, lipids, and ribonucleotides can all be derived by this.

Reductive homologation

This study shows that Miller-Urey experiments produce ___ ____ in discharges and ___-driven plasma impact simulations carried out in a simple prototype of reducing atmosphere containing ammonia and carbon monoxide.

A.K.A. Meteor like impacts with early earth atmosphere can create all 4 __.

RNA nucleobases

Laser

Nucleobases

__ and colleagues showed that RNA molecules, alone, are affected by natural selection.

Spiegelman 1970

Spiegelman’s experiment was adding primer replicase nucleotides in __ consecutive transfers and incubating led to mutated strands of moderate length.

75

__ did the same experiment as Spiegelman but in a different way. Added __ __ (inhibits replication) which produced also mutated strands of moderate length but they evolved to function in __ __.

Sumper 1975

Acridine Orange

How can RNA replicate without replicase (enzyme)?

Ribozymes

__ are RNA molecules that can act as replication enzymes. (Initial system was very limited in terms of replication).

Ribozymes

Who discovered the system of ribozymes acting as replication enzymes in 2002?

The article title is “ A self-replicating ligase ribozyme.”

Paul and Joyce in PNAS journal

What does ligase do?

Sticks things together

Later on, what two people wrote “Self-Sustained Replication of an RNA Enzyme” that extended to show that 4 oligonucleotides could produce 2 enzymes that __-__.

Self-amplify

Lincoln and Joyce

We moved from RNA to DNA because natural selection would have favored ___ and more ___ systems than RNA and ribozymes. DNA is one such system.

Stable

Efficient

What are ways DNA is more stable than RNA? (Deoxyribose vs ribose)

Double-strand protects bases from interference

DNA replication allows proofreading

DNA has built in repair mechanisms (DNA has higher fidelity = lower mutation = bigger, more complex genomes)

DNA has higher __, which means lower mutation, and lower mutation means bigger, more complex genomes.

Fidelity

Once we moved to the DNA world, how did cells form?

Mutualism, molecular mutualism, hypercycle model

__ is when 2 or more individuals interact in ways which benefit each.

Mutualism

__ is when 2 or more molecular substrates contribute to the replication of each other in a positive way.

Molecular mutualism

The __ model applies to replicators (self-replicating entities). Replicators are found in the same environment and can interact in a cycle ( More A makes more B makes more C makes more D makes more A).

An increase in the rate that A self-replicates is selectively favored, NOT an increase in the beneficial effect that A has on B’s rate of replication, unless the components are enclosed in a membrane and share a collective replication rate.

Hypercycle

Natural selection does or doesn’t favor changes that benefit other species?

Doesn’t

Leading theory of how cell division arose is that replicators may also have been selected to produce some fatty acids for cell membrane, and increased efficiency led to ___ of cell membrane parts.

Doubling ___ __ more than doubles __, which eventually leads to cell instability and splitting.

Overproduction

Surface area and volume

__ is the transfer of genetic material from one organism to another organism that is not its offspring. Can be different species.

Horizontal gene transfer (lateral gene transfer)

What explains how cells became more complex?

Horizontal gene transfer

Darwin’s insight: All species descended from 1 or a few common ancestors. Species with a recent common ancestor share more features bc they share common ancestry. This explains the ___ of ___ and ___.

Origins of diversity

Heritability

What was the title of the article Darwin wrote about species?

The origin of species

The disagreements over how to define species are referred to as the ___ ___

Species problem

Usually, we define species using a ___, which defines what species are or what makes a species a species. There are many, 20+, but we look at 4.

Concept

What are the species concepts?

1. Evolutionary species concept

2. Phenetic species concept

3. Phylogenetic/cladistic species concept

4. Biological species concept

Which species concept is this?

A species is a single lineage of populations which maintain its identity from other such lineages and which has its own evolutionary tendencies and historical fate.

Evolutionary species concept

Who came up with the evolutionary species concept?

Simpson and Wiley

What are keys and problems with the evolutionary species concept?

Keys: shared evol. History, common future fate.

Problems: not clear how to identify or define species.

What species concept is this?

A species is a cluster of phenotypically similar individuals or populations.

Phenetic species concept

Who came up with the phenetic species concept?

Michener and Sokol

What species concept do these keys and problems correspond to?

Keys: measure traits, group similar individuals.

Problems: not clear how to weight importance of characteristics, can incorrectly group, (organisms could look similar due to convergent evolution).

Phenetic

Phenetics species concept is also called ___ concept?

It is used when trying to define species of fossil organisms. Also used in microorganisms to determine species.

Morphological

(Fossils: little/no DNA

Microorganisms: lateral gene transfer)

The ___ concept is “A species is the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry and descent beyond which there is not, and which exhibits a pattern of phylogenetic ancestry and descent among units of like kind”

Phylogenetic/cladistic

Eldredge and Cracraft came up with the ____ species concept?

Phylogenetic/cladistic

Phylogenetic species concept: Use phylogeny to define species. Species barriers are drawn using ___, ___ characters that are unique to one ___ group and absent from all other populations in the phylogeny.

Shared, derived

Monophyletic

___ are the smallest monophyletic group distinguished by a shared, derived, character.

Species

What species concept do these keys and problems describe?

Keys: shared evol. History, focus on diagnosable differences.

Problems: differences can be small/arbitrary, traits may not be ecologically significant, ignores gene flow btw species, species can fuse again (doesn’t guarantee evol trajectory in future)

Phylogenetic/cladistic

Since humans are unique and all look different, what species concept would not work to classify humans as one species?

Phylogenetic

Problems: differences are small, traits may not be ecologically significant

What species concept is this?

A species is a group of actually or potentially interbreeding populations which are reproductively isolated from other such groups.

Biological species concept

Who came up with biological species concept?

Mayr

Problems and keys with biological species concept?

Keys: group of populations, reproductively isolated, gene flow.

Problems: hard to apply to extinct species, confusing within hybridization, doesn’t apply to asexual species.

Most common species concept is___. Uses patterns of gene flow to define species. Either no cross-breeding or hybrid sterility. If there IS gene flow… it is NOT a different species.

Biological

Most species concepts agree on species ____ (phenotypic differences, no gene flow, and monophyletic groups).

Delineations

Why are corner cases so hard?

Hard to classify all populations at all stages of evol history.

Trying to make a ___ process __.

Many forces, such as ___ and ___, affect speciation.

Continuous, discrete

Selection, drift, founder effects, inbreeding

What species concept would you apply to “ “ scenario.

What are the 3 models of speciation?

Allopatric, parapatric, sympatric

In __ speciation, reproductive isolating mechanisms evolve in populations that are geographically isolated.

Allopatric

In allopatric speciation, ___ in this model is due to drift, mutation, and selection.

Divergence

In allopatric speciation, often divided into __ and __ __ models.

Dumbbell

Peripheral isolate

__ speciation occurs when 2 adjacent populations diverge into separate species without a barrier to dispersal. In most of these models, its assumed the hybrid zone will eventually disappear, completing speciation. This assumes that hybrid offspring are at a selective disadvantage across the cline.

Parapatric

__ is a spatial gradient in selective pressures and resulting genotypes and phenotypes.

Cline

The __ __ is an area in which divergent populations encounter each other, mate, and produce hybrid offspring.

Hybrid zone

__ __ is the case where individuals that live in a series of populations connected in a ring-like fashion and gene flow occurs btw adjacent populations. But, where populations come back into contact, there is no gene flow due to significant divergence.

Ring species

(Allopatric + parapatric speciation)

Example of a ring species?

Ensatina salamanders

In __ speciation, populations diverge when no geographic boundary exists between them.

Possible mechanisms: __ __ and __ __.

Sympatric

Resource competition & reproductive competition

Example of sympatric speciation?

Cichlids.

Many ecological niches in lake.

__ __ is the absence of gene flow btw populations.

Reproductive isolation

What are the 2 classes of mechanisms of reproductive isolation?

Pre-zygotic isolating mechanisms

Post-zygotic isolating mechanisms

Habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, and gametic incompatibility are __-__ isolating mechanisms.

Pre-zygotic

Zygote mortality, hybrid inviability, and hybrid sterility are ___-___ isolating mechanisms.

Post-zygotic

What 4 genetic mechanisms are responsible for reproductive isolation?

1. Changes in ploidy.

2. Chromosomal re-arrangement.

3. Dobzhansky-Muller incompatibility.

4. Sex-linked effects (Haldane’s rule).

Changes in __ ( chromosome number ).

Ploidy

Which genetic mechanism of reproductive isolation is this?

Many plants can tolerate changes in ploidy, adapting readily to new environments. Differences in ploidy btw individuals lead to infertile offspring (cannot do meiosis). This leads to reproductive isolation btw ploidy levels

Ex: One population had a fusion of chromosomes.

Changes in ploidy

Which genetic mechanism of reproductive isolation is this?

Over time, as populations isolated, genes & chromosomes may re-arrange (by __ or __). These re-arrangements can cause reproductive isolation btw individuals in a population or btw populations, bc individuals of one arrangement + individuals of the other = dysfunctional gametes.

Chromosomal re-arrangement

(Inversion or translocation)

Which genetic mechanism of reproductive isolation is this?

Dobzhansky-Muller incompatibility

Which genetic mechanism of reproductive isolation is this?

JBS Haldane noted that among hybrids, when 1 sex is absent, it is the heterozygous one, & decreased fitness of heterogametic individuals leads to reproductive isolation.

Sex-linked effects (Haldane’s rule)

Regarding the genetic mechanism for reproductive isolation: sex-linked effects (Haldane’s rule),

Why heterogametic sex? ___ __ is if a recessive gene on X-chromosome has negative effect, it is masked in XX females but not in CY males (this works in opposite for ZW sex determination).

Dominance theory

__ __ are regions of DNA of unknown function that are located in non-coding regions of genes. Dr. Faircloth studies these in his lab. They also use these loci to study evolutionary relationships among different species.

Ultraconserved elements

A __ __ is a visual representation, in the form of a bifurcating __, of the evolutionary relationships between species, genera, families, etc…

Phylogenetic tree

Tree

Linnaeus developed the Linnaean __. It is NOT phylogenetics. It is arranged into hierarchical categories: order, family, genus, species, subspecies. Linnaeus had no clue why these similarities existed and some classifications were wrong.

Taxonomy

Who wrote Systema Naturae?

Carl Linneaus

At a ___-scale, phylogenetics allows us to reconstruct the ___of____ - those historical/evolutionary relationships btw all living organisms.

Tree of life