Exam Four Flashcards
What is another term for macroevolution?
Speciation
Describe “species”
An evolutionary independent unit
Name four biological boundaries to gene flow
Physiological (cellular incompatibility), Morphological (anatomical), Behavioral (mate choice), Genetic (chromosomes, genes, alleles)
Describe the Biological Species Concept or BSC
If members of separate interbreeding populations mate and produce fertile offspring-> same species
If members of separate interbreeding populations cannot mate (physiology, morphology), will not mate (behavior), or mate and produce infertile (can be viable) offspring (genetics)-> different species
Describe the Morphospecies Concept or MSC
Traits/Characteristics
Skeletal and organ system
Describe the Phylogenetic Species Concept or PSC
Where well documented (molecular) phylogeny exists
Judgement on how much distance there needs to be for species vs subspecies
What are the three steps of speciation and what concept does it use?
1-Elimination or reduction in gene flow (1 population becomes 2)
2-Divergence, until
3-Separate species (by BSC)
Define allopatric speciation and describe the two forms
Different range, geographical barrier
Dispersal-From start to “habitat island”
Individuals are able to find compatible places randomly
Vicariance-Geographical barrier forms between a population
Define sympatric speciation
Same range
Define parapatric speciation and why it works
Nearby/Overlapping range
Reduction in gene flow, not elimination-little in ½ and 2/3 , almost none in ⅓
Which species concept is used for fossils?
MSC, morphospecies concept
What kind of speciation is Drosphila clines?
parapatric
What kind of speciation is Hawaiian Drosophia?
Allopatric-> Dispersal
What kind of speciation is snapping shrimp?
Allopatric-> Vicariance
What kind of speciation is hawthorne maggot fly?
Sympatric
What are the four levels of divergence?
Allele, Gene, Chromosome, and Genome
How does mutation lead to divergence at the allele level?
Same mutation do not occur in both populations->
New and different alleles appear in each population independently
How does selection lead to divergence at the allele level with the same selection pressures?
under directional selection patterns, different alleles can be fixed or lost
How does selection lead to divergence at the allele level with different selection pressures?
homozygote advantage pattern means that different alleles can be fixed or lost
How does selection lead to divergence at the allele level with quantitative traits?
Quantitative traits in a adaptive landscape (same selection pressure) can cause different alleles to be fixed or lost
How does nonrandom mating lead to divergence at the allele level?
Two populations can become fixed for contributing or non contributing alleles (inbreeding)
Many alleles fixed or lost
What can nonrandom mating lead to that aids in divergence? Give an example.
Nonrandom mating can become sexual selection, independent preferences in one population reinforce reduction in gene flow (even in the same or overlapping range)
Hawthorne and apple maggot flies
How can drift lead to divergence?
Different alleles fixed or lost in each population (with drift alone)
More likely that they will change then they will follow each other
Describe the founder effect in relation to divergence
Founder effect with small population (dispersal) means that initial allele frequencies are different and drift is much stronger
What are the two ways migration can lead to divergence?
Alleles introduced into one population and not the other (or change threshold level by changing allele frequencies)
Describe genetic distance
Over time two populations will accumulate differences in the actual alleles they have at each locus
How does genetic distance lead to divergence?
If two populations have the same genes, but different alleles at every point, mating may become impossible-> BSC
More genetic distance-> more incompatible
What extra thing does the environment at a single locus include?
The genotype at other genes -> multilocus selection
What is the simplest way to get macroevolution?
Microevolution + time (in thousands of generations)
Relate fitness and speciation by BSC
Fitness of hybrids is 0 (do not survive or infertile)
Describe the two ways new genes are created.
Unequal crossover-Crossover occurs where there are similar sequences, may make
one with a new region and one with a missing region
Reverse Transcription- A mRNA can be put back into the original DNA
Describe redundany in gene families, name some examples, and explain why it might be helpful.
Same function
Ribosomal genes, actin, tubulin, keratin
More is better to produce enough material/protein
How does redundancy, subfunctionalization, neofunctionalization, and nonfunctionalization occur in gene families?
One gene retains the original function, while one or more others change (or lose) the function
Describe subfunctionalization in gene families, name some examples, and explain why it might be helpful.
Altered function,
hemoglobin proteins and visual pigment proteins, the changed gene can be expressed at different times and have different (but similar) skills
Describe neofunctionalization in gene families, name some examples, and explain why it might be helpful.
New function,
Crystallins, can be a preadaptation by providing a new function (or just help)
Describe nonfunctionalization in gene families, name some examples, and explain why it might be helpful.
Loss of function, Vitamin C Synthesis Gene and Olfactory receptors, it is the most common and may prevent the wasting of energy (or just be harmful.
Describe chromosome inversions
Flipping a section a chromosome where there is no difference in phenotype because all genes are present, just in a different order/location
Describe how chromosome inversions are passed on
Inversion heterozygotes have reduced fertility (fitness), but they can still pass on their inversion, Eventually two heterozygoes will mate and produce a homozygote that has no reduced fertility and may have an advantage.
Describe how chromosome inversions lead to speciation
When there is normal, heterozygoes, and homozygotes, the hybrid has a much lower fitness and the homozygote may have some advantages (prevent intermating and create new species)
Describe chromosome translocations and describe how they are passed on (with gametes)
Parts of non-homologous chromosomes are switched, leading to 2 inviable, 1 translocated, and 1 normal gamete. Eventually two intranslocation heterozygotes will mate and produce a homo with no reduced fertility.
Describe the process of polyploidy and relate it to speciation
Diploid plant produces n gametes which go to a 2n zygote. Spindle failure produces a mosaic plant. Two 2n gametes produce a 4n adult. Breeding a 2n gamete with an n produces a sterile 3n adult -BSC
What term describes the speed of polyploidy speciation?
Instant (only a few generations)
Describe the hybrid zones and speciation results of a hybrid that has lower fitness
Narrow and short lived hybrid zones
Reinforcement of divergence
Describe pre and post-zygotic selection
Post-zygotic selection->
Mating and attempting to construct and provision an offspring with low fitness is wasteful
Mate choice preference traits-> Prezygotic selection
Positive assortative mating (inbreeding is selected for)
Describe the relationship between the speed of the formation of pre-zygotic selection and allopatric vs sympatric
Hybrid progeny more likely to be produced in sympatric
At the same level (low) of genetic distance, sympatric taxa have much higher prezygotic isolation
Prezygotic mate-selection traits evolve sooner
Describe the hybrid zones and speciation results of a hybrid that has equal fitness
Hybrid zone is relatively wide and long lived
Parental populations coalesce (after gene flow is reintroduced)
Not enough divergence
Describe the hybrid zones and speciation results of a hybrid that has higher fitness
Hybrid zones depend on whether fitness advantage occurs in new or old habitat
Stable hybrid zone or formation of new species
Describe the formation of higher hybrid fitness in plants
Species a has na chromosomes in gametes and species b has nb chromosomes in gametes, so Na + Nb in zygote (sterile)
Failure of the mitotic spindle in one cell ->2na + 2nb (mosaic plant)
Might have a flower, creates egg and pollen with half, zygote with 2na + 2nb (species C)
Describe the formation of higher hybrid fitness in vertebrates
Coywolf has a genome composed of 65% coyote, 10% dog, 25% wolf
Skilled at catching prey in forests (wolf), fields (coyote), and city (dog)
Broader diet
Define phylogeny
Evolutionary history of a group (taxon)
What two things can a phylogenetic tree tell you?
Pattern of branching events and order of speciation events
Define character
aspect of the phenotype being compared
Define character state
exact value of that trait
In a phylogenetic tree, what is polytomy?
When you can’t tell what diverged from what, looks like two v’s with their creases together and a line from the bottom
In a phylogenetic tree, what are branches and what do they show?
Lineages; common ancestor or leading to taxon
In a phylogenetic tree, what defines sister taxa?
Same branch (recent speciation events)
In a phylogenetic tree, what are clades?
A branch with all the taxa included
In a phylogenetic tree, what is the role of roots?
They allow you to determine the order of events
What is the most common error in phylogenies?
Over-interpretation
In a phylogenetic tree, what is the significance of the order of the taxa on top?
Nothing, cannot show relationship
In a phylogenetic tree, what is the significance of the length of lines?
Nothing, unless a scale is included
What information are unrooted trees based or not based on?
Common ancestors, not order of branching events
In a phylogenetic tree, what is the outgroup?
Closest taxa to the root, no common ancestor with others
What are the four steps to estimating a phylogeny?
Choose characters, generate all trees, add character states, choose the best one
What is the easiest way to choose the best tree in a phylogeny?
Parsimony, the tree with the fewest changes in state (add for each state, may be more than one spot to choose)
What are the four traits of good characters to choose for a phylogeny?
Heritable, Variable, Independent, Homologous
Describe synapomorphies
Traits evolved in a common ancestor and shared by all descendent taxa
Define homoplasy and name two ways it can form
Conflicting information about evolutionary relationships from analogous traits (convergent evolution) or reversal (change back to ancestral)
Describe the method for choosing the best tree based on genetic distance
Closer relative-> more shared alleles
Relate maximum likelihood and transitions/transversions
Purine to purine (A to G and vice versa) or Pyrimidine to pyrimidine (T to C and vice versa) are transitions and are more likely
What was the character used to determine cetacean origins based on morphological characteristics?
Shape of astragalus bone (a tarsal, bone in ankle)-> trochleated head present or absent
What was the character used to determine cetacean origins based on molecular characteristics?
Beta-casein gene (milk protein)
Where were whales originally on their tree and where are they now?
Closely related to artiodactyls, in the hippo clade
Define a transposable element and give the other name
Segment of DNA that can copy itself to another location in the same genome (LINE)
Describe the use of transposable elements in forming a tree
Likelihood that a LINE would copy itself to exactly the same location in two separate transposition events is infinitesimally small (second location is random)
Each different location that a LINE is present or absent in at least one of the taxa is a character
Describe the scaling branch length technique relating to fossils and describe its claim
Radiometric dating of fossils
Divergence (speciation) must predate their simultaneous existence
Describe the scaling branch length technique relating to mutations and describe its claim and cautions
Differences due to neutral mutations should be clocklike (a function of mutation rate)
Caution:
Mutation rates vary between distant taxa
Vary between genes
How was the origin of HIV discovered?
Using parsimony to decide if it was monkeys first or humans (it was monkeys)
How did Hawaiian Drosphila make it to the big island? How do we know?
Local molecular clock used to estimate original colonization of Hawaiian islands-> Long ago of Koko Seamound (there first, then island hop to big island)
What three major groups/clades are birds in?
Tetrapods, amniotes, reptilia
Name three polyphyletic groups that need to be changed according to monophyletic rules
Prokaryotes, dicots, fish
How do we know that leafcutter ants and their fungus coevolved?
The phylogenies match up
Compare IDA with LCUA
LCUA -Last universal common ancestor (most recent)
First living thing is also known as IDA (initial Darwinian form)
Name and describe the experiment used to test the first step to make a living organism
Stanley Miller Experiment took gases and passed them through electrodes, then a cooling jacket, then boiling water. Many repetitions produced amino acids and nucleotide-like molecules. Problem: Gases do not represent atmosphere time
Describe the experiment used to test the second step to make a living organism
Short nucleic acid bathed with other nucleotides created chance of covalent bonds. The nucleic acid grew (larger average over time). Theory: Clay was substrate, shorelines providedcontinuous washing with dissolved building clock nucleotides or amino acids
Why was DNA a poor choice for the first replication?
It replicates by encoding proteins that do the catalysis->
Problem: DNA and the proteins needed to replicate it could not have evolved simultaneously
Describe the experiment in which the third step to make a living organism was tested
RNA attached to bead with a random segment with a PPP end
Another molecule starts with hydroxyl group on a cytosine and includes a tag
The second one is complementary to the first and brings the PPP and HO together
If the phosphodiester linkage is formed, the second section will stay and attach to affinity column
Describe how the fourth step to make a living organism may have occurred
A membrane forms from the arrangement of the phospholipids in water
The formation of a double-layered sheet allows the hydrophobic fatty acid tails to remain together and away from water
Concentration of building blocks and catalytic components leads to faster replication
What are the four steps of the precambrian?
Origin of life, LCUA, divergence into eukarya, multicellularity
What is the first step of the origin of life?
Assemble simple molecules into building blocks for complex polymers
What is the second step of the origin of life?
Assemble polymers that can store information and catalyze reactions
What is the third step of the origin of life?
Self-replication
What is the fourth step of the origin of life?
Add membranes and an energy source to make a living organism
What was discovered that became the molecule for step three? Why was it better than DNA?
Catalytic RNA was both information carrying and catalytic
Name the three examples of the molecule used in step 3
Group 1 and 2 introns, ribonuclease P, peptidyl transferase
Give the window for LUCA and say why
3.85 (sedimentary rocks) to 3.5 (earliest bacteria fossils) BYA
Why can’t we use fossils to see what LUCA was like?
Chance of fossilization is low, chance of discovery is low, cannot deduce characteristics
What characteristics/method is used to find LUCA’s characteristics?
Molecular characteristics shared by all cellular organisms are used to firm a phylogeny of the whole life tree
What did scientists have to look out for when choosing characteristics to find LUCA’s characteristics?
Low mutation rate due to the high genetic distance
What clades/branches did the whole life tree form?
split between bacteria and a clade of eukarya and archaea
Name some monophyletic and non-monophyletic groups on the whole life tree
Mono-> animals, plants, fungi (if remove slime molds)
Non-> protists
List the three situations in which parsimony of the whole life tree would give a trait to LUCA
Alll three, Bacteria and one other, bacteria only
List the two situations in which parsimony of the whole life tree would not give a trait to LUCA
Archaea/Eukarya only or both
What did the tRNA whole life tree reveal?
Horizontal gene transfer (transfer of genes across species) is More common than we thought
What is the most recent theory of the progression of LUCA to modern life?
A community of LUCA’s in which horizontal gene transfer was common
Describe the two theories of the formation of the nucleus
That early eukaryotic engulfs an archean, which later becomes the nucleus
Eukarya arise as a fusion of a bacterium with an archean
Describe the theory of the formation of the mitochondrion
Mitochondria was an intracellular parasite, now they are intracellular symbionts of eukaryotic cells
Describe the theory of the formation of the chloroplast
Came from a bacteria that can photosynthesise
Give the three steps to multicellularity
Colonial aggregates, division of labor, continued differentiation into specialized tissues and organ systems
What factor in the second step to multicellularity allowed increased size?
Transport of nutrients, gases, wastes
What are the three sections of the third step of multicellularity
Need gene regulation, Cell status transmission at division, and reliable spatial patterning
Describe homeotic genes
Make organs and tissues in the right orientation. In order from head to abdomen.
Some duplications have occured, but it’s still the same gene, a mouse gene can go into a fly. Mammals and fish duplicated a cluster.
Give the range of the cambrian radiation
543 to 495 MYA
What are the three problems with the fossil record?
Small # fossilized (not a representative fraction, has taxonomic bias), small # discovered, small # characterized
Describe impression/compression fossils
2-D
Fine sediment can produce striking detail
Describe permimeralized fossils
Dissolved minerals enter cells, precipitate, and replace organics
Describe cast and mold fossils
3-D
Mold-hollow, organism gone
Cast-new material infiltrated mold
Describe the required conditions for preserved remains and list a few examples
Decay must be prevented
Amber resin, frozen, acid peat bogs, quick-dried, oil-saturated
What did the Edicaran fossil field have and what was special about them?
First multicellular animals, mostly radial
What were the two special things about the Burgess Shale fossil field?
Spectacular disparity of body forms
2x as many different forms as today
All major animal phyla represented
Lineages that lead to the major phylums
How did symmetry evolve from asymmetric to radial to bilateral?
Radial vs bilateral cleavage initiated very early in development
Radial cleavage furrow is angled in the start of a whorl
Bilateral cleavage furrow is at right angles
What innovation did triploblasts have?
Added mesoderm to the endo and ectoderms
What was the first type of gastrulation and what came second?
Deuterostome (mouth second) vs protostome (mouth first)
What are the three environmental factors that may have aided the rapid diversification?
More oxygen, more innovation due to multicellularity, predation and the red queen hypothesis
What is the name of the eon that starts with the Cambrian?
Phanerozoic
Name and describe the starting and ending points of the first era of the Cambian radiation
Paleozoic
Cambrian radiation to the end Permian extinction
Name and describe the starting and ending points of the second era of the Cambian radiation
Mesozoic
Permian extinction to the K-T extinction
Name and describe the starting and ending points of the third era of the Cambian radiation
Cenozoic
K-T extinction to modern life
Name the three causes of adaptive radation
New niche, extinction empties a niche, new evolutionary innovation
Describe punctuated equilibrium
Rapid divergence at speciation followed by long periods of stasis
Describe phyletic gradualism
Gradual divergence into reproductive isolation
What are the three possible causes of punctuated equilibrium?
Founder effect
Drift after allopatry
Adaptive landscape
Why may punctuated equilibrium not be necessary?
More and more transitional forms are found, not all are fossilized in the first place
Describe cladogenesis
true speciation
Species A goes to Species B and C
Describe Anagenesis
change from one species to another, they do not coexist in time
Species A goes to Species B
Describe the speed, range, and diversity of mass extincions
Rapid, global, taxonomicaly diverse
Describe the speed, range, and diversity of background extinctions
Slow, local, taxonomically narrow
What is the largest mass extinction?
End Perminan
What was the significance of the K-T extinction? When was it?
End of dinosaur dominance- allowed mammalian radiation
65 MYA
What were the two secondary causes of the severity of the K-T meteor impact?
Herbivore diversity was at a cyclic low just before and sex determination may have been affected
What are the four consequences of mass extinctions?
Random elimination, adaptive radiation, population bottlenecks, and Lazarus taxa
What divergence theory did Darwin like?
Phyletic gradualism
Closest relative
chimp
Ape synapomorphies
absence of tail, joint flexibility, brachiationi
African Great Ape synapomorphies
Elongated skull Enlarged brow ridges Shorter stouter canine teeth Fusion of certain carpals (wrist) Enlarged ovaries and mammary glands Reduced hairiness
When did humans diverge from chimps/bonobos and gorillas?
5 MYA
Group, time, and description-Ardipithecus ramidus
Basal hominins, before 4 MYA, Africa, bipedal and arboreal
Group and time- Australopithecus genus
Early human ancestors or relatives, 4-2 MYA
Group, time, and description- Paranthropus genus
Early human ancestors or relatives, 4-2 MYA, possible limited tool use
Group, time, and description- Homo habilis
Early human ancestors or relatives, 4-2 MYA, slightly larger
Group, time, and description- Homo rudolfensis
Early human ancestors or relatives, 4-2 MYA, cobblestone tool user
Group, time, and description- Homo ergaster
Middle period, 2-1 MYA, ancestral to others
Group, time, and description- Homo erectus
Middle period, 2-1 MYA, left Africa to Asia and long lived
Group, time, and description- Homo neanderthalensis
Recent, <1 MYA, Europe
Group, time, and description- Homo sapiens
Recent, <1 MYA, global
Group, time, and description- Homo floresiensis
Recent, <1 MYA, hobbits, java, mix of homo and ape/australopithecine traits
Group, time, and description- Homo heidelbergensis
Recent, <1 MYA, Europe
Describe the hybridization and assimilation theory of our dispersal
H. Ergaster diverged into E. Erectus (Asia) and H. heidelbergensis (Europe)
H. heidelbergensis diverged into H. neanderthalensis (Europe) and H. sapiens (global)
H. sapiens maintained gene flow after spreading and still had a little (2-4%) of gene flow with H. erectus and H. neanderthalensis
Describe how we find migration history from modern haplogroups
Two basic tenets:
New populations will not carry all haplotypes with them, once populations are separated, they will get different mutations
The oldest population will have the most haplogroups
The youngest population will have the fewest overlap with the original
May carry mutations from their former population
Name the 5 extinction events
K-T, end Permian, late ordovician, end devonian, and end triassic
1-1
2-4
3-2
4-4
Basal hominins (ardipithecus ramidus)
Early (Australopithecus, Paranthropus, homo habilis, homo rudolfensis)
Middle (homo ergaster, homo erectus)
Recent (H neanderthalensis, sapiens, floresiensis, Heidelbergensis)
Are dogs the same species?
MSC, BSC
N,Y
Is brassica the same species?
MSC, BSC
N,Y
Are Drosophia (with compound chromosomes) the same species? (MSC, BSC)
Y,N
Are marine copepods the same species?
MSC, PSC, BSC
Y, N, N
Are all African elephants the same species?
PSC, BSC, MSC
N,N, Y
What are the two clades (not including the one with whales) in artiodactylels?
Cow and deer, pig and peccary
Describe the Panspermia theory
Meteorites brought amino acids to earth
Describe the African replacement model of our dispersal
H. Ergaster diverged into E. Erectus (Asia) and H. heidelbergensis (Europe)
H. heidelbergensis diverged into H. neanderthalensis (Europe) and H. sapiens (global)
(no gene flow from erectus or neanderthalensis)
Where do Old World Monkeys live?
Africa and Asia
Name the four members of African Great Apes
Humans, Common chimps, gorillas, bonobos
When did the Pan and Homo genera diverge from each other?
5-6 MYA
What is the common name for pan paniscus?
Bonobos
