midterm #3 Flashcards
(74 cards)
1
Q
small genomes
- found in
- associated with (2)
A
- viruses, archaea, bacteria
- associated with:
- – rapid cell cycles and reproduction (small circular genome)
- – parasitic life history
2
Q
large genomes
- found in
- features (3)
A
- eukaryotes
- features:
- duplicated gene regions
- introns
- large amounts of non-coding DNA
3
Q
mechanisms giving rise to new genes (4)
A
- gene duplication
- exon shufflng and chimaerism
- de-novo origination
- horizontal gene transfer
4
Q
- gene duplication
- what leads to
- mechanisms how (2)
A
- leads to multigene families consisting of multiple copies of the duplicated gene
- mechanisms:
- unequal crossing-over at meiosis
- whole genome duplication
5
Q
- exon shuffling and chimaerism
A
- when exons are added, lost, or rearranged
- chimaerism: when genes consist of segments from two or more other genes, caused by retrotransposition
6
Q
retrotransposition: process and what it leads to
A
a class of transposable elements
process:
> retrotransposons (sequences on DNA) are transcribed into mRNA
> reverse transcription of mRNA
> re-insertion of new DNA in other part of genome by ribonucleoprotein
- abundant in eukaryotes
- leads to chimaeric gene
7
Q
- de novo gene origination
A
when new coding genes originate from non-coding DNA
-> especially regulatory genes
8
Q
- horizontal gene transfer
A
- widespread in archaea and bacetria, less in eukaryotes
- in eukaryotes, most common between organisms with close physical association (e.g. symbiosis, mitochondria)
9
Q
new genes: most common mechanism in prokaryotes and eukaryotes respectively
A
prokaryotes: horizontal gene transfer
eukaryotes: gene duplication (esp. unequal crossing-over)
10
Q
evidence for endosymbiotic gene transfer between organelles and nucleus (2)
A
- many genes located in nucleus are expressed in organelles
- mitochondrial and chloroplast genomes are much smaller than those of their free-living ancestors
11
Q
duplicated gene copies:
- neofunctionalization
- subfunctionalization
- pseudogenes
A
neofunctionalization:
- acquisition of new functions
- e.g. electrical-organ genes in fishes
subfunctionalization:
- specialization of existing functions
- e.g. duplicated Hox genes in zebrafish
pseudogenes:
- loss of function
- no longer under selection, accumulate mutations
12
Q
concerted evolution
+ what leads to
+ how comes about
A
mutation spreading among gene copies within a gene family
- leads to more similar sequences than expected among gene copies
- mediated by DNA repair machinery, modifies one gene copy to resemble another adjacent copy
13
Q
whole genome duplication (polyploidy)
- results from
- common in ?
- evoutionary significance
- higher levels of gene products
A
- results from errors in mitosis and meiosis
- common in plants, uncommon elsewhere
- lots of potential for new genes
- higher levels of gene products in cell may be disadvantageous tho
14
Q
orthology
paralogy
A
orthologous genes:
- same genes found in different species derived from their common ancestor
paralogous genes:
- different genes within a species that resulted from gene duplication (similar but different genes)
15
Q
paralogy and time estimation (3)
A
- from amount of divergence, can infer age of gene family
- if multiple copies of similar age across many gene families, probably result of whole genome duplication
- evolutionary peaks of gene duplication are associated with whole genome duplication events
16
Q
molecular signatures of natural selection (3)
A
- positive selection: increase in favourable mutations
- purifying selection: decrease in deleterious mutations
- balancing selection: favours heterozygosity for a locus
positive + puriying decrease genetic variability,
balancing increase genetic variability
17
Q
dN/dS ratio
A
dN/dS: ratio of nonsynonymous to synonymous mutations
< 1: purifying selection (decrease deleterious mutations)
> 1: positive selection (increase favourable mutations)
18
Q
selective sweep
A
when positive selection eliminates neutral variation near a mutation in DNA
- DNA sequences with neutral mutations but without favourable mutations are eliminated
- after selective sweep: little variation in sequence area surrounding a positive mutation
19
Q
codon bias
A
among synonymous codons for amino acids, there is a bias in which codos are more often usedto code for an amino acid
- if totally silent, would expect only random frequency variation
- means selection somehow discriminates among synonymous codons
20
Q
factors affecting evolutionary rate of protein-coding genes (3)
A
(1) direct effect on organism’s fitness
(2) translational robustness (ability of proteins to retain structure with mutations)
(3) role of the gene in developmental pathways
21
Q
non-coding DNA in prokaryotes and eukaryotes
A
prokaryotes: most of genome is coding
eukaryotes: most of genome is non-coding
22
Q
transposable elements
A
- sequence of DNA that can change their position within a genome
- two classes, one of which is retrotransposons with reverse transcription
- most TEs are selfish DNA (no function except replicating itself)
- sometimes copies acquire useful novel functinos though
23
Q
heterochrony:
- what
- allometric growth
- paedomorphosis
- peramorphosis
A
-> changes in the timing of developmental events
- allometric growth
- differential growth rate in different structures or dimensions leads to different-sized characters - paedomorphosis
- reproductive maturity with juvenile body form
- due to slowed somatic growth or accelerated sexual maturation - peramorphosis
- reproductive maturity with increased development of adult body form
- due to faster somatic growth or slowed sexual maturation
24
Q
modular repeated structures can evolve by (3)
A
- variation in number
- changes in position (heterotopy)
- diversification of modules (individualization)
25
regulatory genes
- produce transcription factors
- transcription factors bind to enhancers or repressors of genes in regulated pathways
- regulatory genes thus control gene expression
26
trans-regulatory changes
| cis-regulatory changes
trans-regulatory changes:
- mutations in regulatory genes
- e.g. Ftz gene in insects akes on different differentiation functions
cis-regulatory changes:
- mutations in enhancer or repressor regions of target genes
- e.g. lower bone expression in freshwater stickleback
- e.g. Drosophila dark wing spots
27
homeotic selector genes (3)
- regulatory genes controlling the overall body plan
- extremely similar across all multicellular eukaryotes
- act earliest in cell division in ontogeny
- animals: HOX genes
- plants: MADS-BOX genes
28
HOX genes
- what
- produce
- product does
- earliest- and latest-expressed
- clusters
- regulatory genes producing transcription factors
- determine body plan
- ealiest-expressed: posterior-anterior axis
- latest-expressed: body segmentation
- homeobox region codes for transcription factors helping express target DNA
- found in clusters, gene order within clusters corresponds to order of expression
29
HOX genes across animal phyla
- highly conserved across phyla in their sequence and organization
- sponges have homeobox, but no true HOX genes (evolved after sponge-metazoa split)
- # of HOX genes relates to complexity of organisms
- gene order within a cluster corresponds to order of expression
30
homeotic mutations (4)
- mutations in HOX genes
- cause changes in body plan
- hopeful monsters idea: homeotic mutations can produce new and viable life forms
- can inactivate developmental program of one segment, which then adopts default program of another
31
visualization of mRNA expression
mRNA expression:
- used to study expression of specific genes
- use single-strand DNA or RNA probe sequence to detect specific mRNA binding to it
- the probe sequence is stained
32
visualization of protein expression
protein expression:
- extract proteins to generate antibodies
- stain antibodies
- re-insert into tissue for visualization of proteins
33
CRISPR-Cas9
- CRISPR sequences: DNA sequences of prokaryote genomes used to defend against viruses
- enzyme Cas9 uses CRISPR sequence as template to recognize and cut out similar DNA sequences from viruses
- use guide RNA to tell Cas9 what complementary DNA sequence to bind to and cut out
34
MADS-BOX genes
- plants, similar to HOX genes in animals
- originated separately in plants (analogous)
- control:
- - growth initiation and dormancy
- - development of leaves and all structures in the flower
35
ABCDE genes
- types of MADS-BOX genes
- E-class genes: determine whether stem produces flowers
- ABC: determines sequence in which parts of the flower develop, with overlapping expression
36
evolution of ABCDE genes
- in early lineages, expression of ABC-genes is less clear-cut, more fluid transition
- in bilaterally symmetrical flowers: Class II TCP genes control dorsal-ventral differentiation
37
phylogenetic homology
- feature derived from a common ancestor
- may or may not have the same genetic and developmental basis
- generally similar in form and position
38
biological homology
- different, but corresponding features in the same organism (or closely related organism)
- diverse structures across groups with common developmental pathways
- share common underlying genetic and developmental pathway
39
modularity in development
- modular body form in multicellular lineages (made of repeating segments or modules)
- most change in morphology is due to individualization of body modules
- results from changes in regulatory gene expression
40
developmental constraints
- what
- possible causes (2)
- evidence
- limits of phenotype due to characteristics of development
- possible causes:
- - lack of genetic variation or deveolpmental pathways
- - strong correlations among characters
- evidence: axolotl foot is same as salamander if treated with chemical
41
what phenotypic plasticity requires
- requires inducible changes in a developmental program to respond to an environmental cue
42
types of coevolution (3)
1. specific: one species evolves trait value parallel to another species
- e.g. aphids and their bacterial symbionts
2. diffuse or multispecies: a species evolves in response to different pressures posed by multiple species
- e.g. feather lice on pigeons
3. a lineage escapes by evolving an awesome trait and then radiates into different species
- e.g. incense trees and insects
43
ecological processes driving coevolution (3)
1. predator-prey interactions
2. mutualism
3. competition for resources
44
predator-prey coevolution
- one species gains, other loses
- includes pathogen-host, parasite-host, herbivore-plant
- found in all species
45
patterns in predator-prey coevolution (4)
1. stable interaction
2. cyclic oscillations
3. arms race
4. extinction of one or both species
46
virulence
- pathogen's ability to infect or damage a host
- intermediate virulence is more successful strategy for virus (high virulence means lower transmission)
- pathogen and host coevolve, e.g. rabbit mortality initially high but declinied over time
47
virulence is affected by (3)
1. whether the host is infected once or multiple times
2. rapidity of host immune response
3. whether parasite is transmitted horizontally or vertically (offspring)
48
optimal level of virulence depends on (3)
1. competition among paricles within host
2. host defenses (weak host -> higher virulence)
3. ease of transmission (rapid transmission -> higher virulence)
49
mutualism
- mutual beneficial interactions between species
- degrees:
- - degree of interdependence (if obligate, most highly adapted)
- - degree of physical association (if high, symbiosis)
50
mutualism
| - in evolutionary context
- often arises from predator-prey or host-parasite interactions
- viewed as reciprocal exploitation (individuals of each species under pressure to minimize costs and maximize benefits of interaction)
51
obligate mutualism example
fig wasps and figs:
- wasp completes life cycle in fig
- fig is pollinated solely by wasp
52
competition coevolution
- competing for resources
- evolutionary consequence: niche displacement
- - decreased overlap in resources required by two or more species
- - e.g. Darwin finches beak size diverged only in co-existing populations
53
mimicry (broad sense) includes
- crypsis: imitation of background or habitat
| - narrow-sense mimicry: imitation of other species (Batesian and Mullerian)
54
Batesian mimicry
| Mullerian mimicry
Batesian: species w/o defenses imitates species w/ defenses
Mullerian: two species with defenses mimic each other
55
biogeographic realms
major regions with characteristic animal and plant taxa
- each realm inhabited by higher taxa that are most diverse in or even confined to it
- Wallace's Line separates Oriental and Australasian realms
56
types of geographic distributions (4)
1. widespread (e.g. N.A. and Eurasia)
2. regional (e.g. western N.A.)
3. endemic or localized (restricted to small geographic area)
4. disjunct (containing gaps)
57
endemism: associated with habitats that are... (3)
- distinct
- isolated
- stable over long periods
58
types of dispersing (2)
- range expansion: gradual spread across continual habitat
| - jump dispersal (long-distance): movement across a barrier of unfavourable habitat
59
explanations for present-day distributions of related species (3)
1. dispersal into new areas
2. vicariance (subdivision of original geographic range into separate areas)
3. extirpation (from previously occupied ranges, leaving gaps)
60
phylogenetic niche conservatism
inheritance of similar ecological requirements from a common ancestor
- leads to related species occupying similar habitats
- limits possible geographic range
- e.g. all palm trees lack frost tolerance
61
fossil record:
- what it measures (2)
- limitation
- rates of morphological evolution (changes in specific characters)
- rates of diversification (originations and extinctions)
- gaps, gives simplified picture
62
fossil record: distorted rate of phenotypic change
- usually rapid change in fossils for a short time period
| - mean rates of change thus appear slower when measured over long timeframes
63
punctuated equilibrium
- what is
- what causes rapid changes
- same set of fossial data
-> proposes alternating periods of (1) rapid change, then (2) stasis
- founder effect speciation causes rapid changes (not well supported tho)
- same set of fossil data can support multiple types of morphological evolution (phyletic gradualism, punctuated equilibria, punctuated gradualism)
64
stasis in fossil record
- living fossils
- why stasis might happen (3)
living fossils: species existing today present in fossil record for millions of years
hypotheses:
- stabilizing selection in stable environments
- genetic/developmental constraints
- ephemeral divergence (variation occurred, but not detected in record)
65
saltational evolution:
- what is
- mechanism
- evolution by large jumps
- mutations in regulatory genes
- - not necessarily deleterious
- - not bidirectional (easy to lose something, hard to gain structure)
66
evolution of novel features (3)
1. modification of existing features (e.g. sesamoid bones as false thumbs)
2. duplication and divergence of features
3. de novo
- complex structures (e.g. eyes) can develop via intermediate stages
67
complexity increase?
- mostly yes, but many exceptions
| - more complex not necessarily better, depends on environment
68
adaptation increase?
- within specific lineages in specific settings, yes
| - completely context-dependent tho, unnecessary question
69
trends (+ 4 types)
directional shifts over time
1) local: in particular clades
2) global: in all organisms
3) active (driven): proceeding in a particular direction
4) passive (partial): equally likely to proceed in different directions
70
diversification: general trends (2)
- most groups tend to become more taxonomically diverse
| - diversification often follows decrease of diversity in other groups
71
diversification: biases in fossil record (3)
1. species that existed more recently more likely to be found as fossils
2. uncommon species less likely to be found
3. durations are underestimated (when species originated and went extinct)
72
biases in fossil record: corrections (3)
1. look at whole genera
2. exclude unreliably detected species
3. exclude species known only from recent fossils
73
possible explanation for increasing diversity over time
> orgainsms occupy more ecological space in present than in past
> species can create new niches for other species
> more biotic factors, stacking-up of niches
(also, key adaptations such as herbivory)
74
Cope's rule
| + active and passive trend examples
-> population lineages tend to increase in body size over time
- active trend: Equidae size increased in all taxa since Eocene
- passive trend: North American mammals some lineages increased, some didn't, mean shifts towards larger size
