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Evolution and Behaviour > Leactures 8-11 > Flashcards

Leactures 8-11 Flashcards

1
Q

What definition did Reverend William Paley give for adaptations in 1802 book ‘Natural Theology’

A

Organisms appear contrived as it towards an end and that they show relation in parts
- organisms did not need to be perfect—same way broken watch still appears designed

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2
Q

Example and explanation of self-organisation

A
  • self organisation is where order or patterns occur spontaneously in systems
  • rapid cooling of molten basalt 50-60 mya—hexagonal columns
  • also happens in biology
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3
Q

What are some of the important extensions to Darwin’s theory?
x 3

A
  1. Hamilton and inclusive fitness
  2. Fisher and Price with the fact other processes may decrease fitness
  3. Grafen formalised link with apparent design and mathematics of allele frequency change
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4
Q

Hamilton’s and concept of inclusive fitness

A
  • social evolution, idea that actions have consequences for members of same population, rather than just their own reproductive success
  • includes biological altruism and spite
  • personal fitness=own reproductive rate
  • inclusive fitness=direct + indirect fitness
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5
Q

What does eusocial mean?

A

The structuring of populations where the majority of the organisms are sterile
- e.g naked mole rates or ants

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6
Q

Fisher and Price

A

Fisher = rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time
- price explained this so that it was true- by stating he didnt mean total evolutionary change but only on allele frequency change due to NS where environments remain constant
- then natural selection always acts to increase fitness but that other processes may decrease it
(like drift)

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7
Q

Grafen

A

connect understanding of mathematics of allele frequency change and then the idea of apparent purpose/design

  • HOW- correspondences between allele frequency changes and an optimisation programme
  • that natural selection when isolated as a component of evolutionary change is an optimising process leading to organisms that appear designed as if to maximise inclusive fitness
  • also- all genes with same pattern of inheritance tend to correspond to same optimisation programme
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8
Q

What is an optimisation programme?

A

pretends that organisms are agents employing strategies to maximise inclusive fitness

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9
Q

Active research is on marginal cases where unclear if a trait has an adaptive function
- give troglobite example

A
  • troglobite is an animal that only lives in caves
  • many convergent features
  • no eyes and lack of pigment
  • regressive evolution—all came from a species with both eyes and pigment
    2 ideas
    1. directional (so has adaptive purpose)
    2. Drift (due to relaxed selection)
  • eye loss = directional
  • pigmentation = drift
  • Protas et al in Maxican cave tetra using QTL mapping found this
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10
Q

What is a fitness landscape?

A

AKA adaptive topography or surfaces of selective value

  • metaphor introduced by Wright in 1932
  • visualising evolution
  • fitness valleys with global optimum and local optima
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11
Q

2 types of fitness landscape

A
  1. organism level
    - vertical axis is individual fitness
    - other axes represent either genotype of phenotype
    (only useful is fitnesses are not frequency dependent)
  2. population level
    - vertical is population mean fitness
    - other can be population mean phenotype
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12
Q

Example of individual-level phenotypic landscape

A

Brodie (1992)

  • garter snakes
  • colour pattern and escape behaviour
  • Juvenile snakes better is longitudinal stripes and straight line escape or blotched colours and multiple reversals during escape
  • intermediates didnt have as high a fitness
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13
Q

What is the shifting balance theory?

A

Wright - used to explain how evolve from local optimum to peak
- large natural populations frequently subdivided

Phase 1 - small Ne enables cross fitness valleys with aid of genetic drift
Phase 2 - natural selection pushes subpop to new, sometimes higher fitness peaks
Phase 3 - subpops at higher peaks send out more migrants so gene flow to other pop

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14
Q

Problems with shifting balance theory of evolution

A
  1. phase 1 requires small Ne and low migration but then 2 needs large Ne and 3 needs high migration rate
  2. shown can work but only if limited range of conditions
  3. others same solving non-problem as natural population rarely stuck at suboptimal peaks as landscapes change over time and high dimensionality of peak-world fitness means that ridges are likely to be common and dont need to cross fitness valley
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15
Q

Experiments are difficult for shifting balance theory, two main experiments give conflicting evidence

A
  1. Weber 1996 - Drosophila fight speed

2. Lenski and Travisano 1994 - E.coli

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16
Q

Weber experiment 1996

A 
wind tunnel automatically select for faster flies
- 9 million flies (over all)
- 100 generations
- top 4.5% of speed roughly
2 increased to 170cm per second
  • flies showed little to no decline in fitness compared to control lines and no decrease in flying speed when selection relaxed so no fitness valley
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17
Q

Lenski and Travisano 1994

A

E.coli in new environment for 10,000 generations

  • regular intervals fitness of 9 replicate lines compared to ancestral strain (kept frozen)
  • all populations increased in fitness initially but some later plateaued at suboptimal levels-stuck at local fitness peaks?
  • though a few experimental errors like maybe bottleneck built into experimental design? as all from single clone
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18
Q

What is the neutral theory of molecular evolution?

A

Kimura in 1968

the vast majority of molecular evolution was due to drift
- so most substitutions and polymorphisms were effectively neural

  • do not deny widespread action of negative selection
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19
Q

What observations do the neural theories aim to explain?

x 6

A
  • substitution rate was higher than expected
  • roughly constant in different lineages
  • unreleased to rate of phenotypic evolution
  • highest in less important proteins and parts of proteins
  • molecular diversity much higher than expected
  • diversity higher in larger populations
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20
Q

How to test neutral theory

A
  1. examine distributions of fitness effects

- in labs by introducing mutations or by bioinformatics methods

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21
Q

What is speciation?

A

The formation of two or more species from a single ancestral population

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22
Q

What 5 traits do populations need to fulfil to be species?

A
  1. Unique phenotypic character found in no other population
  2. Multivariate distributions of quantitive trait value that does not overlap with distributions found in other population
  3. Monophyly (most recent common ancestor of population has no descendants outside of population
  4. Distinct ecological niche
  5. Not hybridising with other populations

(in practice not all of these species criteria are filled)

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23
Q

What is the biological species concept?

A

Made by Mayr
- biological species are groups of interbreeding populations that are reproductively isolated from other such groups

  • so speciation is the evolution of reproductive isolation
24
Q 
Reproductive isolation (RI) (barriers to gene flow) classifications
2 main
A
  1. Prezygotic isolation
    - acting before fertilisation
  2. Postzygotic isolation
    - Acting after hybridisation
25
Q

What are the subsets of prezygotic isolation?

A
  1. Premating isolation
    - temporal = flowers open at different times
    - Habitat = Potential mates live in different places
    - behavioural = lack of sexual attraction, because no mating ritual/it is not right
  2. Post-mating isolation
    - mechanical = flower shape prevents pollen transfer
    - gamete = failure of gametes to unite
26
Q

Subsets of post-zygotic isolation

A
  1. Intrinsic = not habitat-specific
    - hybrid sterility
    - hybrid inviability (die before reproductive age)
    - hybrid breakdown (fitness problems of offspring of hybrids)
  2. Extrinsic = hybrids have low fitness in parental habitats
27
Q

Example of habitat isolation as a form of pre-zygotic reproduction isolation

A

Alpheus

  • shrimp genus
  • Caribbean sea and Gulf of Panama separated roughly 3 million years ago in pliocene
  • sister species on either side
28
Q

Why is hybrid speciation particularly common in plant species

A
  • Partially sterile hybrids can arrive because so many hybrids (probability increases) - fix if better at surviving in different niche
  • deal with different chromosome numbers more easily - by polyploidy
  • selfing where self fertilise
29
Q

2 types of polyploidy

A
  1. Autopolyploids = all chromosomes from same species

2. Allopolyploids = chromosome doubling follows interspecific hybridisation so chromosome sets derived from both species

30
Q

What percentages of plants have arisen from polyploidy?

A

estimated

  • 70% flowering plants
  • 95% mosses and ferns
31
Q

gradual speciation can occur in two ways

A
  1. genetic divergence can lead to reproductive isolation
  2. Reproductive isolation can turn into genetic divergence
  • barriers to gene flow can vary over time and across the genome
  • also either diversifying selection leading to ecological speciation
  • or RI by genetic drift
32
Q

Rundle Drosophila experiment 2003

A
  • 78 populations of drosophila to repeat bottlenecks to see if RI evolved
  • after crossing it was found that no RI evolved
33
Q

Duffy, Burch and Turner 2007

A

Bacteriophage φ6 which infects multiple pathovars of bacterium species

  • starting with a phage with broad host range
  • 4 lines
  • 150 generations on new host
  • 3/4 populations lost ability to infect one or more of alternative host
  • 1 pop completely lost ability
  • so evolved as byproduct of host adaptations (RI)
34
Q

What is reinforcement speciations?

A

Evolution of prezygotic RI as an adaptation to avoid costly matings
- if offspring unfit due to hybridisation then the individuals will choose no to mate with individuals from other populations to prevent the chance of reduced fitness

35
Q

Evidence for reinforcement = Noor 1995

A

1 = Drosophila persimilis and pseudoobscura
- postzygotically isolated as male offspring are sterile but also have partially overlapping regions of range

  • in lab pseudoobscura collected from overlap regions much less likely to mate with persimilis males
36
Q

Cichlids in African great Lakes

A

Lakes = Victoria, malawi and Tanganyika

  • a lot of choosiness based on colour but now might be reversing speciation due to murky waters from human activities
  • remove reproductive isolation
37
Q

What are phylogenetic trees?

A
  • a representation of the complete pattern of ancestry among a group of species with a phylogeny
38
Q

What are the leaves/tips of a P-tree?

A

The species themselves

  • branches represent the evolutionary lineages that connect them
  • the length of these branches represents amount of evolutionary change in a trait or the length of evolutionary time
39
Q

What are nodes of P-trees?

A

The points where lineages divide and are therefore the most recent common ancestor of all the species (tips) connect to this node

40
Q

What is the root of a P-tree

A

Most recent common ancestor of all species the tree contains

  • unrooted trees that do not contain a root node cannot be used to infer ancestry and decent
41
Q

How to estimate phylogenetic tree?

x 4

A
  1. record data from each tip of interest
  2. Make assumptions about the evolutionary process
  3. Identify phylogenies that are likely to have yielded the data, given the assumptions
  4. Test these phylogenies and the assumptions made
42
Q

What is the ideal data recorded from tips to construct phylogenies?

A

Characteristics that are shared by some but not others and unlikely to have evolved more than once

43
Q

How do we date phylogenies?

A

Geochronology

  • include fossil taxa in the phylogeny
  • Infer ages of rocks from which the fossils were found in
  • additional inferences from quality of fossil record (often need to assume certain taxa missing because had not evolved and not because they were not preserved as fossils
44
Q

What is the basis of molecular clocks?

A

The idea that if evolution takes place at a roughly constant rate, the amount of evolutionary change along a branch will be proportional to the length of time that branch represents
- use to estimate relative ages

45
Q

How to calibrate molecular clocks?

A

fossil dates from single node—>turn relative to absolute dates

46
Q

What are relaxed clock methods?

A

Takes into account that the rate of molecular evolution does vary

47
Q

Example of using dated phylogenies?

A

HIV pandemic in humans

  • 2 major strains are closely related to two strains of SIV found in chimpanzees and sooty mangabeys
  • Estimated dates and locations of transfer events it is likely viruses passed into humans via bush meat trade
48
Q

Why can genetic and species trees disagree?

A

the evolutionary history of genes does not need to be identical to evolutionary history of the populations or species whose genomes contain those genes

  • hybridisation events
  • multi-gene families
49
Q

What are multi-gene families?

A

what happens when number of copies of a given protein-coding gene can change quite rapidly over evolutionary time
- as nodes in genealogies of gene families can represent either speciation or duplication events

50
Q

What is a pseudogene?

A

A gene with a premature stop codon and so no longer makes a functional protein

51
Q

In a phylogeny of three species, the branching points correspond to speciation evens and the nodes to populations of most recent common ancestor.

What problems arise when estimating a species tree from this data?

A

We can estimate a gene tree as nodes are most recent common ancestors of individual genes

  • however ancestral populations in species tree and ancestral genes in gene tree are not the same
  • ancestral gene pool contained many genes
  • each of the three genes sampled from the present day species might have descended from a different gene in their common ancestral population. Meaning most recent ancestral population closer than the gene
52
Q

What 2 consequences from the difference between gene and species trees?

A
  1. Nodes in gene trees can be older than the equivalent nodes in a species tree
  2. branching order might differ between gene tree and species tree = INCOMPLETE LINEAGE SORTING
53
Q

how have made a phylogeny for the entirety of life?

A

rRNA genes

54
Q

example of incomplete lineage sorting

edwards 2005

A

Inferred phylogenies of australian grass finches from 25 different genes
- two sister species (sometimes considered subspecies)
P.acuticauda and P.hecki
- however for 11/25 genes one of the species was more closely related to a third species P.cinta

55
Q

How can there be cases on phylogenetic trees were three or more leaves are from one branch point

A
  • maybe three geographic isolations at once
  • changes could have happened relatively quickly and so if cannot resolve the genetic material to specify certain changes
  • like cichlid fish, hard to know which evolved first
  • or unclear hybridisation events

Evolution and Behaviour (8 decks)

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