BIOB51 Lecture 5 and Lecture 6 Notes UTSC Evolutionary Biology

BIOB51 – Lecture 5
Methods of Evolutionary Analysis: Scientific Method:

• Observation:
  o You see something and want to understand how it works
  
• Hypothesis:
  o An educated guess regarding the system you have a question about
  
• Predictions:
  o If the hypothesis is true, then...
  
• Test: gather data and compare different groups
  

o Experiment test:
▪ The independent variable is altered and the effect should be looked upon the dependent variable
o Observation test: the two variables are related to one another but one is naturally manipulated
o The strongest tests are made when predictions are opposed of alternative hypothesis
▪ Null hypothesis: one alternative hypothesis.

• The groups are the same
  
• There isn’t an effect of one variable on the other
  

• Draw conclusions:
o Have to make sure a sampling error doesn’t occur o The statistical tests depend on:
▪ Magnitude of difference
▪ Sample size
▪ Amount of variation in data
o The smaller the p-value, there is a significant difference ▪ p < 0.05
Planned experiment:
• The independent variable is manipulated by the researcher Natural experiment:

• The independent variable is manipulated naturally
  
• The variation in the other variable can be measured
  Observational study:
  

• The measurement of natural variation in proposed X
  
• Causation cannot be interpreted from this study.
  Guppies – Observational Studies:
  • Live in Trinidad in streams and rivers
    
  • They are a model for evolutionary studies since they are very variable for phenotypic and
    life history traits (the patterns of life)
    
  • General hypothesis: selection for larger body size upstream
    o Upstream there are predators called Killifish
    ▪ These eat the guppies when they are small ▪ When guppies are big, they cannot be eaten
    o Downstream there are predators called Pike cichlid
    
    • ▪  These predators are size independent
      
    • ▪  It doesn’t matter how big or small the guppies are, they will be eaten
      regardless
      
    • ▪  Large body size doesn’t affect predation
      
  • Prediction: upstream guppies will evolve larger adult size o The prediction was consistent with the results
    o However, confounding factors need to be looked at.
    ▪ Biotic: prey availability
    ▪ Abiotic: water temperature, pH ▪ Measurement issues: guppy age
    
    • Fishes grow at every stage of life
      
    • Upstream fish are older since they have more time to grow
      
    • Downstream fish are younger since they get eaten before they get
      old
      
  • Observational study 2:
    

  o Predation affects evolution of maternal reproductive life history o Life history is the pattern of life events
  o Predictions:

  ▪ Larger offspring can reach the safe size more quickly • Female guppies upstream

  ▪ More offspring, more are likely to survive • Female guppies in downstream

  o Tradeoff: changes in one trait lead to changes in the opposite direction in other traits

  Planned Experiment:

  • Alternative hypothesis strengthen the test:
    
  • The confounding factors need to be controlled:
    
  • Sample size is important:
    

  
  

BIOB51 – Lecture 6
Natural Experiment 2 (Darwin’s Finches):

• Adaptive radiation: when a few groups of organisms underwent evolution to form different lineages. For example, the finches all had different diets and different types of beaks, according to what they ate
  
• Question: why do Galapagos finches have diverse beaks?
  
• Macroevolutionary explanation: a single lineage of birds went through adaptive
  radiation with different lineages evolving to specialize on different types of food
  

1. Some eat insects, some eat seeds, one type eats blood (the vampire finch)
▪ Uses its beak to slice into other bird’s necks and then sucks the blood
▪ The vampire finch adapted to this feature because the vegetation was low
in that area, but had an increased amount of other birds • Macroevolutionary patterns arise from microevolutionary processes

1. Hypothesis: natural selection favours birds with beaks that can exploit the available food (they will be less likely to starve)
   
2. Prediction: there should be a shift in the type of food available, which should cause a matching shift in the beak characteristics of the surviving/reproducing birds
   
3. For example, a study was conducted on the Geospiza fortis (medium ground finch)
   
   • ▪  The larger-beaked G. fortis is more efficient at eating larger seeds because it has a big body size
     
   • ▪  The smaller-beaked G. fortis is better at eating smaller seeds
     
   • ▪  Natural event: In 1977, a drought occurred on Daphne Major.
     
     • Peter and Rosemary Grant studied all the birds on this island, with more than 30 years of data
       
     • When there was a lot of rain, small soft seeds were produced
       
     • When there is a drought, large and hard seeds were produced more.
       These were produced more in 1977, than the small seeds
       
     • The beak size of G. fortis increased as years passed because of the
       drought, from the shift of small seeds to large seeds
       
     • In 1985-85, another event occurred, which was called El Nino.
       

o These were wet years, so small seeds were commonly produced more than bigger seeds.
o This caused the beak size to decrease
• Another drought occurred in 2003-2004 on Daphne Major.
o The beak size decreased even more than the original population size
o This is because there was a new bird. In 1995, another species was found, which was known as Geospiza magnirostris.

▪ This was physically much larger than the G. fortis. It became a competitor for G. fortis.
▪ G. fortis starts to have small beak size over the years because even the largest bird was smaller than G. magnirostris.
• The overall population of G. fortis decreased throughout all these droughts
• Data Set Results: this data shows:

1. Evolution is dynamic: there is no goal
   ▪ Populations can change repeatedly
   ▪ Populations can change in one direction and then back again
   
2. Evolution of traits under selection may lead to correlated evolution in other
   traits:
   
   • ▪  As beak size increases, the body size increases, and the shape of the beak becomes more pointed
     
   • ▪  This could be due to genetic linkages Comparative method:
     

• Macroevolutionary questions are asking where the origin of major differences among taxa are
  o What are the factors leading to the evolution of some traits
  o What are the hypotheses about the origin of adaptations
  o What are questions about evolutionary history
  o The technique is to compare patters of origin of traits across taxa
  
• For example,
  o Gorilla Gorilla: the testes size is different when compared to a human and other
  species of monkeys and primates
  
• Hypothesis 1: larger testes are present in larger species because larger endocrine glands
  are required to maintain adequate testosterone levels in the body
  
• Prediction: the mass of testes will be proportional to body weight across species
  
• Data: the testes weight increases with body weight across primates
  o However, there are some outliers and variation
  ▪ Physiology isn’t sufficient enough to explain all the variation
  ▪ It might be the different mating system that is affecting the testes size
  

• This is because of sperm competition, which is the competition among the sperm of different males for fertilization of the eggs of a single female.
o Gorillas have a single-male mating system
o Chimps have a multi-male mating system, which is when
the female reproduces with many males. This is described
above.
o One male adaptation to win the fertilization of the women
is the increased amount of ejaculate.

▪ More sperm is produced by larger testes

• Hypothesis 2: there is an evolutionary response to sperm competition, which indicates
  that the evolution of testes size depends on the mating system
  
• Prediction: larger testes (Y) evolve when females evolve to mate with more than one
  male (X)
  
• Test: we must control for body size
  

o For gorillas with a single-male mating system, their sperm competition will be low and their testes size will be small
o For chimps with a multi-male mating system, their sperm competition will be high and their testes size will be big
• Result: the multi-male mating system organisms are away from the average (larger than predicted), while the single-male mating system organisms are near the line (smaller than predicted).
o However, the evolutionary history isn’t considered; instead each species is treated as an independent data point
o Hypothetical evolutionary sequence:

• ▪  In a hypothetical
  situation, there is an ancestral primate with a single-male mating system. An evolutionary event happens, and then there becomes two different mating systems, a single male and a multi-male mating system.
  
• ▪  There are now two taxa;
  the single male has small testes and the multi-male has bigger testes
  
  • n=1 (1 evolutionary event)
    
  • X has changed, and Y might change
    
• ▪  There are then more evolutionary events that aren’t related to the mating
  system. They are instead due to inheritance, not due to independent evolutionary events
  

• X hasn’t changed so we cannot use these taxa as part of the hypothesis
▪ The problem is that the hypothetical data is from independent origins only. • To solve it is by looking at the evolutionary history and finding the
independent evolutionary events that replicated the tests of the hypothesis.
o In this way, phylogeny is controlled
▪ Phylogeny: is the evolutionary history of a group of
organisms/taxa

▪ Phylogenetic tree/phylogeny (cladogram): is a diagram that shows patterns and sequences of evolutionary change among organisms as one ancestral lineage diversifies
▪ Phylogenies are hypotheses which can be tested • Can be tested through the fossil record;

shows evidence of patterns of organisms

• Tools:
o Monophyletic clade (clade): is
an ancestral species and all of its descendants

• ▪  For example, E, F, G, H is one clade
  
• ▪  Another clade is D, E, F, G, and H
  

• Traits and evolutionary relationships: o Pleisiomorphy: an ancestral
character

• ▪  It is a trait found in the
  common ancestor of a clade
  
• ▪  For example, all mammals
  have lungs, limbs, and
  amniotic eggs
  o Apomorphy: derived trait
  
  • ▪  It is an evolutionary novelty (shown after the ancestral node)
    
  • ▪  It is a character that is present in another species that wasn’t present in the ancestor
    

▪ Phylogenetic tree/phylogeny (cladogram): is a diagram that shows patterns and sequences of evolutionary change among organisms as one ancestral lineage diversifies
▪ Phylogenies are hypotheses which can be tested • Can be tested through the fossil record;

shows evidence of patterns of organisms

▪ It is a defining feature of species o Synapomorphy: shared derived trait
▪ It is found after the ancestral node and is shared by two or more lineages ▪ It is a defining feature of a clade
▪ It defines the evolutionary relationship among taxa
▪ It is a type of apomorphy
▪ In a synapomorphy:

• Each branching event is defined by one or more synapomorphies
  
• Every clade is defined by one or more synapomorphies
  
• As a lineage is traced from the root to the tip, each branch adds
  another synapomorphy

For example, the fact that mammals have fur and lactate is a trait that only mammals have. It differentiates them from other tetrapods
How to construct a phylogeny?

• The most closely related species should share the most traits since they have changed less since that point
  
• The most distantly related species will share fewer traits
  
• This is because of descent with modification
  Types of traits used:
  
  • Molecular characters: such as DNA sequence
    
  • Morphological characters: such as feathers, etc
    
  • Both of these characters can be combined into making total evidence trees
    
  • When more traits are used, it is easier to identify and remove homoplasies.
    
  • Also, unidentified homoplasies will have less effect on the final phylogeny
    How are these traits scored?
    
    • Discrete data: only certain states are possible, such as the presence or absence of wings
      
    • Distance data: is the continuous range of values. For example, the average egg weight,
      and the number of sensory hairs
      Homologous traits: are when there are similar traits due to inheritance from a common ancestor
      

• They show information about phylogenetic relationships
Homoplasy (analogous traits): are similar due to convergent evolution instead of inheritance.

• This isn’t important for phylogenetic relationships
  
• For example, some hummingbirds can hover midair for nectar
  o This evolved in only some taxa Using Phylogenies:
  

• Hypothesis: lungs evolved from swim bladders
o An example of a fish was Tiktalik who had the beginnings of limbs
▪ This could mean fish came onto land
o Darwin’s reasoning behind this hypothesis is that the lung and swim bladder are
homologous
o Also, fishes appeared in the fossil record earlier than tetrapods
o Furthermore, swim bladders are more common in extant (surviving) fish than
lungs
• In the phylogenetic tree, lungs are more common than swim bladders
o There are two hypothesis:
▪ The swim bladder was gained first (the plesiomorphic state)
• Eventually lost the swim bladder and gained lungs

▪ The lungs were gained first (the plesiomorphic state)
• Eventually lost the lungs and gained a swim bladder
o Occam’s razor: we look for the simplest explanation with the best pattern
▪ It doesn’t mean it will be the correct one, it just means it might be the
simplest
o Parsimony: a way of deciding among alternative explanations based on
minimizing the total amount of complexity required

• ▪  We look at the tree with the fewest proposed evolutionary changes should
  be the starting hypothesis
  
• ▪  For example, the tree where lungs evolved first has the fewest
  evolutionary changes (it has 5 evolutionary changes)
  
• ▪  This means that lungs evolved before swim bladders
  Notes about Phylogeny:
  

• Characters, phylogenetic trees, and the fossil record all show evolutionary relationships when they come together
What explains the diversity of testes size in primates?

• Hypothesis 2: evolutionary response to sperm competition
  o The evolution of testes size depends on the mating system
  
• Prediction: larger testes (Y) evolve when females evolve to mate with more than one male (X)
  
• Test: it requires identification of natural experiments in the past when a new mating system evolved in a taxon changed
  

o Solution: use the phylogeny of primates to find independent data points, to see where the mating system (X) has changed
▪ This is based on DNA sequence analysis o Felsentein’s independent contrasts:
▪ Compare traits in sister taxa with different mating systems (change in X) • Sister taxa: are taxa
that share more common traits with each other than other taxa. For example, F and G are sister taxa
▪ They have the same common ancestor • Independent contrasts:
o Each line connects a pair of sister taxa where the mating system (X) has changed o It is relative testes weight because there is a physiological relationship between
the testes size and body size.
▪ If it is negative, the testes weight falls below the expectation from

physiology

▪ If it is positive, the testes weight falls above the expectation from physiology
o The results indicated that the evolution of mating systems with high sperm competition correlated with the evolution of relatively large testes
▪ P < 0.005
Fossil Record:

• It can be used to test macroevolution questions about the origin of major differences among taxa
  o For example, what was the evolutionary precursor to this trait? How did this trait change over time?
  
• Technique: is to reconstruct the history of the trait o Establish the ancestral condition
  o Understand transformational sequences
  Mathematical Modelling:
  
  • Questions: there are macro or micro-evolutionary questions
    
  • It allows researcher to:
    o Test logic of proposed hypotheses
    o Identify areas where further study is needed
    o Predict evolutionary outcomes given initial assumptions
    
  • All the above methods are falsifiable