Have a look at this short video. Do you think it works?
It is supposed to show that new species form when traits are subject to trade-offs. However, in the actual model, those traits govern resource use, but here they are illustrated as morphological traits: tails, wings, legs, whiskers, ears, and eyes. The traits vary over time, resulting in four different species.
Now that you have watched it, my question is whether the nature of the traits in the model is adequately conveyed? What do you think?
The data is from our new paper, Trade-offs drive resource specialization and the gradual establishment of ecotypes in BMC Evolutionary Biology.
Press:
Evolutionary compromises drive diversity (MSU Today)
Compromise is key to evolving new creatures (Futurity)
A Winged Cat Helps Explain The Principle Of Evolutionary Trade-Offs (io9)
Evolutionary compromises drive diversity (Fox 47 News)
Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development1 week ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.1 week ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
Death of the fittest
This is imho an excessively beautiful figure! I keep staring at it getting thrills, and bliss pours over me as I explore its intricacies. This is evolution.
Click to enlarge.
(You should enjoy this figure while listening to one or several of these:)
What are we looking at? Fitness over time of all individuals in a population of size 100. The blue line is average population fitness. The red line is the lineage that leads to the most fit individual after 100,000 updates.
And the real treasure? All the black lines which are all the other lineages that died out. Only the individuals who descend from the ancestor on the red line are alive near the end (technically, the most recent common ancestor (MRCA) is close to but obviously not quite at the end of the simulation).
We see two interesting facts:
(You should enjoy this figure while listening to one or several of these:)
What are we looking at? Fitness over time of all individuals in a population of size 100. The blue line is average population fitness. The red line is the lineage that leads to the most fit individual after 100,000 updates.
And the real treasure? All the black lines which are all the other lineages that died out. Only the individuals who descend from the ancestor on the red line are alive near the end (technically, the most recent common ancestor (MRCA) is close to but obviously not quite at the end of the simulation).
We see two interesting facts:
- Offspring that have deleterious mutations (that decrease fitness) survive for quite a long time, and those individuals even have offspring of their own some times. In fact, we can see that there are even deleterious mutations on the line of descent (the red line goes down on five occasions).
- Offspring that have beneficial mutations (that increase fitness) don't always survive. In fact, most of them eventually die and those beneficial mutations are lost. Evolution does not imply survival of the fittest.
Deleterious mutations do not prohibit evolution; deleterious mutations hitchhike on the back of beneficial mutations and go to fixation that way (there is no epistasis in this model).
The simulation
I made this simulation in Matlab. Constant population size of 100. Mutation rate of 0.01. Effect of mutations is drawn at random from a uniform distribution of selection coefficients between -0.05 and 0.05. One individual reproduces per computational update (Moran process), and chance of reproducing is proportional to fitness.
73rd Carnival of Evolution: World Cup Edition
Welcome to the 2014 Carnival of Evolution World Cup of evolution blog posts.
We have an exciting post ahead of us today where we will find the winner of the inaugural CoE World Cup. Entered posts will be scored based on several parameters, and matches will be determined probabilistically.
The scoring system works like this:
+1 for mentioning "evolution" or "evolve"
+1 for posts about biological evolution
-1 for saying "develop" or "development" when meaning "evolve" or "evolution"
-1 for being very short
-2 for being very long
0 to +5 points based on the interest of the referee (the CoE host)
+2 for posts about peer-reviewed articles
+4 for posts whose authors clearly present opinions of their own
+1 per picture (up to three) included in the post
+1 for attracting any comments
+1 extra for each original picture (max 3)
+3 for showing videos
+25 for reports on rabbit fossils from the Cambrian
-5 for any hint of panadaptationism
-2 for each logical fallacy
-4 for any mention of aquatic ape theory
-7 for agreeing with Lynn Margulis that everything is endosymbiosis
-3 if talking about the work of others without citation
-5 to -1 for any wrong statements about evolution
19 posts entered into the CoE World Cup, so three posts needs to be eliminated for the round of 16. These were the three lowest scoring posts:
The remaining 16 posts were paired up at random and the winner of each match determined randomly, with the probability of winning given by the score. For example, two scores of 10 and 15 will give the posts 40% and 60% chances of winning, respectively.
The following list of the remaining 16 posts have three numbers each: their ID number, their score, and their randomly assigned spot in the round of 16.
This gives us the following schedule of games [spot: post ID (score)]:
Game 1 is between Was Fisher W(right)? (score = 16) and The intricate world of cone snail venoms (score = 12). This gives them chances of winning of 52.1% and 42.9%. The CoE World Cup Random Number Generator™selects.... Was Fisher W(right)? and eliminate
Game 6 pits Visualizing coevolution in dynamic fitness landscapes (score = 14, P = 45.2%) against Of Population Structure and the Adaptive Landscapes (score = 17, P = 54.8%). Victorious is Of Population Structure and the Adaptive Landscapes and out is
Game 8 - the last of the round of 16 - is between The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process (score = 11, P = 42.3%) and Evolution 2014 (score = 15, P = 57.7%). Somewhat surprisingly The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process wins this one and sends out
And that concludes the round of 16. Some surprises along the way so far. The least likely post to win actually won in 3 out of 8 games, and we had to say goodbye to two of the overall favorites, Wright's Shifting Balance Process and Add it up: the genetic basis of ecological adaptation.
On to the quarter-finals...
The first quarter-final has Was Fisher W(right)? (score = 16, P = 51.6%) versus Is evolution predictable? (score = 15, P = 48.4%). A tough game, but The CoE World Cup Random Number Generator™doesn't hesitate and chooses Was Fisher W(right)? sends out
The second quarter-final is between The Function Wars: Part I (score = 13, P = 46.4%) and Our skulls didn't evolve to be punched (score = 15, P = 53.6%). And the outcome is that The Function Wars: Part I wins and the loser is
The third quarter-final is a battle between the surprise post Spontaneous mutations - friend of foe? (score = 13, P = 43.3%) and Of Population Structure and the Adaptive Landscapes (score = 17, P =56.7%). Can the surprise post do it again? Noooo! Of Population Structure and the Adaptive Landscapes wins and there is no more
The fourth and last quarter-final has the underdog Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 47.6%) against The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process (score = 11, P = 52.4%). By The CoE World Cup Random Number Generator™the winner is Nicholas Wade and the blurring of boundaries between science and fantasy and going home is
That concludes the quarter-finals. We'll take a short break before we begin the semi-finals.
And we're back.
The first semi-final is an exiting match between Was Fisher W(right)? (score = 16, P = 55.2%) and The Function Wars: Part I (score = 13, P = 44.8%). Who will go to the 2014 CoE World Cup final? Aaaand... it's The Function Wars: Part I!!!! The post has done it again. This means goodbye to
We now turn to the second semi-final that stands between the favorite Of Population Structure and the Adaptive Landscapes (score = 17, P = 63.0%) and the underdog Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 37.0%) It's amazing it has made it this far. Let's see how they do today: Of Population Structure and the Adaptive Landscapes wins as expected and sends home
We are thus left with just two posts for the final match that will decide who wins the 2014 Carnival of Evolution World Cup.
It is The Function Wars: Part I (score = 13, P = 43.3%) versus Of Population Structure and the Adaptive Landscapes (score = 17, P = 56.7%). Both posts have played really well so far, surviving some really close calls. Both posts have a lot to offer on evolution, though one is severely disadvantaged by its excessive length. Can The Function Wars: Part I overcome this obstacle today, or will Of Population Structure and the Adaptive Landscapes prevail as most people expect?
The game is on, and it is over before we know it as the CoE World Cup Random Number Generator™ takes a mere 0.000349 seconds to decide that... The Function Wars: Part I is the winner of the 2014 CoE World Cup!!!! What a glorious and surprising victory! The readers go wild!!! In second place we thus have
Congratulations to the post from Sandwalk and to writer Larry Moran!!!
That concludes the inaugural Carnival of Evolution World Cup 2014.
Come back next month for more blogging about evolution. We still don't have a host, so if you're interested please contact the administrator by email, Facebook, or Twitter. You can submit posts via all three of those as well.
We have an exciting post ahead of us today where we will find the winner of the inaugural CoE World Cup. Entered posts will be scored based on several parameters, and matches will be determined probabilistically.
The scoring system works like this:
+1 for mentioning "evolution" or "evolve"
+1 for posts about biological evolution
-1 for saying "develop" or "development" when meaning "evolve" or "evolution"
-1 for being very short
-2 for being very long
0 to +5 points based on the interest of the referee (the CoE host)
+2 for posts about peer-reviewed articles
+4 for posts whose authors clearly present opinions of their own
+1 per picture (up to three) included in the post
+1 for attracting any comments
+1 extra for each original picture (max 3)
+3 for showing videos
+25 for reports on rabbit fossils from the Cambrian
-5 for any hint of panadaptationism
-2 for each logical fallacy
-4 for any mention of aquatic ape theory
-7 for agreeing with Lynn Margulis that everything is endosymbiosis
-3 if talking about the work of others without citation
-5 to -1 for any wrong statements about evolution
19 posts entered into the CoE World Cup, so three posts needs to be eliminated for the round of 16. These were the three lowest scoring posts:
On guenon monkeys using facial recognition to prevent inbreeding.
D-brief. Carl Engelking.
Score = 7
On spiders hiding from predators by looking like bird poop.
Ecologica. Sam Hardman
Score = 8
On Twitter data from the 2014 Evolution conference.
The molecular ecologist. Jeremy Yoder.
Score = 9
The remaining 16 posts were paired up at random and the winner of each match determined randomly, with the probability of winning given by the score. For example, two scores of 10 and 15 will give the posts 40% and 60% chances of winning, respectively.
The following list of the remaining 16 posts have three numbers each: their ID number, their score, and their randomly assigned spot in the round of 16.
This gives us the following schedule of games [spot: post ID (score)]:
Game 1 is between Was Fisher W(right)? (score = 16) and The intricate world of cone snail venoms (score = 12). This gives them chances of winning of 52.1% and 42.9%. The CoE World Cup Random Number Generator™selects.... Was Fisher W(right)? and eliminate
On conus snail venom and how they are administered.
Teaching biology. Marc Srour.
Game 2 is between Is evolution predictable? (score = 15, P = 42.9%) and Wright's Shifting Balance Process (score = 20, P = 57.1%). Two very strong posts. And the winner is Is evolution predictable? and we must say farewell to the top seeded
On, well, Wright's Shifting Balance Theory.
Evolution in Structured Populations. Charles Goodnight.
Game 3 is between The Function Wars: Part I (score = 13, P = 56.5%) and A bizarre blood-sucking Jurassic maggot (score = 10, P = 43.5%). The Function Wars: Part I beats
On a fossil of an aquatic fly larva from the Chinese mid-Jurassic.
Why evolution is true. Matthew Cobb
Game 4 is between The simulations behind the fitness landscape visualizations (score = 13, P = 46.4%) and Our skulls didn't evolve to be punched (score = 15, P = 53.6%). A win for Our skulls didn't evolve to be punched and a loss to
On the computational details behind the simulations.
Pleiotropy. Bjørn Østman
Game 5 is between Add it up: the genetic basis of ecological adaptation (score = 17, P = 56.7%) and Spontaneous mutations - friend of foe? (score = 13, P = 43.3). Again the weaker post Spontaneous mutations - friend of foe? beats the odds and sends out
On the genetic and genomic changes that underlie adaptation to divergent environments.
Eco-evolutionary dynamics. Katie Peichel.
Game 6 pits Visualizing coevolution in dynamic fitness landscapes (score = 14, P = 45.2%) against Of Population Structure and the Adaptive Landscapes (score = 17, P = 54.8%). Victorious is Of Population Structure and the Adaptive Landscapes and out is
On the biology of the models behind the video.
BEACON. Bjørn Østman.
Game 7 sees Historical Contingencies at the Birthday Party (score = 12, P = 54.5%) against On Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 45.5%). A close match where Nicholas Wade and the blurring of boundaries between science and fantasy prevails and goodbye to
On the probability of convergent evolution.
Synthetic Daisies. Bradly Alicea.
Game 8 - the last of the round of 16 - is between The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process (score = 11, P = 42.3%) and Evolution 2014 (score = 15, P = 57.7%). Somewhat surprisingly The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process wins this one and sends out
On the distribution of topics at the 2014 Evolution conference.
A great tree. Lewis Spurgin.
And that concludes the round of 16. Some surprises along the way so far. The least likely post to win actually won in 3 out of 8 games, and we had to say goodbye to two of the overall favorites, Wright's Shifting Balance Process and Add it up: the genetic basis of ecological adaptation.
On to the quarter-finals...
The first quarter-final has Was Fisher W(right)? (score = 16, P = 51.6%) versus Is evolution predictable? (score = 15, P = 48.4%). A tough game, but The CoE World Cup Random Number Generator™doesn't hesitate and chooses Was Fisher W(right)? sends out
On the probability to leave descendants based on trees contracted from nucleotide sequences.
Neherlab. Richard Neher.
The second quarter-final is between The Function Wars: Part I (score = 13, P = 46.4%) and Our skulls didn't evolve to be punched (score = 15, P = 53.6%). And the outcome is that The Function Wars: Part I wins and the loser is
On whether humans skulls evolved in response to taking a lot of punches.
Laelaps. Brian Switek.
The third quarter-final is a battle between the surprise post Spontaneous mutations - friend of foe? (score = 13, P = 43.3%) and Of Population Structure and the Adaptive Landscapes (score = 17, P =56.7%). Can the surprise post do it again? Noooo! Of Population Structure and the Adaptive Landscapes wins and there is no more
On measuring mutation rate and mutational effects in yeast.
The molecular ecologist. Ryosuke Kit.
The fourth and last quarter-final has the underdog Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 47.6%) against The 1984 founder event debate: Its relation to Phase 1 of Wright’s Shifting Balance Process (score = 11, P = 52.4%). By The CoE World Cup Random Number Generator™the winner is Nicholas Wade and the blurring of boundaries between science and fantasy and going home is
On the role of genetic drift in Wright's Shifting Balance Theory.
Evolution in Structured Populations. Charles Goodnight.
That concludes the quarter-finals. We'll take a short break before we begin the semi-finals.
And we're back.
The first semi-final is an exiting match between Was Fisher W(right)? (score = 16, P = 55.2%) and The Function Wars: Part I (score = 13, P = 44.8%). Who will go to the 2014 CoE World Cup final? Aaaand... it's The Function Wars: Part I!!!! The post has done it again. This means goodbye to
On genetic drift and epistasis.
Evolution in Structured Populations. Charles Goodnight.
We now turn to the second semi-final that stands between the favorite Of Population Structure and the Adaptive Landscapes (score = 17, P = 63.0%) and the underdog Nicholas Wade and the blurring of boundaries between science and fantasy (score = 10, P = 37.0%) It's amazing it has made it this far. Let's see how they do today: Of Population Structure and the Adaptive Landscapes wins as expected and sends home
On what science can and cannot comment on.
it is NOT junk. Michael Eisen.
it is NOT junk. Michael Eisen.
We are thus left with just two posts for the final match that will decide who wins the 2014 Carnival of Evolution World Cup.
It is The Function Wars: Part I (score = 13, P = 43.3%) versus Of Population Structure and the Adaptive Landscapes (score = 17, P = 56.7%). Both posts have played really well so far, surviving some really close calls. Both posts have a lot to offer on evolution, though one is severely disadvantaged by its excessive length. Can The Function Wars: Part I overcome this obstacle today, or will Of Population Structure and the Adaptive Landscapes prevail as most people expect?
The game is on, and it is over before we know it as the CoE World Cup Random Number Generator™ takes a mere 0.000349 seconds to decide that... The Function Wars: Part I is the winner of the 2014 CoE World Cup!!!! What a glorious and surprising victory! The readers go wild!!! In second place we thus have
On fitness landscapes.
Evolution in Structured Populations. Charles Goodnight.
And the winner of the 2014 Carnival of Evolution World Cup is
On ENCODE and the definitions of function.
Sandwalk. Larry Moran.
Congratulations to the post from Sandwalk and to writer Larry Moran!!!
That concludes the inaugural Carnival of Evolution World Cup 2014.
Come back next month for more blogging about evolution. We still don't have a host, so if you're interested please contact the administrator by email, Facebook, or Twitter. You can submit posts via all three of those as well.
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