Field of Science

The Black Queen Hypothesis In the game of Hearts, the object is to not get certain cards. The most vile of them all is the dreaded black queen of spades, which is as bad as all the other bad cards put together.

In a recent theory paper, Jeff Morris, Rich Lenski, and Erik Zinser present the Black Queen Hypothesis to explain why some organisms lose genes that are apparently important for survival.

Prochlorococcus is a bacterium that is able to live in an environment full of a toxic peroxide, HOOH, because they have a gene, KatG, that produces catalase-peroxidase, a compound that neutralizes HOOH. But then why are some forms of Prochlorococcus able to survive in this environment even without a functional copy of KatG? Here is their Black Queen Hypothesis:

In the context of evolution, the BQH posits that certain genes, or more broadly, biological functions, are analogous to the queen of spades. Such functions are costly and therefore undesirable, leading to a selective advantage for organisms that stop performing them. At the same time, the function must provide an indispensable public good, necessitating its retention by at least a subset of the individuals in the community—after all, one cannot play Hearts without a queen of spades. The detoxification of HOOH fulfills both of these criteria, and therefore the BQH predicts that this function will be performed by helpers that comprise only a fraction of the community.
In other words, the mutant form of Prochlorococcus that does not have KatG survives because of the public good produced by the original Prochlorococcus with a functional copy of KatG. And it does not cause the original type to become extinct, because it depends on it for removing HOOH from the environment.

Initially, all Prochlorococcus has the gene, KatG, that allows the bacteria to produce catalase-peroxidase. This allows the cells to live in an environment with a peroxide, HOOH (blue), which is otherwise toxic. The HOOH diffuses into the cells, where it is neutralized by catalase-peroxidase. This creates a gradient such that there is less HOOH the closer you get to the center of the colony.
A mutant is born (red cell) that has lost KatG, and so cannot produce catalase-peroxidase. If it were to live in an environment with HOOH, it would die. However, it can live close to other Prochlorococcus that are resistant to HOOH (blue), because these resistant cells remove HOOH from the environment.
Because producing KatG comes at a slight cost in fitness, those who don't spend the resources producing it has a slight reproductive advantage over those who do. As a result, the mutant Prochlorococcus will soon increase in number.
An equilibrium is established such that the original KatG producing Prochlorococcus and the mutant form coexist, because the higher the number of mutant cells results in less HOOH being removed from the environment. Negative frequency-dependent selection thus ensures that both types can exist side by side, because it is favorable to be the less frequent type.

Negative frequency-dependent selection works like this: If chance would have it that more is born of the mutant type, then there isn't enough space for them where HOOH is being removed, and some will die. However, the original KatG producers are still fine, so they will have a fitness advantage and grow in number. If it happens that there are few mutants, they they again has a fitness advantage over the original type, and now they will grow in number.

Jeff Morris

Luckily, Jeff works three doors down the hall from me, and so I was able to go talk to him about the BQH. The BQH is formulated mathematically as if the organisms/bacteria are in a homogeneous well-mixed environment. However, this is of course, as they discuss in the paper, not 100% realistic. Bacteria often exist in microenvironments, and it matters where the mutant cells are in space in relation to the original KatG producers; if they are too far away, HOOH is not removed from their environment, and they die. Jeff agrees that this heterogeneity - as portrayed in the figures above, where HOOH isn't removed equally from all of space - changes the dynamics somewhat, most probably by shifting the equilibrium frequencies of the two types, such that there are fewer mutants in a heterogeneous environment compared to a well-mixed homogeneous environment.

Jeff has this to add (personal correspondence):

No modern Prochlorococcus (that we've found so far) has katG. Almost all other cyanobacteria do, however, so we infer that Pro lost it at some point. The "helpers" in the modern ocean are entirely different species. So really what you're describing in the blog is the hypothetical process by which the first Pro to lost katG was able to invade its ancestral population.

The neat thing is that, because other species exist that aren't in competition with Pro but still degrade HOOH, the katG-deficient Pro was able to sweep its ancestor to extinction. In general BQH stands out (along with Red Queen) in considering interspecies interactions more explicitly than most evolutionary ideas.
Read more about the BQH on BEACON's blog and Science Daily.

Morris JJ, Lenski RE, & Zinser ER (2012). The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio, 3 (2) PMID: 22448042.

The evolving carnival

The CoE blogger thinks Carnival of Evolution is evolving. Doofus! There's no population, no real inheritance, and not even a genetic code to be transmitted. All it amounts to then is akin to memes, and they really don't evolve the same as genes. I like the stats, though:
Figure 1: Number of posts included in CoE by month from its conception in August 2008 through May 2012. Not all months are included, because not all past editions are accessible. Numbers are approximate (counted one time by one person).

Notice that very consistent increase in body size of CoE over through time. A one-tailed t-test with unequal variance on the first half of editions vs. the second half gives p= 4.7072e-5, which is highly significant. That is, the average change in size from the first half (18.81) to the second (33.95) is not due to random fluctuations in number of posts included in the editions. CoE is definitely evolving. Creationists, go redacted!

There are still a few days left to submit to the next edition, which will be hosted on Pharyngula (clue: get linked to and get 29,000 in a day).


Yet more papers from the ToCs that I'd like to live longer to read.
  • Evidence of non-random mutation rates suggests an evolutionary risk management strategy
  • Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift
  • The evolution of sex is favoured during adaptation to new environments
  • The extended evolutionary synthesis and the role of soft inheritance in evolution
  • Group adaptation, formal darwinism and contextual analysis
  • The effects of migration and drift on local adaptation to a heterogeneous environment

Is Eigenfactor really a good measure?

I have just been alerted to Eigenfactor - a new measure of how influential scientific journals are. A one-page article in PNAS discusses its use, and explains how it is calculated:
The Eigenfactor™ algorithm corresponds to a simple model of research in which readers follow chains of citations as they move from journal to journal. Imagine that a researcher goes to the library and selects a journal article at random. After reading the article, the researcher selects at random one of the citations from the article. She then proceeds to the journal that was cited, reads a random article there, and selects a citation to direct her to her next journal volume. The researcher does this ad infinitum.
A comparison of journals reveals that the journals we already know to be the best(?) have high Eigenfactors:
But, when I went to and read the FAQ, I saw this:
1. How do I interpret a journal's Eigenfactor™score? A journal's Eigenfactor score is our measure of the journal's total importance to the scientific community. 
With all else equal, a journal's Eigenfactor score doubles when it doubles in size. Thus a very large journal such as the Journal of Biological Chemistry which publishes more than 6,000 articles annually, will have extremely high Eigenfactor scores simply based upon its size.
Whaaat?! That seems misleading, doesn't it? Just because a journal publishes more articles certainly doesn't mean it is more prestigious to publish in. I realize that that wasn't the question; the question was which journals are most influential, and this I can see. However, what does that matter for the author who has to choose the journal to submit to? Take PLoS journals. If you submit to PLoS Biology or PLoS Computational Biology, then upon rejection they'll suggest you to submit to PLoS ONE. Why? Well, clearly because it is way easier to get accepted there - PLoS ONE is a much larger journal (with a policy of accepting papers as long as they are not erroneous).

Looking up the Eigenfactor of these journals, I get this:

PLOS ONE: 0.319571
PLOS Biology: 0.159932
PLOS Computational Biology: 0.060394

 PLoS ONE is thus twice as influential as PLoS Biology, and over five times as influential as PLoS Comp Bio. However, no sane author I know would prefer to publish in PLoS ONE over PLoS Biology, so what's the use, then? None, as far as I am concerned.

CoE #47: All the evolution news fit to blog

47th Carnival of Evolution has been posted on Evolving thoughts. All the evolution news that fit to blog includes this interesting post on the caveman diet:
Except for Captain Caveman and Fred Flintstone, were there other overweight cavemen? Would we be healthier if we adopted the diet that ancient humans ate thousands of years ago?
What is your favorite diet? 
The Atkins diet? South Beach diet? Ever heard of the paleolithic (paleo) diet?


Last weeks interesting papers on evolution:
  • Adaptive evolution of facial colour patterns in Neotropical primates
  • Selection in a fluctuating environment leads to decreased genetic variation and facilitates the evolution of phenotypic plasticity
  • Footprints of positive selection associated with a mutation (N1575Y) in the voltage-gated sodium channel of Anopheles gambiae
  • Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
  • In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids