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Name: I am also a verb
Joined: April 19, 2009

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About

What's the deal with your nickname? How did you get it? If your nickname is self-explanatory, then tell everyone when you first started using the internet, and what was the first thing that made you say "wow, this isn't just a place for freaks after all?" Was it a website? Was it an email from a long-lost friend? Go on, spill it.

I am a Cascadian bicycle commuting stridently feminist phage biologist in Flanders. I am interested in T4 physiology, molecular genetics, why cows and other ruminants tend to align on a north/south axis, what I'm going to eat next, viral ecology and evolution, ambitiously experimental beer and wine projects, how nucleoid occlusion could possibly work, making art out of what is lying around, the mysterious intersections of biofilm ecology and defense against parasitoid DNA in pseudomonads, post-classical Hellenic concepts of religion and sexuality, the intricacies of nucleotide substitution and modification of in phage takeover of cellular metabolism, microbial eschatology, as well as the therapeutic applications of bacteriophages and studying the virus-host interactions, immunological responses, pharmacokenetics, pharmacodynamics, phage genetics and genomics, enrichment strategies, and regulatory frameworks we need to understand to do it right.

For a while I was making monster posts about especially neat scientific papers that are especially accessible to the lay public and publicly available on the internet because people seemed to really like them, and I think engaging with actual science as it is practiced is particularly important for an understanding of science as it is presented. I've stopped however as it did get kind of GYOBey and got my own blog for them [LinksToTheDamnPaper.org] with Scientist and ChuraChura. If you miss my science posts you can always go there where we update it with a new awesome science paper presented for a lay audience daily, here is the metafilter post.

The rest of this profile basically just a handy personal html based reference for finding things again that I've done on metafilter:
-After a Meta thread where I was mistakenly identified as a proficient Classical Greek translator, ocherdraco wrote an awesome Sapphic-style poem in the voice of one bacterium communicating to another about bacteriophages.

-Inspiring THE MOST BADASS SONG EVER by flapjax at midnite with this comment, flapjax is apparently just that awesome.

-This comment, which inspired litleozy to write a short play about it, how cool is that?

-My comments have been empirically demonstrated to put midnight fussy newborns back to sleep when read aloud in an enthusiastic Julie Andrews voice (n=1).

-I also have a habit of dropping science explanations and history into threads on The Blue:
  • This comment about a fascinating story of mysterious origin in Phage Biology that made the sidebar!
  • Zombies, Vibrio cholerae is the pleasant dude who rolls around on the back of a truck with a jumpsuit and a NASCAR hat picking up the garbage in front of your home, CTX-f is the agent that turns him into a poison-syringe/grappling-hook wielding madman looking to feed off of your guts
  • On how the Selfish Gene concept was already outdated by the time Dawkins took it from the two guys who developed it as well as how the gene ontology it relies on is inherently flawed and must be abandoned
  • This commentdescribing a model I have for explaining one of the reasons why women drop out of STEM careers progressively over time and also why female dominated professions are less well paid
  • This comment describing as best I can why anti-vaxxers are generally not idiots, but also why they are unambiguously wrong
  • "There is some promise in other areas of research into fighting bacteria. Doubtless blasdelb will eventually drop into this thread to talk about bacteriophages."
  • This explanation of the promise that synthetic biology has
  • A detailed answer explaining why its not ok that the depicted fictional sailor is drinking clear liquid from a torpedo, not ok at all.
  • This comment detailing how the discoverer of bacteriophages has saved hundreds of billions of dollars worth of agricultural produce and countless lives by finally vanquishing one of the great biblical plagues, which sadly few even remember
  • A tragedy that would dwarf all of the great wars of the twentieth century combined by an order of magnitude in a matter of months. Civil liberties would be among the least of our concerns, there are monsters more terrible than the worst of tyrants, and they are very real.
  • On the nature of symbiosis and a bacteriophage that infects an endosymbiotic bacteria and enables the bacteria to protect its host, a pea aphid, from a parasitoid wasp allowing the pea aphid to infect legume fields and the fantastically complex but understandable system of interdependant and hostile relationships between each of these various actors
  • An explanation of treatment strategies to either skirt around or take advantage of the extraordinary specificity of bacteriophages.
  • My shot at explaining why I am not so concerned about the safety of GMOs even in the context of corporate control, why I am much more concerned about how the anti-GMO movement is affecting the fairness and social justice of how GMOs are integrated in society than the nefariousness of any CEO, and finally the parallels I do see between the anti-GMO and anti-vaxx movements.
  • On where O157:H7 comes from but also why, at least in meat, it is not so much a scientific problem as a social and moral one.
  • This comment is a an explanation of how we tell different bacteria apart, it even includes an exercise you can do so that you can see where a real 16S ribosome gene one of my students sequenced places the bacteria they found in the tree of life.
  • -Some especially neat posts:
  • This FPP where I accumulated all of the molecular movies I had found up until then, I still use it for reference constantly. Plus Follow-up, there will be more.
  • This FPP, which is now a part of the cannon of metafilter responses to racism, as well as the follow-up post.
  • A lot of people really liked History Cookbook about ancient recipes.
  • This post compiling ever single extant film that Charlie Chaplin ever appeared in.
  • This post bringing together episodes of Current TV's long-form journalism series Vanguard and a followup post were also pretty cool
  • This thread on the Pervocracy blog, which is all kinds of awesome even if the thread did derail immediately
  • Welcome to Muppet Labs where the future is being made today! All of Muppet Labs
  • All of Swedish Chef B?rk! B?rk! B?rk!
  • -TIME FOR SOME STORIES
  • This story of how my sailing instructor ended up sailing into Ocean City in a sailboat soaked with blood and oil with no motor, no rudder, and deep gashes in his legs that made the sidebar!
  • "Then the absolutely predictable happened. The can went off like a beef cannon, it detonated with aspects of the stew projectile breaking the sound barrier and everything" That made the sidebar!
  • Two stories from a month long hiking trip in western North Carolina, in the first I get surprised by a dead woodpecker falling out of the sky while taking a shit, and the second is the tale of a spontaneous scrotum piercing I also received on that trip
  • When I was a young rascal interested in other peoples daughters, I got to meet parents with a pretty diverse set of strategies for containing the existential threat I represented, and they had widely varied levels of success:
  • I can roundly confirm that Cockburns is an excellent name for the liquor and state that I have no intention of repeating the experiment.
  • An old war story picked up in a senior center from a woman on her way out, contains Wild Bill Donovan on behalf of the OSS, sex, early commandos, and state secrets
  • -And some answers I've given that I thought were particularly good on Ask:
  • I'm glad I was there to provide the right answer but this question still scares the crap out of me for how much colossal damage AskMe is capable of doing in its ignorance to presumably real people.
  • My comprehensive answer to questions about gardening with urine, that made the sidebar
  • I still can't believe that after 46 largely ignorant and often offensive answers to this technical question relating to FERPA, mine was the first to actually answer the question being asked
  • I'm glad my experience ended up seeming useful to this question about female on male rape
  • The root of all relationship wisdom
  • It is also kind of cool that my experience in microbiology has been useful in these threads
  • -Metafilter is an odd place for the religious, even when well educated, but I seem to do alright:
  • A detailed answer to a question about why Christians seem to hate sex so much
  • A super detailed assessment of the relationship between Christianity and homosexuality
  • A very detailed of how we know what we know about the life of Jesus and the first century church
  • On the role of adelphopoiesis, porneia, and homosexuality in the early Christian Church.
  • On pre-Christian infanticide in the Roman World
  • On why, in spite of everything, Christianity does have something maybe worth listening to on the topic of abortion.


  • \*P*\*******
    *\*R*\******
    **\*I *\*****
    ***\*N*\****
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    OF METAFILTER


    Here is a handy list of 170 mefites I will never get onto an elevator alone with.

    Microbial Evolution is a really cool, amazingly promising and oddly neglected field where evolutionary biologists tend to not understand microbiology well enough to do anything meaningful with it and microbiologists seem to mostly only play with it as an afterthought - but there is still so much amazing and fascinating work being done with it. Here is a pretty paired down collection of Blasdelb's favorite papers in microbial evolution, with the free access ones marked with *** so as not to tease you. They have also been selected to present different aspects of the field, and while some knowledgable observers might claim a phage bias, I think that is totally defensible. As always if you would like copies of those papers that are not publicly available - for the purpose of this academic discussion that we will be having - feel free to memail me with an email address I can send PDFs you want to.

    Fitness of RNA virus decreased by Muller's ratchet. Nature. 348(6300):454-5.
    Why sex exists remains an unsolved problem in biology. If mutations are on the average deleterious, a high mutation rate can account for the evolution of sex. One form of this mutational hypothesis is Muller's ratchet. If the mutation rate is high, mutation-free individuals become rare and they can be lost by genetic drift in small populations. In asexual populations, as Muller noted, the loss is irreversible and the load of deleterious mutations increases in a ratchet-like manner with the successive loss of the least-mutated individuals. Sex can be advantageous because it increases the fitness of sexual populations by re-creating mutation-free individuals from mutated individuals and stops (or slows) Muller's ratchet. Although Muller's ratchet is an appealing hypothesis, it has been investigated and documented experimentally in only one group of organisms--ciliated protozoa. I initiated a study to examine the role of Muller's ratchet on the evolution of sex in RNA viruses and report here a significant decrease in fitness due to Muller's ratchet in 20 lineages of the RNA bacteriophage phi 6. These results show that deleterious mutations are generated at a sufficiently high rate to advance Muller's ratchet in an RNA virus and that beneficial, backward and compensatory mutations cannot stop the ratchet in the observed range of fitness decrease.

    ***Mitigating Mutational Meltdown in Mammalian Mitochondria PLoS Biol 6(2): e35.
    Mitochondria are remarkable microorganisms. About two billion years ago, their distant free-living ancestors hooked up with a truly foreign lineage of archaebacteria and started a genomic merger that led to the most successful coevolved mutualism on the planet: the eukaryotic cell. Along the way, evolving mitochondria lost a lot of genomic baggage, entrusted their emerging hosts with their own replication, sorted out genomic conflicts by following maternal inheritance, and have mostly abstained from sex and recombination. What mitochondria did retain was a subset of genes that encode critical components of the electron transport chain and ATP synthesis enzymes that carry out oxidative phosphorylation. Because mitochondria house the biochemical machinery that requires us to breathe oxygen, it was first assumed that mitochondrial genes would show very slow rates of molecular evolution. So it was big news almost 30 years ago when mitochondrial DNA (mtDNA) evolution was observed to be quite rapid [1]. How could the genes for a highly conserved and critical function sustain the consequences of high mutation pressure and permit rapid rates of nucleotide substitution between species? Without the benefits of recombination, where offspring can carry fewer mutations than either parent, mutations should accumulate in mitochondrial genomes through the random loss of less-mutated genomes, a process referred to as Muller's ratchet [2,3]. How have mitochondria avoided a mutational meltdown, or at least significant declines in fitness?

    Adaptive radiation in a heterogeneous environment Nature 394, 69-72.
    Successive adaptive radiations have played a pivotal role in the evolution of biological diversity. The effects of adaptive radiation are often seen but the underlying causes are difficult to disentangle and remain unclear. Here we examine directly therole of ecological opportunity and competition in driving genetic diversification. We use the common aerobic bacterium Pseudomonas fluorescens, which evolves rapidly under novel environmental conditions to generate a large repertoire of mutants. When provided with ecological opportunity (afforded by spatial structure), identical populations diversify morphologically, but when ecological opportunity is restricted there is no such divergence. In spatially structured environments, the evolution of variant morphs follows a predictable sequence and we show that competition among the newly evolved niche-specialists maintains this variation. These results demonstrate that the elementary processes of mutation and selection alone are suifficient to promote rapid proliferation of new designs and support the theory that trade-offs in competitive ability drive adaptive radiation.

    Plasmids Spread Very Fast in Heterogeneous Bacterial Communities Genetics. 2002 Dec;162(4):1525-32.
    Conjugative plasmids can mediate gene transfer between bacterial taxa in diverse environments. The ability to donate the F-type conjugative plasmid R1 greatly varies among enteric bacteria due to the interaction of the system that represses sex-pili formations (products of finOP) of plasmids already harbored by a bacterial strain with those of the R1 plasmid. The presence of efficient donors in heterogeneous bacterial populations can accelerate plasmid transfer and can spread by several orders of magnitude. Such donors allow millions of other bacteria to acquire the plasmid in a matter of days whereas, in the absence of such strains, plasmid dissemination would take years. This "amplification effect" could have an impact on the evolution of bacterial pathogens that exist in heterogeneous bacterial communities because conjugative plasmids can carry virulence or antibiotic-resistance genes.

    Massive Horizontal Gene Transfer in Bdelloid Rotifers Science
    Horizontal gene transfer in metazoans has been documented in only a few species and is usually associated with endosymbiosis or parasitism. By contrast, in bdelloid rotifers we found many genes that appear to have originated in bacteria, fungi, and plants, concentrated in telomeric regions along with diverse mobile genetic elements. Bdelloid proximal gene-rich regions, however, appeared to lack foreign genes, thereby resembling those of model metazoan organisms. Some of the foreign genes were defective, whereas others were intact and transcribed; some of the latter contained functional spliceosomal introns. One such gene, apparently of bacterial origin, was overexpressed in Escherichia coli and yielded an active enzyme. The capture and functional assimilation of exogenous genes may represent an important force in bdelloid evolution.

    Sex increases the efficacy of natural selection in experimental yeast populations Nature
    Why sex evolved and persists is a problem for evolutionary biology, because sex disrupts favourable gene combinations and requires an expenditure of time and energy1. Further, in organisms with unequal-sized gametes, the female transmits her genes at only half the rate of an asexual equivalent (the twofold cost of sex)2. Many modern theories that provide an explanation for the advantage of sex incorporate an idea originally proposed by Weismann more than 100 years ago: sex allows natural selection to proceed more effectively because it increases genetic variation3, 4, 5. Here we test this hypothesis, which still lacks robust empirical support, with the use of experiments on yeast populations. Capitalizing on recent advances in the molecular biology of recombination in yeast, we produced by genetic manipulation strains that differed only in their capacity for sexual reproduction. We show that, as predicted by the theory, sex increases the rate of adaptation to a new harsh environment but has no measurable effect on fitness in a new benign environment where there is little selection.

    ***Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms PNAS
    Giant viruses such as Mimivirus isolated from amoeba found in aquatic habitats show biological sophistication comparable to that of simple cellular life forms and seem to evolve by similar mechanisms, including extensive gene duplication and horizontal gene transfer (HGT), possibly in part through a viral parasite, the virophage. We report here the isolation of “Marseille” virus, a previously uncharacterized giant virus of amoeba. The virions of Marseillevirus encompass a 368-kb genome, a minimum of 49 proteins, and some messenger RNAs. Phylogenetic analysis of core genes indicates that Marseillevirus is the prototype of a family of nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes. The genome repertoire of the virus is composed of typical NCLDV core genes and genes apparently obtained from eukaryotic hosts and their parasites or symbionts, both bacterial and viral. We propose that amoebae are “melting pots” of microbial evolution where diverse forms emerge, including giant viruses with complex gene repertoires of various origins.

    ***High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection PNAS
    Core genes comprising the ubiquitous backbone of bacterial genomes are not subject to frequent horizontal transfer and generally are not thought to contribute to the adaptive evolution of bacterial pathogens. We determined, however, that at least one-third and possibly more than one-half of the core genes in Escherichia coli genomes are targeted by repeated replacement substitutions in the same amino acid positions—hotspot mutations. Occurrence of hotspot mutations is driven by positive selection, as their rate is significantly higher than expected by random chance alone, and neither intragenic recombination nor increased mutability can explain the observed patterns. Also, commensal E. coli strains have a significantly lower frequency of mutated genes and mutations per genome than pathogenic strains. E. coli strains causing extra-intestinal infections accumulate hotspot mutations at the highest rate, whereas the highest total number of mutated genes has been found among Shigella isolates, suggesting the pathoadaptive nature of such mutations. The vast majority of hotspot mutations are of recent evolutionary origin, implying short-term positive selection, where adaptive mutations emerge repeatedly but are not sustained in natural circulation for long. Such pattern of dynamics is consistent with source-sink model of virulence evolution.

    ***Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution PNAS
    Mobile genetic elements have impacted biological evolution across all studied organisms, but evidence for a role in evolutionary emergence of an entire phylogenetic clade has not been forthcoming. We suggest that mobile element predation played a formative role in emergence of the phytoplasma clade. Phytoplasmas are cell wall-less bacteria that cause numerous diseases in plants. Phylogenetic analyses indicate that these transkingdom parasites descended from Gram-positive walled bacteria, but events giving rise to the first phytoplasma have remained unknown. Previously we discovered a unique feature of phytoplasmal genome architecture, genes clustered in sequence-variable mosaics (SVMs), and suggested that such structures formed through recurrent, targeted attacks by mobile elements. In the present study, we discovered that cryptic prophage remnants, originating from phages in the order Caudovirales, formed SVMs and comprised exceptionally large percentages of the chromosomes of ‘Candidatus Phytoplasma asteris’-related strains OYM and AYWB, occupying nearly all major nonsyntenic sections, and accounting for most of the size difference between the two genomes. The clustered phage remnants formed genomic islands exhibiting distinct DNA physical signatures, such as dinucleotide relative abundance and codon position GC values. Phytoplasma strain-specific genes identified as phage morons were located in hypervariable regions within individual SVMs, indicating that prophage remnants played important roles in generating phytoplasma genetic diversity. Because no SVM-like structures could be identified in genomes of ancestral relatives including Acholeplasma spp., we hypothesize that ancient phage attacks leading to SVM formation occurred after divergence of phytoplasmas from acholeplasmas, triggering evolution of the phytoplasma clade.

    Snowdrift game dynamics and facultative cheating in yeast Nature
    The origin of cooperation is a central challenge to our understanding of evolution1, 2, 3. The fact that microbial interactions can be manipulated in ways that animal interactions cannot has led to a growing interest in microbial models of cooperation4, 5, 6, 7, 8, 9, 10 and competition11, 12. For the budding yeast Saccharomyces cerevisiae to grow on sucrose, the disaccharide must first be hydrolysed by the enzyme invertase13, 14. This hydrolysis reaction is performed outside the cytoplasm in the periplasmic space between the plasma membrane and the cell wall. Here we demonstrate that the vast majority (99 per cent) of the monosaccharides created by sucrose hydrolysis diffuse away before they can be imported into the cell, serving to make invertase production and secretion a cooperative behaviour15, 16. A mutant cheater strain that does not produce invertase is able to take advantage of and invade a population of wild-type cooperator cells. However, over a wide range of conditions, the wild-type cooperator can also invade a population of cheater cells. Therefore, we observe steady-state coexistence between the two strains in well-mixed culture resulting from the fact that rare strategies outperform common strategies—the defining features of what game theorists call the snowdrift game17. A model of the cooperative interaction incorporating nonlinear benefits explains the origin of this coexistence. We are able to alter the outcome of the competition by varying either the cost of cooperation or the glucose concentration in the media. Finally, we note that glucose repression of invertase expression in wild-type cells produces a strategy that is optimal for the snowdrift game—wild-type cells cooperate only when competing against cheater cells.

    Siderophore production and biofilm formation as linked social traits ISME
    The virulence of pathogenic microbes can depend on individual cells cooperating in the concerted production of molecules that facilitate host colonization or exploitation. However, cooperating groups can be exploited by social defectors or ‘cheats’. Understanding the ecology and evolution of cooperation is therefore relevant to clinical microbiology. We studied two genetically linked cooperative traits involved in host exploitation by the opportunistic human pathogen Pseudomonas aeruginosa. Clones that defected from cooperative production of iron-scavenging siderophores were deficient in biofilm formation. The presence of such clones in mixed biofilms with a wild-type clone led to reduced biofilm mass. The fitness advantage of siderophore-deficient mutants in the presence of wild-type bacteria was no greater in biofilm than in planktonic culture, suggesting that these mutants did not gain an additional advantage by exploiting wild-type biofilm polymer. Reduced biofilm formation therefore represents a pleiotropic cost of defection from siderophore production.

    Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes Science
    Although common among bacteria, lateral gene transfer—the movement of genes between distantly related organisms—is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of four insect and four nematode species that range from nearly the entire Wolbachia genome ([over] 1 megabase) to short ([over] 500 base pairs) insertions. Potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.

    Nature
    The evolution of competitive interactions among viruses was studied in the RNA phage phi6 at high and low multiplicities of infection (that is, at high and low ratios of infecting phage to host cells). At high multiplicities, many phage infect and reproduce in the same host cell, whereas at low multiplicities the viruses reproduce mainly as clones. An unexpected result of this study was that phage grown at high rates of co-infection increased in fitness initially, but then evolved lowered fitness. Here we show that the fitness of the high-multiplicity phage relative to their ancestors generates a pay-off matrix conforming to the prisoner's dilemma strategy of game theory. In this strategy, defection (selfishness) evolves, despite the greater fitness pay-off that would result if all players were to cooperate. Viral cooperation and defection can be defined as, respectively, the manufacturing and sequestering of diffusible (shared) intracellular products. Because the low-multiplicity phage did not evolve lowered fitness, we attribute the evolution of selfishness to the lack of clonal structure and the mixing of unrelated genotypes at high multiplicity.

    Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism Science
    Bacteriophages are known to carry key virulence factors for pathogenic bacteria, but their roles in symbiotic bacteria are less well understood. The heritable symbiont Hamiltonella defensa protects the aphid Acyrthosiphon pisum from attack by the parasitoid Aphidius ervi by killing developing wasp larvae. In a controlled genetic background, we show that a toxin-encoding bacteriophage is required to produce the protective phenotype. Phage loss occurs repeatedly in laboratory-held H. defensa–infected aphid clonal lines, resulting in increased susceptibility to parasitism in each instance. Our results show that these mobile genetic elements can endow a bacterial symbiont with benefits that extend to the animal host. Thus, phages vector ecologically important traits, such as defense against parasitoids, within and among symbiont and animal host lineages. [My less technical explanation]

    Evidence for an early prokaryotic endosymbiosis Nature
    Endosymbioses have dramatically altered eukaryotic life, but are thought to have negligibly affected prokaryotic evolution. Here, by analysing the flows of protein families, I present evidence that the double-membrane, Gram-negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium. The resulting taxon has been extraordinarily successful, and has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth's oxygen atmosphere. Their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin: an endosymbiosis between a clostridium and actinobacterium.

    ***Timing of transmission and the evolution of virulence of an insect virus Proc Biol Sci.
    We used the nuclear polyhedrosis virus of the gypsy moth, Lymantria dispar, to investigate whether the timing of transmission influences the evolution of virulence. In theory, early transmission should favour rapid replication and increase virulence, while late transmission should favour slower replication and reduce virulence. We tested this prediction by subjecting one set of 10 virus lineages to early transmission (Early viruses) and another set to late transmission (Late viruses). Each lineage of virus underwent nine cycles of transmission. Virulence assays on these lineages indicated that viruses transmitted early were significantly more lethal than those transmitted late. Increased exploitation of the host appears to come at a cost, however. While Early viruses initially produced more progeny, Late viruses were ultimately more productive over the entire duration of the infection. These results illustrate fitness trade-offs associated with the evolution of virulence and indicate that milder viruses can obtain a numerical advantage when mild and harmful strains tend to infect separate hosts.

    ***Virulence-transmission trade-offs and population divergence in virulence in a naturally occurring butterfly parasite PNAS
    Why do parasites harm their hosts? Conventional wisdom holds that because parasites depend on their hosts for survival and transmission, they should evolve to become benign, yet many parasites cause harm. Theory predicts that parasites could evolve virulence (i.e., parasite-induced reductions in host fitness) by balancing the transmission benefits of parasite replication with the costs of host death. This idea has led researchers to predict how human interventions—such as vaccines—may alter virulence evolution, yet empirical support is critically lacking. We studied a protozoan parasite of monarch butterflies and found that higher levels of within-host replication resulted in both higher virulence and greater transmission, thus lending support to the idea that selection for parasite transmission can favor parasite genotypes that cause substantial harm. Parasite fitness was maximized at an intermediate level of parasite replication, beyond which the cost of increased host mortality outweighed the benefit of increased transmission. A separate experiment confirmed genetic relationships between parasite replication and virulence, and showed that parasite genotypes from two monarch populations caused different virulence. These results show that selection on parasite transmission can explain why parasites harm their hosts, and suggest that constraints imposed by host ecology can lead to population divergence in parasite virulence.

    The Selection Landscape of Malaria Parasites Science
    Malaria parasites have to survive and transmit within a highly selective and ever-changing host environment. Because immunity to malaria is nonsterilizing and builds up slowly through repeated infections, commonly the parasite invades a host that is immunologically and physiologically different from its previous host. During the course of infection, the parasite must also keep pace with changes in host immune responses and red-blood-cell physiology. Here, we describe the “selection landscape” of the most virulent of the human malaria parasites, Plasmodium falciparum, and the adaptive mechanisms it uses to navigate through that landscape. Taking a cost-benefit view of parasite fitness, we consider the evolutionary outcomes of the most important forces of selection operating on the parasite, namely immunity, host death, drugs, mosquito availability, and coinfection. Given the huge potential for malaria parasite evolution in the context of the recently renewed effort to eradicate malaria, a deeper understanding of P. falciparum adaptation is essential.

    ***Lenski Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli PNAS
    The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that “replayed” evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 × 1012 ancestral cells, nor among 9 × 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

    ***Optimization of DNA polymerase mutation rates during bacterial evolution PNAS
    Mutation rate is an important determinant of evolvability. The optimal mutation rate for different organisms during evolution has been modeled in silico and tested in vivo, predominantly through pairwise comparisons. To characterize the fitness landscape across a broad range of mutation rates, we generated a panel of 66 DNA polymerase I mutants in Escherichia coli with comparable growth properties, yet with differing DNA replication fidelities, spanning 10(3)-fold higher and lower than that of wild type. These strains were competed for 350 generations in six replicate cultures in two different environments. A narrow range of mutation rates, 10- to 47-fold greater than that of wild type, predominated after serial passage. Mutants exhibiting higher mutation rates were not detected, nor were wild-type or antimutator strains. Winning clones exhibited shorter doubling times, greater maximum culture densities, and a growth advantages in pairwise competition relative to their precompetition ancestors, indicating the acquisition of adaptive phenotypes. To investigate the basis for mutator selection, we undertook a large series of pairwise competitions between mutator and wild-type strains under conditions where, in most cases, one strain completely overtook the culture within 18 days. Mutators were the most frequent winners but wild-type strains were also observed winning, suggesting that the competitive advantage of mutators is due to a greater probability of developing selectably advantageous mutations rather than from an initial growth advantage conferred by the polymerase variant itself. Our results indicate that under conditions where organism fitness is not yet maximized for a particular environment, competitive adaptation may be facilitated by enhanced mutagenesis.

    Different Trajectories of Parallel Evolution During Viral Adaptation Science
    The molecular basis of adaptation is a major focus of evolutionary biology, yet the dynamic process of adaptation has been explored only piecemeal. Experimental evolution of two bacteriophage lines under strong selection led to over a dozen nucleotide changes genomewide in each replicate. At least 96 percent of the amino acid substitutions appeared to be adaptive, and half the changes in one line also occurred in the other. However, the order of these changes differed between replicates, and parallel substitutions did not reflect the changes with the largest beneficial effects or indicate a common trajectory of adaptation.

    ***Competitive fates of bacterial social parasites: persistence and self-induced extinction of Myxococcus xanthus cheaters Proc Biol Sci.
    Cooperative biological systems are susceptible to disruption by cheating. Using the social bacterium Myxococcus xanthus, we have tested the short-term competitive fates of mixed cheater and wild-type strains over multiple cycles of cooperative development. Cheater/wild-type mixes underwent several cycles of starvation-induced multicellular development followed by spore germination and vegetative population growth. The population sizes of cheater and wild-type strains in each pairwise mixture were measured at the end of each developmental phase and each growth phase. Cheater genotypes showed several distinct competitive fates, including cheater persistence at high frequencies with little effect on total population dynamics, cheater persistence after major disruption of total population dynamics, self-extinction of cheaters with wild-type survival, and total population extinction. Our results empirically demonstrate that social exploitation can destabilize a cooperative biological system and increase the risk of local extinction events.

    ***Triassic origin and early radiation of multicellular volvocine algae PNAS
    Evolutionary transitions in individuality (ETIs) underlie the watershed events in the history of life on Earth, including the origins of cells, eukaryotes, plants, animals, and fungi. Each of these events constitutes an increase in the level of complexity, as groups of individuals become individuals in their own right. Among the best-studied ETIs is the origin of multicellularity in the green alga Volvox, a model system for the evolution of multicellularity and cellular differentiation. Since its divergence from unicellular ancestors, Volvox has evolved into a highly integrated multicellular organism with cellular specialization, a complex developmental program, and a high degree of coordination among cells. Remarkably, all of these changes were previously thought to have occurred in the last 50–75 million years. Here we estimate divergence times using a multigene data set with multiple fossil calibrations and use these estimates to infer the times of developmental changes relevant to the evolution of multicellularity. Our results show that Volvox diverged from unicellular ancestors at least 200 million years ago. Two key innovations resulting from an early cycle of cooperation, conflict and conflict mediation led to a rapid integration and radiation of multicellular forms in this group. This is the only ETI for which a detailed timeline has been established, but multilevel selection theory predicts that similar changes must have occurred during other ETIs.