April 8, 2011

This week's picks

Workers influence royal reproduction
"worker aggressive and non-aggressive behaviour towards queens predicted which queen monopolized reproduction. In contrast, among-queen interactions were rare and did not predict queen reproduction. Furthermore, parentage analysis showed workers favoured their mother when present"
[Maybe "inclusive fitness" is useful after all!]

Updated chronology for the Miocene hominoid radiation in Western Eurasia
"Eurasian pongines [orangutans and extinct relatives] and African hominines [humans, chimps, bonobos, and extinct relatives] might have independently evolved in their respective continents from similar kenyapithecin ancestors [apes living 14 million years ago], resulting from an early Middle Miocene [5-23 MYA] intercontinental range extension followed by vicariance [geographic separation, reducing or eliminating interbreeding so allowing evolutionary divergence]. "

Ribozyme-Catalyzed Transcription of an Active Ribozyme "we recombined traits evolved separately in different ribozyme [catalytic enzyme made of RNA rather than protein] lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. "

An evolutionary process that assembles phenotypes through space rather than through time "assortative mating between fast-dispersing individuals at the invasion front results in an evolutionary increase in dispersal rates in successive generations"

Fork-tailed drongos use deceptive mimicked alarm calls to steal food
"false alarm calls when watching target species handling food, in response to which targets flee to cover abandoning their food"

Moving calls: a vocal mechanism underlying quorum decisions in cohesive groups
"a sharp increase in the probability of changing foraging patch when the number of group members joining the chorus increased from two up to three"

Differences in the temporal dynamics of phenotypic selection among fitness components in the wild "The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival."

Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias "Rickettsia sp. nr. bellii swept into a population of an invasive agricultural pest, the sweet potato whitefly, Bemisia tabaci, in just 6 years. Compared with uninfected whiteflies, Rickettsia-infected whiteflies produced more offspring, had higher survival to adulthood, developed faster, and produced a higher proportion of daughters. The symbiont thus functions as both mutualist and reproductive manipulator. "

The evolutionary biology of child health "cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes"

Tradeoffs associated with constitutive and induced plant resistance against herbivory "Across all 58 plant species, we demonstrate a tradeoff between constitutive and induced resistance, which was robust to accounting for phylogenetic history of the species. Moreover, the tradeoff was driven by wild species and was not evident for cultivated species."

Towards a quantitative understanding of the late Neoproterozoic carbon cycle
"all of the main features of the carbonate and organic carbon isotope record can be explained by the release of methane hydrates from an anoxic dissolved organic carbon-rich ocean into an atmosphere containing oxygen levels considerably less than today"

May 15, 2010

Evolution of DNA methylation in animals, plants, and fungi

This week, I will try to explain what DNA methylation is and some of the reasons why it's important, before discussing this week's paper on how DNA methylation has evolved.

The paper is "Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation", published in Science by Assaf Zemach and others from the lab of Daniel Zilberman.

DNA methylation usually refers to the attachment of a methyl (CH3) group to a cytosine, one of four DNA bases (C, in DNA's A,T,C,G alphabet). Here's a link showing one way cytidine can get methylated. And this Wikipedia article shows cytosine in place in double-stranded RNA. (DNA would be similar, but with T instead of U.)

The functions of DNA methylation mostly come from the reduced transcription of RNA from methylated stretches of DNA. Surprisingly, when a new DNA copy is made (e.g., when one of our cells divide), methylation patterns are generally copied, too. Together, these two facts explain many of DNA methylation's functions.

First, DNA methylation is key to imprinting, whereby genes inherited from one parent are often shut down, perhaps for life, by methylation. Imprinting often reflects an unconscious battle between male and female parents over whether to maximize growth of this particular offspring, whatever the consequences for the mother's future survival and reproduction, or take or more long-term view. Earlier, I discussed the possible role of imprinting in mental illness.

Continue reading "Evolution of DNA methylation in animals, plants, and fungi" »

March 5, 2010

Evolution via less-fit intermediates

A central hypothesis in my forthcoming book, "Darwinian agriculture: where does Nature's wisdom lie?" is that past natural selection is unlikely to have missed simple, tradeoff-free improvements. This implies (as discussed in a recent post on drought-tolerant wheat) that tradeoff-blind biotechnology is less likely to succeed, relative to crop-improvement methods that consider tradeoffs, as long as biotechnology is limited to simple changes, like increasing the expression of an existing gene.

More complex improvements (those whose evolution would require a series of steps) are another story, however. Just because some hypothetical horse would kick ass, if it did evolve, doesn't guarantee that it will evolve. The problem is that you can't get from genotype A to some very different genotype Z, except through one or more generations of individuals with intermediate genotypes.

It's fairly easy to get from A to Z, provided that B is at least as fit as A, while C is at least as fit as B, and so on. This can be the case, as shown by experiments on the five-step evolution of antibiotic resistance, discussed in a previous post. But is this the only way a population can evolve a superior genotype? Or does evolution sometimes reach new heights (faster-flying birds, scummier pond scum, etc.) through intermediates that are significantly less fit?

Evolution via less-fit intermediates would expand evolution's options, making it even harder for biotechnology folks to come up with something missed by evolution. And that's what this week's paper seems to show.

"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness" was recently published in Nature by Margarita Meer and colleagues.

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August 5, 2009

Highly conserved, but how important?

Today Pharyngula takes a break from his exhaustive documentation of the existence of wackos and evil-doers among religious and political conservatives -- who would have guessed? -- to discuss highly conserved non(protein)coding DNA. It seems reasonable that if a DNA sequence is highly similar between humans and fish, whose last common ancestors lived way back in the good old days, then it's probably doing something important. But a paper I discussed earlier showed that highly conserved noncoding regions can sometimes be deleted without any apparent ill effects. Of course, this is also true of some protein-coding genes; we apparently have a lot of backups. Actually I'm not sure computer and circuit-board analogies are that useful.

February 11, 2008

Ancient temperatures inferred from DNA

"Where was you hid to see all that?" he cried. "It seems to me that you knows a great deal more than you should."? - The Complete Sherlock Holmes
"Our DNA is a coded description of the worlds in which our ancestors survived. And isn't it an arresting thought? We are digital archives of the African Pliocene, even of Devonian seas; walking repositories of wisdom out of the old days. You could spend a lifetime reading in this ancient library and die unsated by the wonder of it."? -- Richard Dawkins, Unweaving the Rainbow

Like many of the characters baffled by Sherlock Holmes, I am repeatedly amazed by the detailed inferences my fellow scientists are able to draw about events in the distant past. This week's paper:
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
is a good example. Eric Gaucher and colleagues at the University of Florida and DNA2.0 Inc. used protein sequences from a variety of modern bacteria species to infer the protein sequences of their distant and more recent ancestors...

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