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May 31, 2013

This week's picks

Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size "areas deprived of large avian frugivores for several decades present smaller seeds than nondefaunated forests, with negative consequences for palm regeneration"

Molecular evolution of peptidergic signaling systems in bilaterians "phylogenetic reconstruction tools... show that a large fraction of human PSs [peptide-based signaling systems] were already present in the last common ancestor of flies, mollusks, urchins, and mammals"

Honey constituents up-regulate detoxification and immunity genes in the western honey bee Apis mellifera "apicultural use of honey substitutes, including high-fructose corn syrup, may thus compromise the ability of honey bees to cope with pesticides and pathogens and contribute to colony losses"

Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes" "the oldest known fossil 'ape', represented by a partial mandible... the oldest stem member of the Old World monkey clade, represented by a lower third molar... recovered from a precisely dated 25.2-Myr-old stratum in... the East African Rift in Tanzania."

Experimental evidence that evolutionarily diverse assemblages result in higher productivity "Species produced more biomass than predicted from their monocultures when they were in plots with distantly related species and produced the amount of biomass predicted from monoculture when sown with close relatives."

March 8, 2013

Cooperation, inducible defense, cancer, and more

Here are some papers that look interesting this week.

Prairie Dogs Disperse When All Close Kin Have Disappeared "cooperation among kin is more important than competition among kin for young prairie dogs"

Variants at serotonin transporter and 2A receptor genes predict cooperative behavior differentially according to presence of punishment "Participants with a variant at the serotonin transporter gene contribute more, leading to group-level differences in cooperation, but this effect dissipates in the presence of punishment."

Plant mating system transitions drive the macroevolution of defense strategies
the repeated, unidirectional transition from ancestral self-incompatibility (obligate outcrossing) to self-compatibility (increased inbreeding) leads to the evolution of an inducible (vs. constitutive) strategy of plant resistance to herbivores."

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics "we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression"

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality"
"natural selection against optimal codons to achieve adaptive responses to environmental changes"

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote "> 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally"

Recent land use change in the Western Corn Belt threatens grasslands and wetlands
"a recent doubling in commodity prices has created incentives for landowners to convert grassland to corn and soybean cropping... onto marginal lands characterized by high erosion risk and vulnerability to drought."

December 24, 2011

BRCA linked to reproduction-versus-longevity tradeoff

This is amazing. BRCA mutations have been linked to increased risk of breast cancer and ovarian cancer. Yet these mutations are not that rare. Hasn't natural selection been doing its job? Or is there some benefit that balances the risk?

The authors of "Effects of BRCA1 and BRCA2 mutations on female fertility," recently published in Proceedings of the Royal Society, hypothesized that women with a BRCA mutation might have more children, even if they don't live as long, on average.

Today, enough couples use birth control that the number of children born depends on preferences for family size, not just innate fertility. So the authors compared women (with and without the mutation) born before 1930. They used the Utah Population Database, which has data on births, deaths, and family relations for large numbers of Utah residents. Most of those women are no longer alive, however, so how can we know whether they had the BRCA mutation or not?

The authors used a variation on ancestral state reconstruction. When two women had the same BRCA mutation -- apparently there are various versions -- the authors assumed that their most-recent common ancestor had that mutation also. They also identified a number of controls -- women who presumably did not have a BRCA mutation, because none of their descendants did -- from the same time period.

So, was there any difference in fertility between women with versus without a BRCA mutation?

Continue reading "BRCA linked to reproduction-versus-longevity tradeoff" »

July 31, 2010

Evolutionary history of yucca moths

I've written a few posts about ancestral-state reconstruction, where we use molecular or other information from living species to infer the traits of their shared ancestors. But I really like this post in which PhD student Jeremy Yoder describes his own work.

There's a nice diagram showing the general approach, then he looks at yucca moths and their relatives to figure out what their ancestors did. Yucca moths, like fig wasps, lay their eggs in flowers. Their larvae eat seeds, but the moths pollinate the flowers, so it's not too bad a deal overall. Their ancestors, he concludes, fed inside developing flowers, but without pollinating them. Maybe the world is getting a little more cooperative, after all.

June 4, 2010

Cancer's deep evolutionary roots

This week's paper, "Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa" was published in BMC Biology by Tomislav Domazet-LoŇ°o and Diethard Tautz. Each of our cells is descended from an unbroken lineage going back to the first living cell. Most cells in an adult, however, are at the end of the line and will have no descendants. Exceptions include sex cells, stem cells, and cancer cells.

We consider cancer an aberration, but think back to the first multicellular life, which may have resembled Trichoplax. A Trichoplax has an upper and a lower layer of cells, and not much in between. They can reproduce by dividing in half, producing two offspring with hundreds of cells each (video). Or they can bud off propagules containing a small number of cells. They also seem to be able to reproduce sexually, from a fertilized single-cell egg, although complete development from an egg hasn't been documented. A Trichoplax can reform from separated cells, sometimes combining cells from two individuals. In such a chimeric organism, cells with different genotypes could compete for resources and reproductive opportunities, undermining collective success. Similar problems can occur when social amoebae get together to form a stalk for their spores. Even in a genetically uniform organism, a mutant cell could start reproducing (perhaps generating many propagules) at the expense of the whole. Today, we call cells that reproduce at the expense of the whole cancers, but something similar would presumably have been a problem for the earliest multicellular organisms.

Presumably? The authors of this week's paper used "phylostratigraphic tracking" to see when the ancestors of our cancer-suppressing genes evolved. Sure enough, there was an evolutionary burst of such genes right around the time when multicellular animals first evolved.

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" »

May 6, 2010

Do legume hosts benefit from suppressing rhizobial reproduction?

This week's paper is by my PhD student Ryoko Oono, with major contributions from Imke Schmitt (University of Minnesota faculty) and Janet Sprent, who was an expert on legume-rhizobium evolution long before I started working on the problem.

"Multiple evolutionary origins of legume traits leading to extreme rhizobial differentiation" has been published on-line in New Phytologist.

Rhizobia are soil bacteria, but a lucky few accept invitations from legume plants to infect their roots, multiply a million-fold or more inside a nodule, and then convert ("fix") atmospheric nitrogen into a form that the plant can use. When the plant dies (or sometimes sooner), an unknown fraction of the rhizobia in each nodule escape back into the soil.

Below left is what rhizobia look like in the soil and in the nodules of some legume hosts, including soybean. In other hosts, including pea, they swell up and/or change their shape (below right, same scale) as they differentiate into the nitrogen-fixing bacteroid form. The swollen form is apparently nonreproductive (like worker bees), but copies of their genes can still end up back in the soil. This is because some of their clonemates in the same nodule haven't become bacteroids yet and so retain the ability to reproduce, like queen bees.
Bacteroids.jpg
The extreme differentiation shown above right is imposed by the legume host. But why? Are swollen bacteroids somehow more beneficial to the plant? Or are bacteroid swelling and their losing the ability to reproduce side-effects of some other process that may or may not benefit the plant?

Ryoko reasoned that, if a plant trait has evolved repeatedly over the course of evolution, then it is probably beneficial to the plant. On the other hand, a trait that has been abandoned repeatedly is probably harmful. But has either of these happened?

Continue reading "Do legume hosts benefit from suppressing rhizobial reproduction?" »

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.

Continue reading "Evolution via less-fit intermediates" »

May 31, 2008

Traditional values in bees

The beehive was an early Mormon icon, symbolizing hard work and cooperation. To an evolutionary biologist, however, a beehive could symbolize reproductive skew, a situation where some individuals reproduce much more than others. Extreme reproductive skew is one of the defining characteristics of eusocial species, of which honey bees are a prime example. Reproductive skew can differ between the sexes. In honey bees, the queen lays most of the eggs, and most females don't reproduce at all. Polygamous species and groups show the opposite pattern: males vary much more in reproductive success than females do. Maybe an inverted beehive would have been a better symbol. Note that the cells in our bodies behave somewhat like a eusocial bee colony; any children we have are directly descended from a few sex cells, while brain cells and skin cells play the supporting role of worker bees.

This week's paper, "Ancestral monogamy shows kin selection is key to the evolution of eusociality" was published in Science by William Hughes and others. Like humans, some bees are monogamous, meaning that the queen mates with only one male, so her daughters (the workers) are all sisters. In other bee species, the queen mates with several males, so her daughters are half-sisters. Relatedness generally favors cooperation, although there are some possible complications, discussed below.

This week's paper asks how mating behavior affects the evolution of eusociality. They reasoned that, if mating system doesn't matter, then today's eusocial species could be descended from either monogamous, polygamous, polyandrous (each female has multiple mates), or promiscuous ancestors. Alternatively, eusociality may evolve more easily with one of these mating systems than with the others.

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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...

Continue reading "Ancient temperatures inferred from DNA" »