Evolution – Page 19 – Jonathan Eisen's Lab

The latest genomics buzz

The latest buzz in genomics is about the honeybee genome. The people working on this genome have really done a good job of organizing themselves (a sort of model social genomics network in a way). They have a veritable slew of papers coming out this week on various things about the genome and about honeybees that were learned by making use of the genome.

There is an entire issue of Genome Research dedicated to studies of the honeybee (see the press release here) including papers on rates of evolution, circadian rhythms, chemical sensing, sex and death (of course), and even the royal jelly. If you don’t know what royal jelly is, do a google search for that. There is also an overview article in Nature and a genome report in Science. In total 170 researchers were involved in these papers.

Mind you, I am disappointed that these were not published in Open Access journals. And this is particularly sad given that the funding came from the NHGRI, the same group of sanctimonious individuals who kept talking about how the “public” human genome project was “open” in every way for the betterment of humanity. Unfortunately, what they mean by “open” even for the human genome project is a bit of a misnomer. They meant that people could look at the data immediately. But they restricted how people could use the data, despite their attempts to pretend otherwise. Consistent with this, the groups funded by the NHGRI generally do not publish their papers in Open Access journals. Shame shame shame.

OK, enough sniping. The honeybee is so fascinating biologically in so many ways that this genome sequence deserves a bit of extra attention. First, honeybees are social creatures. They have in fact been one of the key models in studying both the evolution of social behavior but also communication among organisms.

Another aspect of their biology that is very interesting is their genetic structure. Like other hymenoptera they have what is know as a haplodiploid life cycle with males being haploid (the result of unertilized eggs) and the females being diploid. This unusual genetics is another reason that honeybees and other hymenoptera have been studied extensively by biologists for many years. In fact, a great little bit of history about this is in a book on the history of studies of altruism from Princeton University press. One of Darwin’s biggest concerns in the origin of life related to the self sacrifical behavior, especially that in honeybee colonies. Apparently, honeybees were a topic of conversation among non scientists and the non reproductive worker castes were well known to the public. Darwin struggled quite a bit to come up with a good explanation that was consistent with natural selection for why some individuals would sacrifice their lives for others.

Dawrin actually cam up with a good logical explanation for this – that some individuals would sacrifice if they were related to others who would benefit. Bees and their relatives played a large part in studies that have revealed in much greater detail how altruism can evolve. They may not be as warm and fizzy as some other organisms being sequenced, but they certainly were a good pick for a genome sequencing project.

World’s Smallest Genome of a Cellular Organism?

A one page paper in Science reports on what I think is one of the most exciting findings in microbial genomics in years. The reports describes the sequencing and analysis of the genome of a bacterial endosymbiont of an aphid. This bacteria, known as Carsonella, has a TINY genome – only 160 kbp in length. This is ~ 3 fold smaller than the previously known smallest genome – that of Nanoarchaeum equitans which has a genome of 490 kbp.

I think almost certainly this symbiont should be considered an organelle. It is missing many cellular functions found even in the most reduced symbionts. Thus in essence it may not be the smallest genome of a cellular organism. But who cares how we define it. If it is a new organelle – that is amazing. If it is a tiny cellular genome – that is amazing too.

One thing that strikes me as strange is the fact that the paper is only one page long. It contains so little detail on what was done and what was found in the genome that the story is woefully incomplete. This I would guess is somehow related to a rush to publish but also likely due to it being published in Science, which has severe page restrictions.

This paper has been getting ENORMOUS press coverage for valid reasons. But I agree with Craig Venter (see the New Scientist article) that this genome is not of much relevance to efforts to create a “minimal” genome. This is because the ideal minimal genome is one that can support independent life. Carsonella, is far from independent and thus represents a really wild evolutionary story, but nothing of much relevance to minimal genome studies.

Some related links:

Commentary by Siv Andersson
NPR Story
Nancy Moran’s Home Page (one of the corresponding authors of the paper)
World Science article

Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H., Moran, N., & Hattori, M. (2006). The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella Science, 314 (5797), 267-267 DOI: 10.1126/science.1134196

Open Access Biology highlights – The Intriguing Life of Endosymbionts

Two new articles published in the last issue of PLoS Biology bring forth some wildly interesting details about the lives of endosymbiotic bacteria.

One of the articles is about the role Wolbachia may play in speciation in Drosophila species. Wolbachia are a type of bacteira that are found to infect a wide diversity of invertebrate species. These bacteria are transmitted directly from mother to offspring much like mitochondria. Interestingly, many have evolved specialized means of negatively impacting male offspring. In the PLoS Biology study, the researchers were working on a type of Wolbachia known to cause cytoplasmic incompatability in which infected male offspring cannot produce offspring with uninfected females. Since these males can produce offspring with infected females, this helps contribute to the spread of the Wolbachia in the population. To make a long story short, the current paper proposes that not only can Wolbachia apparently lead to speciation through behavioral affects on the host, but that these affects can be stimulated even in species not infected by Wolbachia, if another similar species in the same area is infected. To learn more about the study read the synopsis here. I am personally interested in this story because we published the first Wolbachia genome a few years ago in PLoS Biology.

The second story to me is even more interesting. This relates to a bacterial symbiont that is found in the gut of a stinkbug species. The paper is important because the symbiont in this case does not live inside the cells of its host as do many other gut symbionts of insects. Instead, the symbiont lives in an extracellular capsule. Interestingly, the symbiont is transmitted to offspring not directly in eggs as in many other symbionts, but indirectly. The mother deposits a mass of the bacteria near the eggs and these are then consumed by the young just after hatching (the video of this is amazing).

The paper shows that these symbionts possess many of the genomic features found in other transmissable symbionts – including small genomes, high AT contents, and high rates of evolution (you can read more about this in my recent paper on symbionts of the glassy winged sharpshooter here or in my earlier blog). Many previously thought that these genomic features were related to the intracellular lifestyle of symbionts. But given that the same features are found in these extracellular symbionts, this suggests that the shared genome features are probably related to experiencing population bottlenecks in transmission from mother to offspring. See the synopsis of the paper here.

Human Evolution and Neanderthals

Well, I suppose everyone should have seen this coming. An announcement has been made of plans to sequence the genome of a Neanderthal. The plan is to take DNA extracted from a Neanderthal fossil, and sequence it using a relatively new method from a company known as 454 Life Sciences.

I am torn about this project. Yes, it is cool to read DNA sequence from an extinct species, especially one that has not been around for some time and one of direct relevance to understanding human evolution. On the other hand, I would personally find it much more interesting to try and sequence an ancient Homo sapiens first. This is because the comparison of the Neanderthal to modern humans may not be the right comparison. It would be better to first compare an ancient Homo sapiens sample to modern humans, maybe with both being done with the same methods to be used in the Neanderthal study. This would be for two reasons. First, we do not really know how well the method(s) they are using work. And second, if the methods work well, it is possible that some of the differences they observe would actually be due to degradation or damage to the DNA sample. Therefore, if they simultaneously did work on an ancient Homo sapiens they might better be able to calculate which differences are do to real differences in the Neanderthal DNA and which are due to damage to the sample.

Assuming they do something like this and they are able to detect differences in the Neanderthal genome. What then? In the end, the major area of interest will be population genetic analyses trying to figure out how long Homo sapiens and Neanderthals were separated for and whether there was any interbreeding. To figure this out, they will need more Neanderthal samples and ancient human samples. Nevertheless, it is always good to do something that brings attention to the public for scientific research.

Ancient DNA

Studies of “ancient DNA” are becoming all the rage these days in various circles. The term “ancient DNA” refers to DNA isolated from very old samples, lets say at least 1000 years old.

Many years ago, it was considered almost taboo among biologists to say you worked on ancient DNA. It was the cold fusion of biology. This was becuase a variety of esteemed scientists basically said it was impossible for one to study ancient DNA since DNA was not stable enough to survive for so long a period of time. It is clear now that these people were pontificating without any real evidence, but at the time, they carried a lot of weight.

At first, the papers published on ancient DNA seemed to support the naysayers. Many many early claims were found to be flawed. But as researchers learned the problems, they also learned how to circumvent them. They learned how to keep samples very clean and avoid the possibility of contamintions. And they learned how to help deal with fragile DNA (it is sort of the chemical equivalent of dealing with a crumbling manuscript of days past).

And most recently, ancient DNA has gotten a new kick in the pants. This comes from applications of methods originally designed for genome sequencing projects (like the human genome project) to the field of ancient DNA. The genome sequencing methods allow researchers to characterize in more depth samples that supposedly contain ancient DNA. The deeper sampling allows more statistical approaches to analyzing the data and this in turn allows one to test a variety of possible explanations for what one observed (e.g., one can do a test that distinguiushes contamination from other possibilities).

And one can tell that ancient DNA is really a hot topic again as it is getting covered in all sorts of popular mags (see the recent article in Wired magazine for example here).

What can one do by studying ancient DNA? Well, basically the same things that anthropologists and paleontologists and archaeologists and evolutionary biologists have been trying to do by examining fossils. Only now, by looking at the DNA contained within fossils, one can both test (i.e., confirm, deny) inferences made from other information OR one can frequently make inferences that were impossible previously (the article in Wired is about Eddy Rubin’s studies of Neanderthal DNA that to them suggests that many anthropology-based claims about human-Neanderthal interbreeeding are wrong). Note – for full disclosure (which someone nagged on my previously for not doing), I am just starting to work with Eddy Rubin on some ancient DNA analyses, but I had nothing to do with the Neanderthal work described in the article.

The real question I think for ancient DNA studies is now no longer can they work. The question is – how far back can they go? Most likely, as one goes further and further back in time, the DNA will be in worse and worse shape. And thus what one can learn from looking at it will decrease significantly. But here is where the genome sequencing methods come into play. If one can get a large enough sample size, it may not matter so much that the DNA is in bad shape. For example, if one had one blurry picture of someones face, you would not know what they looked like. But if you had 10000 blurry pictures of the same face, you could reconstruct it with high accuracy by combining the information from the different pictures.

So – stay tuned – ancient DNA studies may be turning up some interesting tidbits in the near future. We are not likely to get to Jurassic Park territory soon – but it is not longer as absurd as it once seemed to many.

John McCain on Evolution

Just got very interested in reports of a Q&A session John McCain had a the Aspen Music Festival, as reported in the Aspen Times here. He was apparently, his normal self. Most interesting to me is his quote in response to a question about evolution

“I think Americans should be exposed to every point of view,” he said. “I happen to believe in evolution. … I respect those who think the world was created in seven days. Should it be taught as a science class? Probably not.”

It’s too bad more of the Republican party is not like him on this issue. I would bet he really cannot stand Bush but he has been trying to be a little more policial recently and thus has not said anything too critical. But it is good to know that at least one (and maybe only one) of the possible Republican candidates for president is not as anti-science as the core of the party seems to be these days.

God, Evolution, and Science

Apparently Francis Collins has a new book coming out on how he balances his religious beliefs with his work as a scientist.

Well, that is all fine and dandy and I personally view science and religion as separately areas for the most part. However, if you look at some of Collins’ interviews you realize that in fact his science appears to be compromised by his strict (i.e., fundamentalist) interpretation of certain aspects of religious belief.

For example see his PBS interview. In this he says that “Moral Law” comes from some higher power and gives the following example:

“If I’m walking down the riverbank, and a man is drowning, even if I don’t know how to swim very well, I feel this urge that the right thing to do is to try to save that person. Evolution would tell me exactly the opposite: preserve your DNA. Who cares about the guy who’s drowning? He’s one of the weaker ones, let him go. It’s your DNA that needs to survive. And yet that’s not what’s written within me.”

What an absolute load of crap. What he is saying here is that since someone might do something that is not in their own direct self interest it cannot therefore have evolved. Apparently, Collins has either never taken an evolution course or did not pay attention in one if he did. Does he suggest that soldier ants are following some moral code to sacrifice themselves for the colony? What about skin cells? Or birds that warn of coming predators? Basically, Collins is using his position as the head of NHGRI to foment anti-evolutionary points of view. It is one thing to express an opinion that one has faith and that one follows ones faith rather than following science. But instead Collins repeatedly says things that are hostile to the field of evolutionary biology. He may not intend it, but that is the way it is. It is a shame too as NHGRI (the intitute he is the head of) has done some good things for the world. His blather about evolution however, is not one of them.

This is not to say the evolution and religion are not compatible, but the way to make them compatible is NOT to mislead people about what the science of evolutionary biology reveals. It’s funny in a way – Collins claims he believes in “theistic evolution” or the idea that God created the natural laws, including those of evolutionary biology, and that those laws are how the hand of God works. But then I do not understand why it is OK to ignore those laws when convenient.

Glassy winged sharpshooter symbionts

For those interested in wine production, or symbioses, you maybe interested in a paper we published a few days ago. It was on a study we did of bacterial symbionts of an insect known as the glassy winged sharpshooter. This insect is a vector for Pierce’s Disease in grapes – a nasty disease that if it is found in a vineyard might lead to the vineyard being sacrificed for the greater good.

Anyway – we did a study of bacteria that live inside the insect that make nutrients for their insect host and without whcih the insect will die. An understanding of these symbionts will hopefully lead to better methods to control the spread of this invasive insect.

Our paper can be found in PLoS Biology here.
A synopsis of our article is here.
An article in Science Now about our study is here
An article in the Central Valley Business Times is here.
Nature highlighted it in their “Research highlights” section
And ASM article about this here
Link to our collaborator’s lab (Nancy Moran)

Some new links about our paper

For more information about the sharpshooter and Pierce’s Disease seee the following links

Pierce’s Disease Control Program for State of California: here
Glassy winged sharpshooter media information here
Introduction to Pierce’s Disease here

Wu, D., Daugherty, S., Van Aken, S., Pai, G., Watkins, K., Khouri, H., Tallon, L., Zaborsky, J., Dunbar, H., Tran, P., Moran, N., & Eisen, J. (2006). Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters PLoS Biology, 4 (6) DOI: 10.1371/journal.pbio.0040188