Misinterpreting Phylogenetic Trees

Last night, Marta told us about the history of phylogenetic trees and touched on their modern incarnations. In yet another serendipity (we seem to be finding them everywhere), I just saw something this morning that expands on the modern part of the history, as well as supports Bob's comments last night about how misleading circular phylogenetic tree diagrams can be. I think it was Brad who first told us about the UC Berkeley evolution site, at http://evolution.berkeley.edu. There is a newly posted article that talks about how to read and interpret phylogenetic trees. It's written at an accessible level, and is completely understandable to those of us (guilty) who are not expert in biology.

One of the most interesting sections of the article is towards the end, where the author spells out the ten most common mistakes people make in interpreting phylogenetic trees.

I won't go through all ten, but here are a couple of the more interesting ones:

Misconception Number 1: Higher and Lower. Of particular interest to me since my first paper is on the idea of hierarchy of the natural world, the first misconception is that further up the tree is "higher" or "better" and further down the tree is "lower" or "less good." As the author puts it, "there is no scientifically defensible basis on which to rank living species in this way."


Misconception Number 2: Mainline vs. Sidetrack. Just by virtue of the use of the tree diagram, you visually see what looks like a main line of evolution, in the case of figure A from the root to a human, and all the other lines look like sidetracks. It's important not to take that seriously, as one could (as in figure B) simply reconfigure the exact same diagram to make the fish look like the main line and the human a sidetrack. Even T.H. Huxley made this conceptual error when he wrote that certain fish "appear to me to be off the main line of evolution—to represent, as it were, side tracks starting from certain points of that line."

Misconception Number 6: Long Branch Implies No Change. Visually, it can appear that the result of a long, unbranching line is more related to, or closer to, the root ancestor than something that is at the end of lots of branches. How many branches there are between the initial and terminal nodes is in no sense a measure of the how much evolutionary change there has been. Referring back to the figures A and B above, figure A could be misinterpreted to suggest that humans are very similar to the ancestral form, and figure B could be misinterpreted to mean that we are quite different. Of course, the diagrams are logically identical, and to draw either conclusion from the diagrams themselves would be a fallacy. (This is not to say, of course, that there are not some forms more like the ancestral forms than others, just that reading the long line of the diagram to be a measure of that similarity is a logical error).


Misconception Number 9: More Intervening Nodes Equals More Distantly Related. The author doesn't actually use this illustration to make this point, but it makes it quite clearly. If you interpret figure a naively, you might guess that frogs are more related to fish than to humans, being "closer" in a left to right sense. Figure B shows you another rendering of the identical phylogenetic tree that makes frogs look closer to humans. Of course, the right way to think about it is to look for the common ancestor. Frogs are more closely related to humans than to fish because the most recent common ancestor of the frog and the human is more recent than the most recent common ancestor between frogs and fish, a relationship that is apparent from either diagram.

Overall, none of this is rocket science, and we should be able to figure these things out on our own, but as the T.H. Huxley example shows, even the experts can think carelessly, and this article is a useful corrective. The url is http://www.springerlink.com/content/v41w288751r82653/fulltext.html

Greg Priest

P.S. I am apparently a moron, unable to perform the simple tax of putting a live link that actually works into my posts. The links are correct, but the way I have inserted them is not working. Robbie has given me careful instructions, but I still am incapable of getting it right. I will get him to show me live, and meantime, you can copy the links into your browser.

Saving Wild Salmon, in Hopes of Saving the Orca

So what does the president elect have to do with Science (let alone Darwin)? That's exactly what I said when I opened the science section of the NY Times this afternoon. Well there was no answer to be found. Just a questions. "What’s a president to do on issues like climate and population, particularly in an era of huge deficits and pressing real-time problems?" Nice hook. It got me, but gave me very little satisfaction...

But I did see an interesting article about Alexandra Morton a "supky hero" and the Jane Goodall of killer whales. "Alexandra Morton is a self-trained biologist, has been battling fish farms in British Columbia that she says are endangering wild salmon runs that in turn are adversely affectly the orca's ecosystem.

In 1984, 26 years old and armed only with a bachelor’s degree and enthusiasm for her task, she [and her family] moved to the Broughton Archipelago, in the Queen Charlotte Strait of British Columbia, where the whales, or orcas, were abundant." Her husband died 2 years later, but she stayed on and has earned the respect of scientist, fisherman and fishery experts alike.

Ray Hilborn, a researcher at the University of Washington. “She doesn’t come from a science background but she has had a lot of influence in highlighting the issue,” he said. Daniel Pauly, director of the Fisheries Center at the University of British Columbia, calls her “a spunky hero.”

Like the Grants, Morton has remain in one place long enough to identify issues that are missed even by specialists. She's in the NY Times because “the problem with this whole issue is if nobody sees it nothing happens,” she said one day recently as she motored past one of the farming operations. And because most of the fish farmed here end up in trucks heading down I-5 to California, she said, “it can’t just be the Canadian public. It has to be the American public.”

http://www.nytimes.com/2008/11/04/science/04prof.html?pagewanted=3&ref=science

-Pamela Alexander-Beutler

The HMS Beagle Trust

Fundraising is underway to build a replica of the HMS Beagle, which will set sail on a two-year voyage commencing in 2009. The Beagle’s mission is to conduct scientific research (in particular, Metagenomics and DNA Barcoding) in much the way Darwin did while circling the globe 177 years ago.

The Trustees of this UK registered charity describe the undertaking as follows:

The HMS Beagle Project
Bringing the adventure of science to life

We aim to rebuild the ship that carried Charles Darwin around the world. The voyage of the new Beagle will inspire global audiences through unique public engagement and learning programmes, and original scientific research in evolutionary biology, biodiversity and climate change.

She will cross the North and South Atlantic, the Pacific and Indian Oceans, round both Cape Horn and the Cape of Good Hope. She will sail in her ancestor's wake, with international crews of young scientists and sailors aboard applying the tools of modern science to the work started by Darwin and Captain Fitzroy 170 years before.

The replica Beagle is not intended to be a museum ship; she will be equipped with laboratories and equipment to allow contemporary, original research. This is not only in keeping with Charles Darwin’s legacy but also creates an opportunity to engage students and teachers in the excitement of real scientific discovery.

You can peruse the details, or make a donation, at http://www.thebeagleproject.com/index.html

The HMS Beagle Trust also sponsors a blog, which is worth a look: http://thebeagleproject.blogspot.com/

The latest entry points to the Galapagos Conservation Trust (GCT) website, which is raising funds to save the Floreana mockingbird from extinction. An earlier post highlights that the Trust and NASA will work together “…on a joint science, education and outreach programme centered on a direct link between the International Space Station and the new Beagle as she retraces the 1831-1836 voyage that carried a certain young naturalist around the world.”



Finally, I came across an article that claims the remains of the original HMS Beagle, which became a coastguard vessel before being sold for scrap in 1870, were located in 2004. Here’s a link to the article: http://news.bbc.co.uk/2/hi/science/nature/3490564.stm



Roxanne Enman

Another brief note from the New York Times, this time about genetic variations--or the lack thereof--in commercially produced chickens. The link to this article is http://www.nytimes.com/2008/11/04/science/04obchicken.html?scp=1&sq=&st=nyt .

A new study shows that commercially produced chickens are less genetically diverse than they were 50 years ago....a troubling development since that means diseases can spread more easily through a larger number of chickens that lack varying means of resistance to these diseases. Rather than natural selection developing varieties that evolve into separate species on the one hand, or the variation under domestication described by Darwin in chapter 1 of "Origin of Species," which as he puts it, leads to a greater variety than what would be found in nature (using the example of his beloved pigeons), this article shows instead a form of domestication that unwittingly leads to uniformity. According to this study, published in the Proceedings of the National Academy of Science, around 50 percent of the ancestral breeds of these chickens have been lost.

However, this study was able to "reverse engineer," and through genetic studies reconstruct the genetic characteristics of the ancestral breeds and identify what is missing from the contemporary chickens. So, on one level an interesting contrast to Darwin's apparent view of evolution leading to a continuously growing level of diversity.

Brad Bauer

Cloning of Extinct Species?

Scientists working at the RIKEN Research Institute in Japan recently cloned mice, frozen for more than a decade and whose cells had burst, using the Somatic Cell Nuclear Transfer technique, and prompting speculation that nuclear transfer might be used to “resurrect” extinct species.

Somatic Cell Nuclear Transfer involves transplanting the nucleus from a somatic cell (any cell of the body other than a reproductive cell) into an egg cell.

“In this process, the nucleus of a somatic cell is removed and inserted into an unfertilized egg that has had its nucleus removed. The egg with its donated nucleus... divides until it becomes an embryo[, which] is then placed inside a surrogate mother [to] develop…” (http://biology.about.com/od/biotechnologycloning/a/aa062306a.htm).

Typically cells burst when frozen, damaging the DNA inside them. The article explains that “[c]hemicals called cryoprotectants can prevent this, but they must be used before the cells are frozen.” Because the cloned mice had damaged cells, and a cryoprotectant had not been used, the Japanese research team speculates that nuclear transfer might be used on other organisms frozen for long periods without cryopreservation (for example, to resurrect extinct species like mammoths, who have often been found preserved in ice). They further believe that the technique might be used to preserve endangered species.

The team reported in the Proceedings of the National Academy of Sciences. Here’s the link to the article: http://www.newsdaily.com/stories/tre4a26nv-us-clones-frozen/

Roxanne Enman

Extinction and evolution

Among checking on election news this afternoon during my lunch break, I found this article on the New York Times, which I thought could be of interest: http://www.nytimes.com/2008/11/04/science/04conv.html?pagewanted=1.


Namely, it is about the work that Prof. Stuart Pimm of Duke University is doing to study--and combat--the extinction of species (no, that is not Prof. Pimm in the picture, but one of the animals that he studies, the golden lion tamarin of Brazil). In studying Darwin one can read about the "tree of life," with the emphasis being on those branches of the tree that continue to evolve, but what happens to those dead-end branches that do not? Pimm's work gives current and vivid examples of such cases.

Unsurprisingly, the culprits that prevent such further evolution are often human beings, through the expansion of the human population and corresponding alteration of natural habitat, whether in the destruction of rain forests in Brazil, or the development (real-estate and agricultural)and importation of foreign species to the Hawaiian Islands, an example that Pimm discusses at the beginning of this article. When he first visited Hawaii over thirty years ago, he thought that it would harbor a rich and diverse native flora and fauna, like the Galapagos, and was disappointed at the paucity of native species (10 types of animals, with a further 10 on the brink of extinction).

Trying to think about this in Darwinian terms, I am reminded of Paul Ewald's book, "The Evolution of Infectious Diseases," which I began reading on the train this morning. One of the problems that Ewald outlines is that infectious diseases adapt more quickly than the biological beings that act as hosts for them (such as humans, animals, etc.) Using this analogy, it looks like human beings play the role of "infectious diseases" when compared to the wildlife that can't adapt quickly enough to ward off or at least adapt to our incursions.

One area of course where this analogy breaks down is that there are people like Pimm who are trying to find ways to save species, and there are no infectious diseases I know of that are trying to spare us the worst that they have to offer. If you take a look at the interview with Pimm, listen to his audio segements as well, where he discusses efforts to save the Florida panther (through importing female panthers from Texas)as well as saving the habitat of the golden lion tamarin in Brazil, purchasing land between shrinking islands of forest habitat so that "it will be possible for lonely hearts to meet members of the opposite sex and go forth and multiply."

Brad Bauer

Stephen Hawking Heads to the Vatican, on Behalf of Darwin

In October, I posted about the Anglican and Vatican unofficial apologies to Charles Darwin. Again, I found the whole news thread a non-issue. Still, I can’t resist giving you all an update: Pope Benedict XVI has invited Stephen Hawking to the Vatican, which is holding a week-long conference organized by the very offical sounding Pontifical Academy of Sciences.

In a London Times article, Hawking, explained that he took part in another scientific conference at the Vatican 30 years ago. At that time, he suggested that since the universe had no identifiable beginning, there had been no creation. Now, on his return to the Vatican, he’s hoping that the current is Pope was unaware of his remark for fear that he'll “share the fate of Galileo.”

The article reiterated the Catholic Church’s view on evolution, which included yet again a reminder that there’s no reason to formally apologize to Darwin. It also pulls out the cliché that oh-so-many Americans are fundamentalist Christians. Personally, I preferred the heydays of Dallas and Dukes of Hazzard, when most Brits simply assumed all Americans talked like a Texan or Daisy Duke.

Here’s the Pope’s latest thinking on the e-word, according to the Times:

The Catholic Church accepts evolution, but sees it as part of the divine plan. Pope Benedict has been described as a ‘theistic evolutionist’ who believes that God created life through evolution, and thus that there is no inherent clash between religion and science.

Laura Moorhead