Reconstructing the tree of life

May 01, 2014 by Marlene Cimons
Antonis Rokas, Associate Professor and Cornelius Vanderbilt Chair of Biological Sciences at Vanderbilt University pictured in front of the "Tree of Knonwledge" structure on the Vanderbilt campus. Credit: Steve Green, Vanderbilt University

In 1837, Charles Darwin drew a tree of life, a primitive sketch suggesting that all organisms shared a common ancestry. Today, scientists still are trying to reconstruct these evolutionary branches, but using tools, such as genomic data and sophisticated statistical algorithms, that Darwin never could have envisioned.

"We are historians of biology, trying to infer events that happened billions of years ago," says Antonis Rokas, an associate professor of biological sciences at Vanderbilt University. "We take data from what we know today—the DNA of different organisms—and by comparing the sequences and evaluating how similar they are and how different they are from each other, we try to infer the between them."

Yet in doing so, phylogeneticists, as they are known, sometimes produce results that are surprising, and even contradictory.

The National Science Foundation (NSF)-funded scientist says it is not unusual for high quality research to report genealogies that conflict with each other over the origins of certain organisms.

"Some are surprising and unexpected, and difficult to decipher," he says.

In an attempt to sort out the reasons for the conflicts, and refine the techniques, Rokas and graduate student Leonidas Salichos assembled and analyzed more than 1,000 genes from each of 23 species of yeast, including Saccharomyces cerevisiae, better known as baker's yeast used to make bread, wine and beer, and Candida albicans, sometimes the source of infections.

"Yeasts are a great model for studying ancient branches, since they have very compact genomes, two orders of magnitude smaller than the human genome," Rokas says. "Humans and chimpanzees branched away from each other relatively recently—only 5 or 6 million years ago. With yeast, we're looking at branching events that took place hundreds of millions of years ago."

Their study, published in the journal Nature, found that the histories of the more than 1,000 genes all were slightly different from one another, as well as different from the genealogy the researchers built from a simultaneous analysis of all the genes.

"We found 1,070 genes, and made 1,070 trees, and each one was different," Rokas says.

"One explanation may have to do with the fact that you are looking at such a small part of the genome," he adds. "It's like trying to sample the skin color of the United States by looking at only one city. You will get different results if you look at New York, or Nashville, or Washington, D.C."

Rokas and Salichos found that genetic data is less reliable during periods of rapid "radiation," or diversification, when there is a sudden appearance of many . "A lot of the debate on the differences in the trees has been between studies concerning the 'bushy' branches that took place in these 'radiations'," Rokas says.

"When you see a lot of conflict, and have lots of data, you expect to see gene differences when you have radiations," he adds. "We don't know what happened. We have 23 yeasts, and what we observed is their DNA sequences in the present. We do these comparisons to try to understand how they came about, and who is most closely related to whom. By looking at these genes, we see consensus in many parts and conflict at the base of the tree. What we understand about evolution leads us to believe that in a small window of time, several new species originated."

The work is important not only because it tackles the enduring mysteries associated with evolution, but, on a practical level, "the process is exactly the same as what we do when we are trying to identify where a new pathogen is coming from," Rokas says. "If there is a new agent of disease or infection, we try to culture it first to see what family of bacteria or viruses it is related to. This allows public health officials to understand very quickly what they are dealing with."

Moreover, "it also allows us to understand the evolution of life on Earth and how a variety of different traits that we associate with different organisms have come about, for example, such characteristics as big brains in humans, compared to other organisms, walking on two legs, loss of hairiness."

Rokas is conducting his research under an NSF Faculty Early Career Development (CAREER) award, which he received in 2009 as part of NSF's American Recovery and Reinvestment Act. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education, and the integration of education and research within the context of the mission of their organization. NSF is funding his work with $688,000 over five years.

The grant's educational goal "is to promote understanding of phylogenetics and its importance for comprehending evolution across the educational continuum," he says, adding that the program has trained three postdoctoral scholars, all of whom have obtained faculty positions, three graduate students, and eight undergraduates, three of whom already have first-author publications. These students include one Hispanic and four women.

The educational component also includes a new undergraduate/graduate course on the computational analysis of genomes; and up to seven advanced graduate training national and international workshops annually, plus numerous lectures at national and international meetings, as well at regional high schools.

If anything, Rokas and his collaborators are discovering that reconstructing the tree of life is anything but simple.

"People expect to find a single tree of life," Rokas says. "They expect there to be one tree that explains how each organism is related to all others."

If that were the case, "then you would expect that different studies would not reach different conclusions," he says. "But you have parts of the tree that are that are easy to infer, where there is consensus, and parts that are challenging. The more ancient the relationships, the harder they are to infer."

His work tries to provide some clarification for why this is the case, "that you should expect to see this when you have these events of rapid diversification, which seemed to have happened rapidly together, at the base of the tree," he says, meaning a very long time ago. "And this means that certain branches of the will be bushy," he says.

Explore further: Sponges squeezed off oldest branch of animal tree

More information: "Inferring ancient divergences requires genes with strong phylogenetic signals." Leonidas Salichos, et al. Nature 497, 327–331 (16 May 2013) DOI: 10.1038/nature12130. Received 06 December 2012 Accepted 28 March 2013 Published online 08 May 2013

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JVK
1 / 5 (10) May 01, 2014
Interesting news about an article published online 08 May 2013

Re: "What we understand about evolution leads us to believe that in a small window of time, several new species originated."

What we know about ecological variation is that it leads to ecological adaptations and species diversity via links from the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. The conserved molecular mechanisms of ecological adaptations have been detailed starting with one-carbon metabolism and the biophysical constraints that prevent mutation-driven evolution.

Instead, nutrient-dependent DNA methylation and the pheromone-controlled physiology of reproduction clearly link ecological variation to ecological adaptation manifested in the morphological and behavioral phenotypes of all species.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
Torbjorn_Larsson_OM
4.6 / 5 (5) May 02, 2014
So massive diversifications take a double hit in phylogenetic resolution, they tend to be old and they tend to involve rapid specification, in both cases persumably because they establish ecological nishes.

Service message to bystanders: don't take the pheromone troll for serious, he is making lies up as he go. The sole intention seems to be to feed his pheromone web business. [Ref: Google his name.] E.g. reproduction and its physiology is not controlled by pheromones. Say, the existence cloning as reproduction mode tests that to rejection. [ http://en.wikiped...oduction ]
TheGhostofOtto1923
3.5 / 5 (6) May 02, 2014
ecological adaptations and species diversity via links from the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man
How are modern western diets affecting the devt of our species? Do you think that refined sugar and msg are morphing us in unnatural directions? Do you think the epidemic of obesity is an example of "ecological adaptation manifested in the morphological and behavioral phenotypes"?

How about all the endocrine disrupters we've been ingesting? And how do fluorine, chlorine, pesticides, and antiseptics affect the biota we are full of?

And what about the agricultural revolution? What were the epigenetic changes which resulted? Would you consider these environmental or not?

Western foods today come from all over the world. What happens when I eat a kiwi fruit? Do you think that this forced amalgamation of global foods is intended to combat the genetic urge to speciate, the true source of tribalism? A conspiracy?
JVK
1 / 5 (6) May 02, 2014
Ecological epigenetics: an introduction to the symposium. See any or all articles from the symposium http://icb.oxford...abstract

Stop your nonsense. Then read any of my reviews:

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Kohl JV.PMID: 24693353 Socioaffect Neurosci Psychol. 2013 Jun 14;3:20553. eCollection 2013. Review.

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Kohl JV. Socioaffect Neurosci Psychol. 2012 Mar 15;2:17338.
.
Human pheromones: integrating neuroendocrinology and ethology.
Kohl JV, Atzmueller M, Fink B, Grammer K.
Neuro Endocrinol Lett. 2001 Oct;22(5):309-21. Review.

From fertilization to adult sexual behavior.
Diamond M, Binstock T, Kohl JV.
Horm Behav. 1996 Dec;30(4):333-53.
TheGhostofOtto1923
3.8 / 5 (4) May 02, 2014
Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Kohl JV. Socioaffect Neurosci Psychol. 2012 Mar 15;2:17338.
You ought to answer at least some of my questions. What is the effect of chocolate on human morphology worldwide? How about fermented grape juice?

What about the introduction of spices and tea in Europe? For that matter what about the chronic ingestion of spoiled foods which created the market for spices in the first place?

Is our taste for salty and fatty foods a cause or an effect of our epigenetic expressions? Are epigenetic expressions deleterious?

What about tobacco and caffeine? Are there morphological expressions which can be attributed to these? How about lead from pipes in ancient rome, or from paint and auto exhaust in recent times?

What exactly are we ingesting that is morphing us into fat, lazy, stupid people? I suspect grains. No self-respecting hunter-gatherer would waste his time eating grass.
TheGhostofOtto1923
3.5 / 5 (4) May 02, 2014
And here's a big one: do any of these culturally-determined and tech-derived uh things have any analogue whatsoever in any other species besides our own? I think not sir. Dogs maybe.

By the way do you eat ham or no? Ah, none of my business.
Anda
3 / 5 (2) May 05, 2014
What do you mean with the ham Ghost? I don't think I like it...

And why someone called JV Kohl wouldn't eat ham. I mean he can talk nonsense and eat ham, right?

Muslims or vegetarians don't eat ham.
So what do you f****** mean?
Uncle Ira
1 / 5 (4) May 05, 2014
Hooyeei, Ol Ira-Skippy is getting smarter me. I saw the name on the thing and know if I peeked that JVK-Skippy would be here selling his stinky love potions.
JVK
1 / 5 (3) May 05, 2014
Cultural evolution:
https://www.faceb...nt_reply

"An odour lexicon: A group of nomadic hunter-gatherers in Thailand have multiple words for smells." May 5th, 2014. http://phys.org/n...ers.html
Uncle Ira
1 / 5 (4) May 05, 2014
Cultural evolution:
https://www.faceb...nt_reply


So do the peoples here JVK-Skippy. We got smells, stinky, putrid, pooyeei, and my favorite one from the google, malodorous. How you like that one? Malodorous? And we got ripe, odoriferous, and more that I can't remember now. How many those Thailand-Skippys got?