Subscribe free to our newsletters via your
. Earth Science News .




WOOD PILE
Evolutionary trees reveal patterns of microbial diversification
by Staff Writers
Urbana IL (SPX) Jul 16, 2015


This is James O'Dwyer, assistant professor of plant biology and member of the Carl R. Woese Institute for Genomic Biology at the University of Illinois. Image courtesy Brian L. Stauffer. For a larger version of this image please go here.

While teaching a class on coarse-graining methods in physics, James O'Dwyer realized that the technique could be used to understand how microbes evolve over time. The results, published in PNAS, reveal microbial family trees with distinct evolutionary patterns that may one day help us understand how harmful microbes evolve.

"The species concept is difficult for microbes," said O'Dwyer, an assistant professor of plant biology and member of the Carl R. Woese Institute for Genomic Biology at the University of Illinois.

Microbes typically reproduce asexually, which makes it difficult to use the traditional biological species concept, which defines species as organisms that can reproduce together. Ecologists and microbiologists have often lumped microbes with similar DNA sequences together as effective, `operational' taxonomic (or classification) units.

In this paper, O'Dwyer and co-authors Steven Kembel from the Universite du Quebec a Montreal and Thomas Sharpton from Oregon State University have sorted these sequence data into a new kind of family tree, that displays sudden bursts of diversification. This is likely the first time that coarse-graining, a physics principle, and ?-coalescents, a set of mathematical models, have been used to address questions in ecology.

What are phylogenetic trees?
A family tree, also known as a phylogenetic tree, uses DNA to show how new species have evolved over time. Phylogenetic trees are typically binary: each branch splits into two distinct lineages and each of those branches eventually splits into two further distinct lineages, and so on. The longer the branch, the longer that lineage persisted before it evolved, or diversified.

When diversification happens relatively quickly, and multiple lineages have similar genes, a branch could appear to split into multiple branches, instead of just two. Ordinarily, biologists would try resolve this ambiguity, by figuring out the order in which lineages diversified.

Introducing a new phylogenetic tree
"In this paper, the lack of knowledge [about microbial taxonomy] is treated as a virtue," O'Dwyer said.

Using phylogenetic trees to understand diversification is like using Google Maps to understand automobile travel, said O'Dwyer. You can zoom in to look at detailed information, studying individual city streets, or you could zoom out to look at the bigger picture of how people are moving across the state using interstates.

So far, ecologists have typically used phylogenetic trees that are "zoomed in" to show all the branches. In this paper, coarse-graining condenses many short binary branches into large nodes that suddenly split into multiple branches, resembling the tines of a fork.

The result is a simpler, "zoomed out" tree that shows bursts of diversification over time. These bursts were found in phylogenetic trees created for 22 microbial communities, chosen to represent a breadth of habitat types: plant, marine, and human gut and skin.

"They provide us with an echo of real ecological processes, like adaptive radiations, when an organism rapidly diversifies due to a change in environment or to fill a new niche," O'Dwyer said. "And these bursts are there throughout these phylogenetic trees, deep within their history."

Finding an ecological theory that fits
The authors tried to use a controversial ecological theory (called neutral theory) to quantitatively describe these patterns. According to this theory, all species are selectively equal; population success or failure is random, like the flip of a coin. Neutral theory trees exhibit gradual diversification, rather than sudden bursts. Instead, they found another family of mathematical models, called ?-coalescents, are better able to describe the unique patterns of diversification.

Real-world applications and future work
These ecological patterns may help us understand the diversification of harmful microbes. The same patterns may also be found in other parts of the tree of life, helping us to understand when and how new species evolve over time.


Thanks for being here;
We need your help. The SpaceDaily news network continues to grow but revenues have never been harder to maintain.

With the rise of Ad Blockers, and Facebook - our traditional revenue sources via quality network advertising continues to decline. And unlike so many other news sites, we don't have a paywall - with those annoying usernames and passwords.

Our news coverage takes time and effort to publish 365 days a year.

If you find our news sites informative and useful then please consider becoming a regular supporter or for now make a one off contribution.

SpaceDaily Contributor
$5 Billed Once


credit card or paypal
SpaceDaily Monthly Supporter
$5 Billed Monthly


paypal only

.


Related Links
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
Forestry News - Global and Local News, Science and Application






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle




Memory Foam Mattress Review
Newsletters :: SpaceDaily :: SpaceWar :: TerraDaily :: Energy Daily
XML Feeds :: Space News :: Earth News :: War News :: Solar Energy News





WOOD PILE
Kidnappers free 12 loggers in Senegal's Casamance: army
Kolda, Senegal (AFP) July 13, 2015
Twelve loggers who were kidnapped four days ago in the southern Casamance region of Senegal have been freed, an army source said Sunday. "We have just observed the return of the 12 forestry workers... in the village of Kolling" on Sunday, the source in the town of Kolda told AFP, requesting anonymity. The kidnappers freed them in the Yassine forest, the source added, saying he had no mor ... read more


WOOD PILE
Free meals offer comfort to Nepal quake victims

Nepal unveils subsidy-heavy $8.19 bn post-quake budget

S. Korea selects China consortium for Sewol ferry salvage

Global warming to fuel migration, terrorism: report

WOOD PILE
Lower cost ultrasound degassing now possible in processing aluminum

New computer program may fix billion-dollar bit rot problem

Brownian motion phenomena of self-powered liquid metal motors

Omnidirectional free space wireless charging developed

WOOD PILE
Rescue saves rare Philippine turtles from 'brink of extinction'

Strong El Nino not expected to answer California drought

China begins construction of 'world's tallest' dam

Managing mining of the deep seabed

WOOD PILE
Strong geothermal heating measured beneath West Antarctic Ice Sheet

Study predicting 'mini ice age' is being second-guessed

Study finds high geothermal heating beneath West Antarctic Ice Sheet

Has US Already Lost in the Arctic

WOOD PILE
Potential of blue LEDs as novel chemical-free food preservation technology

3-D printers poised to have major implications for food manufacturing

Oregon study suggests organic farming needs direction to be sustainable

After China woes, Vietnam's lychee farmers head to new markets

WOOD PILE
NanoSIMS ion probe measures volcanic cycles at Yellowstone

Submerged volcanoes found off Sydney

Bali tackles backlog after volcano hits nearly 900 flights

Hundreds evacuate as Mexico's 'Volcano of Fire' erupts

WOOD PILE
Nigeria's Buhari sacks top military chiefs

At least 11 dead in twin suicide bombing in Cameroon

US condemns 'horrific' attacks by Boko Haram in Chad

South Sudan: four years of freedom, 18 months of war

WOOD PILE
Continued destruction of Earth's plant life places humans in jeopardy

Indonesia jails orangutan trader caught with baby ape

Fossils indicate human activities have disturbed ecosystem resilience

Neuroscientists establish brain-to-brain networks in primates, rodents




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. All websites are published in Australia and are solely subject to Australian law and governed by Fair Use principals for news reporting and research purposes. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA news reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement, agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement All images and articles appearing on Space Media Network have been edited or digitally altered in some way. Any requests to remove copyright material will be acted upon in a timely and appropriate manner. Any attempt to extort money from Space Media Network will be ignored and reported to Australian Law Enforcement Agencies as a potential case of financial fraud involving the use of a telephonic carriage device or postal service.