Nav: Home

Doubling down on DNA

October 19, 2016

Millions of years ago, one species of frog diverged into two species. Millions of years later, the two frogs became one again, but with a few extra chromosomes due to whole genome duplication. Such is the curious case of the African clawed frog, Xenopus laevis, a frog whose genome contains nearly double the number of chromosomes as the related Western clawed frog, Xenopus tropicalis.

In the evolution of species, different events have occurred over millions of years that have increased the number of chromosomes in some organisms. Polyploidy describes an event that increases the number of copies of each chromosome. Vertebrates have undergone at least two different polyploidy events since their original divergence. While it is relatively rare nowadays to observe a mammal, reptile or bird with an abnormal number of chromosomes, polyploidy is common in fish, amphibians and plants.

Prof. Daniel Rokhsar, Professor of Genetics, Genomics and Development at the University of California, Berkeley and head of the Molecular Genetics Unit at the Okinawa Institute of Science and Technology Graduate University (OIST), Prof. Masanori Taira from the University of Tokyo and Prof. Richard M. Harland from the University of California at Berkeley led groups of researchers in examining the genome evolution of the African clawed frog. This large, collaborative project included scientists from a variety of universities and institutions across the globe. The study, published in Nature and featured on the cover, revealed that the X. laevis genome is comprised of two different sets of chromosomes from two extinct ancestors.

Dr. Oleg Simakov, a postdoctoral scholar in the Molecular Genetics Unit at OIST, developed an algorithm to determine the length of time, in millions of years, between the divergence and subsequent fusion of the X. laevis ancestral species. In order to be able to calculate these times, the X. laevis genome had to be correctly annotated. Annotation involves identifying which regions of DNA contain coding genes or non-coding regions. While automation can simplify this process, many mistakes are made. Dr. Yuuri Yasuoka of the Marine Genomics Unit at OIST helped to manually correct the gene annotation. His graduate studies at the University of Tokyo under the guidance of Prof. Masanori Taira allowed him to develop the skills necessary for his role in this project. "Taking advantage of my experiences on the field of developmental biology, I examined genes involved in developmental processes," he clarified.

Dr. Adam Session, a former graduate student in Prof. Rokhsar's lab at the University of California at Berkeley and co-lead author of the Nature publication, elaborated "The most exciting finding from our study is that we can partition the current X. laevis genome into two distinct sets of chromosomes, each descended from a unique ancestral species. While plant studies have been able to show similar results using related species still in existence, this study is the first time this has been done with two extinct progenitor species".

This large collaborative project resulted in new knowledge of genome duplication that can be applied to evolutionary studies of other organisms. "Because X. laevis is a well-studied model system for cell and developmental biology, it is ideal for to studying the effect of polyploidy on evolution," Dr. Simakov explains.
-end-


Okinawa Institute of Science and Technology (OIST) Graduate University

Related Evolution Articles:

Prebiotic evolution: Hairpins help each other out
The evolution of cells and organisms is thought to have been preceded by a phase in which informational molecules like DNA could be replicated selectively.
How to be a winner in the game of evolution
A new study by University of Arizona biologists helps explain why different groups of animals differ dramatically in their number of species, and how this is related to differences in their body forms and ways of life.
The galloping evolution in seahorses
A genome project, comprising six evolutionary biologists from Professor Axel Meyer's research team from Konstanz and researchers from China and Singapore, sequenced and analyzed the genome of the tiger tail seahorse.
Fast evolution affects everyone, everywhere
Rapid evolution of other species happens all around us all the time -- and many of the most extreme examples are associated with human influences.
Landscape evolution and hazards
Landscapes are formed by a combination of uplift and erosion.
New insight into enzyme evolution
How enzymes -- the biological proteins that act as catalysts and help complex reactions occur -- are 'tuned' to work at a particular temperature is described in new research from groups in New Zealand and the UK, including the University of Bristol.
The evolution of Dark-fly
On Nov. 11, 1954, Syuiti Mori turned out the lights on a small group of fruit flies.
A look into the evolution of the eye
A team of researchers, among them a zoologist from the University of Cologne, has succeeded in reconstructing a 160 million year old compound eye of a fossil crustacean found in southeastern France visible.
Is evolution more intelligent than we thought?
Evolution may be more intelligent than we thought, according to a University of Southampton professor.
The evolution of antievolution policies
Organized opposition to the teaching of evolution in public schoolsin the United States began in the 1920s, leading to the famous Scopes Monkey trial.

Related Evolution Reading:

Evolution: The Human Story, 2nd Edition
by Dr. Alice Roberts (Author)

Theistic Evolution: A Scientific, Philosophical, and Theological Critique
by J. P. Moreland (Editor), Stephen C. Meyer (Editor), Christopher Shaw (Editor), Ann K. Gauger (Editor), Wayne Grudem (Editor), Steve Fuller (Editor), Douglas Axe (Editor), C. John Collins (Editor), John D. Currid (Editor), Guy Prentiss Waters (Editor), Gregg R. Allison (Editor), Fred G. Zaspel (Editor), Matti Leisola (Editor), James M. Tour (Editor), Winston Ewert (Editor), Jonathan Wells (Editor), Sheena Tyler (Editor), Günter Bechly (Editor), Casey Luskin (Editor), Paul A. Nelson (Editor), Ola Hössjer (Editor), Colin R. Reeves (Editor), Stephen Dilley (Editor), Garrett J. DeWeese (Editor), Tapio Puolimatka (Editor), John G. West (Editor)

Evolution: A Visual Record
by Robert Clark (Author)

Darwin Devolves: The New Science About DNA That Challenges Evolution
by Michael J. Behe (Author)

Why Evolution Is True
by Jerry A. Coyne (Author)

Evolution
by Douglas J. Futuyma (Author), Mark Kirkpatrick (Author)

Dr. Gundry's Diet Evolution: Turn Off the Genes That Are Killing You and Your Waistline
by Steven R. Gundry (Author)

Grandmother Fish: A Child's First Book of Evolution
by Jonathan Tweet (Author), Karen Lewis (Illustrator)

Evolution & Classification of Life Poster 24x36"
by UsefulCharts.com (Author)

Sydney Brenner's 10-on-10: The Chronicles of Evolution
by Sydney Brenner (Author), Shuzhen Sim (Editor), Benjamin Seet (Editor)

Best Science Podcasts 2018

We have hand picked the best science podcasts for 2018. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Circular
We're told if the economy is growing, and if we keep producing, that's a good thing. But at what cost? This hour, TED speakers explore circular systems that regenerate and re-use what we already have. Guests include economist Kate Raworth, environmental activist Tristram Stuart, landscape architect Kate Orff, entrepreneur David Katz, and graphic designer Jessi Arrington.
Now Playing: Science for the People

#504 The Art of Logic
How can mathematics help us have better arguments? This week we spend the hour with "The Art of Logic in an Illogical World" author, mathematician Eugenia Cheng, as she makes her case that the logic of mathematics can combine with emotional resonance to allow us to have better debates and arguments. Along the way we learn a lot about rigorous logic using arguments you're probably having every day, while also learning a lot about our own underlying beliefs and assumptions.