Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Genetic analysis rewrites salamander family tree

14.09.2004


Biologists take for granted that the limbs and branches of the tree of life - painstakingly constructed since Linnaeus started classifying organisms 270 years ago - are basically correct. New genetic studies, the thinking goes, will only prune the twigs, perhaps shuffling around a few species here and there.


A salamander from the genus Hydromantes, one of the lineages that was reshuffled in the family tree as a result of a new genetic analysis of the lungless salamanders. (Rachel Mueller/UC Berkeley)



Hence the surprise when a new University of California, Berkeley, study of the largest family of salamanders produced a genetic family tree totally inconsistent with the accepted classification, which is based primarily on physical features.

Salamanders formerly classified together because of similar characteristics, such as a tail that breaks at only one spot as opposed to anywhere when stressed, now appear not to be close relatives at all. And salamanders that go through an aquatic larval stage are scattered about on different branches instead of grouped on one limb of the tree: Apparently some salamander lineages lost the larval stage and then reacquired it again.


"For 40 years, we have had a very clear understanding of the evolutionary history of the largest family of salamanders, Plethodontidae," said David Wake, professor of integrative biology at UC Berkeley and an expert on salamanders. "We thought they arose in Appalachian mountain streams and then diverged in a highly patterned way, sequentially abandoning larvae for direct development, gaining highly specialized, projectile tongues, et cetera." "The results were stunningly different than what we anticipated," he said. "Only one of the currently recognized four major groups is supported."

The study, published this week in the online edition of the Proceedings of the National Academy of Sciences, was conducted by Wake’s graduate student, Rachel Mueller, to understand the evolution of the Plethodontid salamanders, a family that comprises 360 species - two-thirds of the world’s 522 known species of salamander. Known for being one of few landlubbing vertebrates without lungs - they breathe through their skin - Plethodontids were thought to have originated in the Appalachians because the southern portion of that chain has the greatest diversity of species.

The new family tree, constructed by comparing the mitochondrial genomes of 22 representative Plethodontid species and five others from different salamander families, offers no support for the out-of-Appalachia theory, Mueller said. "We can infer only a North American origin," Mueller said. "Most likely, where these species are now doesn’t relate to where they were ages ago, because the climate and geology have changed so much, and the species have moved around."

Though results from this one family of vertebrates can’t necessarily be generalized to other families, Mueller said, "this does tell us that, when reconstructing evolutionary relationships, you have to be careful which morphological features you assume are conservative and haven’t evolved much, and which you think are likely to have changed over time."

Three years ago, Mueller teamed up with the Joint Genome Institute (JGI) in Walnut Creek, Calif., to sequence the complete mitochondrial genomes of 24 salamanders, all but two of them Plethodontids. The mitochondrial genome is smaller than the nuclear genome, containing only 37 complete genes in most animals - just those needed to produce energy for the cell. They’re inherited without recombination from the mother, and therefore represent an unbroken female chain going back perhaps 100-150 million years in plethodontid salamanders. By looking at mutations in the mitochondrial DNA, biologists can infer the pattern of evolution. "What is happening now is that by focusing on mitochondrial genes and adding particular nuclear genes, we really are teasing apart issues related to our understanding of the tree of life," Wake said.

Mueller obtained DNA samples from frozen salamander tissue in the collection of UC Berkeley’s Museum of Vertebrate Zoology, and over a two-year period worked with JGI researchers to sequence the brief genomes. Once Mueller annotated the genomes, that is, identified the genes, she compared the complete genome sequences with three other known mitochondrial genomes, for a total sample of 27 species. Using Bayesian statistical techniques, she was able to reconstruct a "robust" family tree of the Plethodontid salamanders.

One feature that has been used to classify salamanders is their larval stage, much like the tadpole stage of frogs. The ancestral Plethdontid salamanders, like all other salamanders, apparently went through a larval stage in fresh water, where the eggs are laid, before losing their gills and swimming tails and emerging onto land. Salamanders that evolved to live totally out of the water, however, lost the larval stage, emerging from the egg as a smaller version of an adult.

The new family tree shows, however, that some terrestrial salamanders regained their larval stage after moving back to the water. This may have happened in three separate lineages of Plethodontids, which is surprising for a seemingly complex feature biologists have assumed arose just once, very early in the history of salamanders.

Tongues also are distinctive in plethodontid salamanders, coming in three different types: ones attached to the jaw so they stick out only slightly; tongues attached by a stretchy muscle, which allows them to be thrown out an appreciable distance to snag food; and so-called "ballistic" tongues that have no muscular attachment at the tip and can be hurled out nearly the length of the salamander’s body. Wake has shown in previous studies that these tongues are not a good way to classify salamanders, because the various types of tongues have evolved several times in different lineages. The new data confirm that, Mueller said.

Mueller’s coauthors, in addition to Wake, include Jeffrey L. Boore, adjunct professor of integrative biology at UC Berkeley and director of evolutionary genomics at JGI; herpetologist and evolutionary biologist Robert Macey of JGI; and former visiting student Martin Jaekel. Mueller, Wake, Macey and Jaekel also are associated with UC Berkeley’s Museum of Vertebrate Zoology.

Robert Sanders | EurekAlert!
Further information:
http://www.berkeley.edu

More articles from Life Sciences:

nachricht Meadows beat out shrubs when it comes to storing carbon
23.11.2017 | Norwegian University of Science and Technology

nachricht Migrating Cells: Folds in the cell membrane supply material for necessary blebs
23.11.2017 | Westfälische Wilhelms-Universität Münster

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Frictional Heat Powers Hydrothermal Activity on Enceladus

Computer simulation shows how the icy moon heats water in a porous rock core

Heat from the friction of rocks caused by tidal forces could be the “engine” for the hydrothermal activity on Saturn's moon Enceladus. This presupposes that...

Im Focus: Nanoparticles help with malaria diagnosis – new rapid test in development

The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.

Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

Im Focus: Novel Nano-CT device creates high-resolution 3D-X-rays of tiny velvet worm legs

Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.

During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

Underwater acoustic localization of marine mammals and vehicles

23.11.2017 | Information Technology

Enhancing the quantum sensing capabilities of diamond

23.11.2017 | Physics and Astronomy

Meadows beat out shrubs when it comes to storing carbon

23.11.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>