Scientists discover a way to sequence DNA of rare animals

Date: January 25, 2017
Source: Louisiana State University

Rare and extinct animals are preserved in jars of alcohol in natural history museum collections around the world, which provide a wealth of information on the changing biodiversity of the planet. These preserved specimens of snakes, lizards, frogs, fish and other animals can last up to 500 years when processed in a chemical called formalin. While formalin helps preserve the specimen making it rigid and durable, it poses a challenge to extracting and sequencing DNA. Furthermore, DNA degrades and splits into small fragments over time. This fragmented DNA is difficult to amplify into long informative stretches of DNA that can be used to examine evolutionary relationships among species when using older DNA sequencing technology. Therefore, scientists have not been able to effectively sequence DNA from these specimens until now.

LSU Museum of Natural Science Curator and Professor Christopher Austin and his collaborator Rutgers-Newark Assistant Professor Sara Ruane developed a protocol and tested a method for DNA sequencing thousands of genes from these intractable snake specimens. Their research was published today in the international scientific journal Molecular Ecology Resources.

"Natural history museums are repositories for extinct species. Unfortunately, naturalists in the 1800s were not collecting specimens for analyses we conduct today such as DNA sequencing. Now with these new methods, we can get the DNA from these very old specimens and sequence extinct species like the Ivory Billed Woodpecker, the Tasmanian Wolf and the Dodo Bird," Austin said.

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DNA Sequencing Shows Evolutionary History Of Butterflies

August 2, 2014

April Flowers for redOrbit.com – Your Universe Online

In the first study of its kind to use large-scale, next-generation DNA sequencing, a team of researchers from the University of Florida have traced nearly 3,000 genes to the earliest common ancestor of butterflies and moths. The findings, to be published in the Proceedings of the Royal Society B: Biological Sciences, create an extensive “Tree of Lepidoptera” and build the evolutionary framework for future ecological and genetics insect research.

Several of the study’s findings were surprising, including the discovery that butterflies are more closely related to small moths than to larger ones. This one finding completely changes the previously held ideas of butterfly evolution. The study also increased the number of butterfly species known by identifying that some previously classified moths were actually butterflies.

“This project advances biodiversity research by providing an evolutionary foundation for a very diverse group of insects, with nearly 160,000 described species,” said Akito Kawahara, assistant curator of Lepidoptera at the Florida Museum of Natural History on the UF campus. “With a tree, we can now understand how the majority of butterfly and moth species evolved.”

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DNA Sequences Reveal the True Identity of the Softshell Turtle Pelodiscus - via Herp Digest

Oct. 5, 2011 — Science News- A research team from the Senckenberg Research Institute Dresden has identified many different genetic lineages in the softshell turtle genus Pelodiscus, representing different species. Traditionally it has been assumed that only the species Pelodiscus sinensis belonged to the genus examined. As a foodstuff, Chinese softshell turtles are the most economically important turtles in the world, with an annual trade volume of many hundreds of millions of specimens.

The accompanying study is being published September 23, 2011 in the Journal of Zoological Systematics and Evolutionary Research.

It is probably safe to say that none of the 300 million turtles that land on a plate in China each year are particularly interested to know the species to which they belong, but for scientists the discovery of different genetic lineages is of enormous significance. Due to its ease of breeding the turtle is often used as a model organism for embryological and physiological studies, so that a correct identification of the species is of paramount importance, not only in the fields of taxonomy and systematics.

Prof. Uwe Fritz, one of the Dresden authors of the study, confirms this: "While until now these turtles have been used as models in many scientific works, nobody actually knew what species they were. This led to considerable contradictions or non-reproducible results, because different species were used in different publications."

The Chinese softshell turtle (Pelodiscus sinensis) is a strange looking animal: its shell is -- as the name already suggests -- soft, the long neck is flexible enough to allow the reptile even to see behind himself, and the trunk-like nose proves to be an excellent snorkel in shallow waters. Around the world there are more than 300 different turtle species, only 30 of which have a soft shell. Instead of an ossified shell, the softshell turtles, with a length of up to 30 centimetres, have a leather-like, flexible skin on their back and belly.

Together with his colleague Heiko Stuckas, Fritz examined the DNA of two 180-year-old softshell turtle shells from the Berlin Natural History Museum (Museum für Naturkunde). In 1834 the greatly shrunken and dried-out samples had served the German zoologist Arend Friedrich August Wiegmann as a basis for describing the species Pelodiscus sinensis.

Tiny pieces of tissue were removed from the shells by the Dresden researchers and parts of the genetic makeup of the turtles were defined with the help of the most up-to-date techniques. What is promising here is above all the analysis of the mitochondrial DNA, as these are present to a much greater degree compared to the DNA of the cell nucleus, thus minimising conservation problem.

Unfortunately, the attempt to gain DNA from the first turtle shell failed completely -- the remnants of the animal were simply too old and too dried out. However, the second shell proved to be a great success for the research team! The analysis of the DNA sequences led to the conclusion that the genus Pelodiscus contains at least four and not -- as previously believed -- one species. For the first time, and with the help of the sequences from the Berlin sample, which is more or less the "original standard" for the species Pelodiscus sinensis, it could be clarified which of the four species is actually the "real" Chinese softshell turtle.

This finding is not only of great importance to the field of science; the turtles themselves can also benefit. At present all species that are collated under Pelodiscus sinensis have been placed on the red list of endangered species by the International Union for Conservation of Nature and Natural Resources (IUCN). However, some of the "newly discovered" species could actually be considered to be even more seriously endangered at present and may therefore enjoy greater protection.

In future, due to the results of the research, the different species will no longer be "lumped together" -- at least by scientists -- but rather can now be named precisely.

New predator enters Australian waters

TWO years ago, recreational fisherman Steve Downs was deep-sea fishing near Rottnest Island when he caught two sharks he was unable to identify. 

It turns out the species had never been seen in Australian waters before.

Mr Downs contacted the Department of Fisheries, which then brought in shark biologist Ryan Kempster, of the University of Western Australia's oceans institute, to try to determine what type of shark it was and whether or not it was a new species.

Fisheries experts in WA have previously spoken about how much there is still to be learnt about sharks, which, in addition to the recent five fatal shark attacks in the state, is why the government has put millions of dollars into shark research. 

What followed was a two-year investigation that included DNA sequencing. 

Mr Kempster said this process proved difficult. 

''DNA sequencing between closely related sharks can be tricky, as it can be so similar,'' he said. ''When I saw them, they had characteristics of many different sharks but not all the characteristics of one species.'' 

The mystery sharks were a male that was just under a metre long and a pregnant female that was about 1.2 metres long. 

The sharks have now been identified as Mandarin dogfish (Cirrhigaleus barbifer), pictured above, a species previously found only between Indonesia and Japan, and also in New Zealand. 

Read more: http://www.smh.com.au/environment/animals/new-predator-enters-australian-waters-20130228-2f965.html#ixzz2OCP1CyBe

Sri Lankan Snake Study Reveals New Species, Rich Biodiversity in Island Country

Mar. 12, 2013 — Alex Pyron's expertise is in family trees. Who is related to whom, who begat whom, how did they get where they are now. But not for humans: reptiles.

In 2011, his fieldwork in Sri Lanka studying snake diversity on the island led him to confirm the identity of 60 known species of snakes. With Sri Lankan collaborators, Ruchira Somaweera, an author on snakes and expert on amphibians and reptiles, and Dushantha Kandambi, a local naturalist and snake expert, the team collected the snakes and of those, Dr. Pyron used DNA sequencing technology on 40 of them. The study led to a greater understanding of how all the snakes are related to each other and their evolutionary relationship other species globally.

"We found that Sri Lanka has been colonized by snakes at least five times by totally different snake groups, which have each diversified heavily within the island," said Dr. Pyron, the Robert Griggs Assistant Professor of Biology at George Washington University in the Columbian College of Arts and Sciences.

Alex Pyron uses DNA sequencing to learn the history of native snakes. 

(Credit: Image courtesy of George Washington University)

Dr. Pyron's findings were recently featured in the March edition of the journal Molecular Phylogenetics and Evolution.

One finding was a blindsnake, which on its own would be noteworthy but in this case, the blindsnake had a history on the island.

"Molecular data, or DNA, has revolutionized all fields, whether finding genes for cancer or detecting new species. In my field, uses of DNA are twofold: to discover if populations are really new species and two, to determine how species are related. We were able to do both of these things in Sri Lanka. We discovered the blindsnake and we suspected it was a new species, but when we sequenced it, we discovered that it was an entirely new lineage of blindsnake. It's still a blindsnake, but a new genus, a group of blindsnakes that had never been discovered or described.

Continued:  http://www.sciencedaily.com/releases/2013/03/130312134910.htm

Mediterranean sharks are Australian immigrants

Antipodean great whites took a wrong turn on the way to South Africa.

Joseph Milton

The elusive great white sharks of the Mediterranean Sea may be descended from a single small Australian population that lost its bearings while visiting South Africa 450,000 years ago.


The great whites (Carcharodon carcharias) were probably returning to the Antipodes but became trapped after passing through the Straits of Gibraltar, according to a team led by marine biologist Leslie Noble of the University of Aberdeen, UK. The sharks have since made the Mediterranean their home because they reproduced there and, like salmon, the young always return to their birthplace.

Little is known about Mediterranean great whites — sightings are rare and tissue samples even rarer — but Noble and his colleagues teamed up with Turkish researchers to get access to samples from four sharks caught in fishing nets: two from Turkey, one from Tunisia and another from Sicily.

Their research, published today in Proceedings of the Royal Society B1, suggests that a combination of climate change, high sea levels and strong ocean currents around the South African coast could have driven the migrating Australian sharks off-course, up the west coast of Africa and east into the Mediterranean. But because the initial population was small, genetic variability in modern Mediterranean sharks seems to be limited — indicating that a lack of diversity could threaten their future survival. Female sharks from the nearby Atlantic do not seem to be migrating to the region, where they could help to replenish the stagnant gene pool.

Lost at sea
The researchers sequenced an area of the four sharks' mitochondrial DNA — DNA that is passed onto offspring from the mother and encodes proteins from cells' energy factories. The team was then able to compare the genetic code with a bank of sequences derived from great whites in waters of different parts of the world, including South Africa, Australia and the Atlantic.

Noble says the team was surprised to find that the section of DNA sequenced was identical in three of the four Mediterranean sharks, and showed that they were most closely related to Australian great whites. The team had expected to see more affinity with the nearer Atlantic or western Indian Ocean populations.

Great white sharks were once thought of as a coastal species, but research has shown that they migrate long distances in the open ocean — although scientists do not know exactly why. Tagged sharks have been seen travelling between the coasts of South Africa and southern Australia, and the authors suggest that it was probably during one of these excursions that a group took a wrong turn.

The researchers used a molecular dating technique based on the number of differences between the DNA of the Mediterranean and Australian sharks to estimate that the sharks got lost during the Pleistocene epoch, around 450,000 years ago. Noble says that this was an period between ice ages: a time of high sea levels, climate change and, perhaps most importantly, an unusually fast-flowing ocean eddy off the east coast of South Africa called an Agulhas ring — which may explain why the sharks went so far astray.


The warm Agulhas Current flows down the east coast of Africa, but periodically an Agulhas ring carries its waters around the southern tip of the continent and into the Benguela Current off the west coast. "When sharks follow the Agulhas Current, the cooler waters of the Benguela probably alert them to turn east," says Nelson, "but an Agulhas ring is like a warm-water bubble." A group of sharks swimming in one of these bubbles could miss the turning and find the western coast of Africa between it and its desired destination.

The researchers speculate that the sharks then swam north until the Mediterranean basin gave them a chance to head east again. Once in the basin, they may have become trapped by the peninsulas and narrow channels of the Medterranean.

A population in peril
Paulo Prodöhl, an evolutionary geneticist at Queen's University Belfast, UK, says that although the finding "comprises a precious and unique data set, the sample sizes are really too small to draw conclusive inferences". But he admits that because shark samples are so hard to get hold of, "you have to work with what you can get".

"We recognize the sample-size problem," says Noble. "We're trying to get another 50 Mediterranean samples, which could dramatically change our inferences — we're very keen to access museum material."

But, he says, "I don't think it removes the central tenet — that as far as we're aware, a significant proportion of the Mediterranean sharks are Australian in origin."


Noble also hopes that the work will highlight the plight of a potentially fragile shark population surviving in a polluted and over-fished sea. He says that great whites occupy a "pivotal role" in the Mediterranean, and the removal of top predators from other marine ecosystems has been disastrous.

"On the east coast of America, shark eradication has caused an 'ecological cascade'," says Noble. Populations of species on which sharks prey, such as seals and dolphins, have exploded, unbalancing the whole system. "It's been instrumental in helping kill off some of the shellfish," says Noble. "I wouldn't like to speculate on the consequences for the Mediterranean if this population became extinct."

http://www.nature.com/news/2010/101117/full/news.2010.616.html