The way of the digital dodo

Wednesday, June 10th, 2009

scanned dodo renderedAn early version of the scanned dodo rendered by project research technician Abby Drake and students in Leon Claessens’ lab.

From PhysOrg, The way of the digital dodo: The laser light glowed brilliant red, forming a moving line as it bounced information from the dodo’s bones back into the high-tech scanner sitting on a tripod on the Museum of Comparative Zoology’s (MCZ) fifth floor.

Again and again, the red line traced the contours of the skeletal bird, one of just a handful of complete skeletons of one of the world’s most famous cases of human-caused extinction.

The flightless bird, about the size of a large turkey, was native to the Indian Ocean island of Mauritius. It became extinct in the mid- to late-1600s from a combination of human hunting, habitat destruction, and predation by introduced animals, including rats, cats, pigs, and dogs.

The laser’s tracings were creating a 3-D digital model of the skeleton, compiled as part of a joint effort between the MCZ’s ornithological collection, overseen by Professor of Organismic and Evolutionary Biology Scott Edwards, and Holy Cross College biologist Leon Claessens, an assistant professor whose doctoral work at Harvard and familiarity with the MCZ’s collections led to the collaboration. Claessens received his doctorate in 2006.

The National Science Foundation-funded, three-year effort aims to create 3-D digital models of each species represented in Harvard’s collection of 12,000 bird skeletons. It will make those digital models available on the Internet for researchers around the world. The collection’s digitization will not only vastly expand access to the collections for researchers who can’t afford to travel to Cambridge, it will also make analysis of the specimens far more rapid, using powerful engineering software that creates thousands of data points on each bone that can be manipulated, measured, and used in calculations.

“This project will be useful for people studying the basic morphology of birds,” Edwards said. “In this era of genomics, the size and shape of bones is still very important.”

Claessens, who has been scanning with a group of his students since the “Aves 3D” project got under way in August, said much of the effort is aimed at disarticulated bones of specimens, so that the scanner can image the entire bone, including the ends and surfaces that might not be accessible in an assembled specimen. Researchers interested in the shape and size of a particular bone across different species will be able to call up those bones digitally, rather than traveling to individual museums with calipers, pencil, pad, and camera, as would be required today. Those interested in other aspects of anatomy can manipulate the bones digitally, even reassembling the bird if needed.

Keep reading on PhysOrg.

Dodo Skeleton Found on Island

Tuesday, September 11th, 2007

Dodo Skeleton Found on Island

Dodo Skeleton Found on Island, May Yield Extinct Bird’s DNA by Kate Ravilious for National Geographic News:

Adventurers exploring a cave on an island in the Indian Ocean have discovered the most complete and well-preserved dodo skeleton ever found, scientists reported yesterday.

Researchers say the find would likely yield the first useful samples of the extinct, flightless bird’s DNA.

If you follow this blog, you know I already linked to the same news on the posts Bones Could Yield Dodo DNA and Flightless Fred has scientists in raptures. However, that National Geographic article is good, as usual, and there more additional information on it.

Until now most of the information about dodos has come from scattered bone fragments. Only one other full skeleton was ever unearthed—in the 1860s—but it has been of limited scientific value, because the person who discovered it never revealed where it was found.

“We need to know about the location to understand the ecology of the dodo,” said Kenneth Rijsdijk, a scientist with Geological Survey of the Netherlands, who plans to study the environment in which the newfound bird was discovered.

The site of the new dodo skeleton and the layout of its bones has been precisely recorded, making the find already very useful to scientists, he added.

“We can take soil samples and discover how and why the animal got there,” Rijskijk said.

What’s more, the location of the new skeleton makes it much more likely to yield DNA, said Beth Shapiro, a geneticist from Oxford University who studies dodo remains. […]

The cave site of the new skeleton is likely to provide the best hope of a decent DNA sample because the bones will not have been exposed to sunlight and the temperature was fairly constant, she added.

“We are really excited about the new find and hope it might tell us much more about the behavior and appearance of dodos,” Shapiro said.

PS.: Photograph from Reuters, inset illustration from Getty Images.

Flightless Fred has scientists in raptures

Friday, August 24th, 2007

Dodo picture from Stuff.co.nz

After Bones Could Yield Dodo DNA, the same news at Stuff.co.nz: The remains of a dodo found in a cave beneath bamboo and tea plantations in Mauritius offer the best chance yet to learn about the extinct flightless bird, a scientist has said.

Update: Unfortunately the link to the news was removed.

Bones Could Yield Dodo DNA

Friday, August 24th, 2007

Bones from the dodo’s foot

From LiveScience Bones Could Yield Dodo DNA: A newly discovered dodo skeleton has raised hopes for extracting some of the legendary extinct bird’s DNA.

Fred the dodo

Late last year, biologists looking for cave cockroaches accidentally discovered a dodo skeleton in the highlands of Mauritius.

Nicknamed “Fred” after one of its discoverers, the skeleton’s bones were badly decomposed and fragile, but there is still a good chance of extracting some dodo DNA because of the stable temperature and dry to slightly humid environment (keys to DNA preservation) of the cave.

(Scientists think Fred ended up in the bottom of the cave because he sought shelter from a violent cyclone but fell down in a deep hole and could not climb out.)

Dodo DNA would be of great scientific value because scientists know very little about the genetics of the dodo. Also, it would allow scientists to figure how long the skeleton was lying in the cave.

Keep reading on LiveScience.

Dodo excavation 2007

Wednesday, August 22nd, 2007

Dido

Do you remember the Dodo Expeditie Weblog? They are back with back. Or I rather say, they were back with the Dodo excavation 2007, because it ended in August 19th. The expedition was documented in a blog, as the previous one, with English and Dutch. The Dutch has a link the images of the new mascot Dido.

The expedition started with a fantastic new discover in its first day, July 29:

As soon as we set foot on Mauritius we headed for an excursion into the vast system of lavatunnels on the hilly side of the island. In the shadow of Julian Hume we entered a cave where speleologists discovered a complete dodoskeleton, only a month ago. This would be the first ever discovered in the Mauritian highlands. Soon it pointed out that also we would be lucky in the catacombs. In the smal chamber where the dodoskeleton was found Julain discovered the pelvis of the extinct Mauritian owl (Mascarenotus sauzieri)! Before this moment nobody knew this part of the postcranial skeleton of this species, it simply never was found. The Mauritian owl was the size of a forest owl, but had much bigger paws to kill reptiles. A most important find. How did the dodo and the owl ended in the cave, and how did they enter? Questions that immediately came to our minds and that we hopefully can answer with future research.

Dido find an owl bone

There are more information (and images) about this last expedition on their weblog posts. Check also the links on the main page of the expedition, including the Research plan. But before, a couple of Dido images:

Dido and the bones

Dido Goodbye

The Dodo Life of Long Ago

Wednesday, January 10th, 2007

Bones found recently on its home, Mauritius

A New York Times‘ article from July about the new expedition to explore Mauritius’ sites: Newfound Island Graveyard May Yield Clues to Dodo Life of Long Ago:

The origins of the dodo are mysterious. Studies on its DNA indicate that it descended from pigeons. The dodo’s closest relative was the solitaire, another extinct flightless bird that lived only on the nearby island of Rodrigues. […]

Plant-eating mammals play a major role in shaping their ecosystems. Dodos may have thinned the Mauritius forests, and some plants may have come to depend on them to spread their seeds.

With almost no fossils to study, scientists had been unable to test these ideas. Now it will be possible, thanks to the discovery of the dodo graveyard. Dr. Rijsdijk and Frans Bunnik, also of the Geological Survey of the Netherlands, found it almost by accident. […]

Based on the underlying geology of the site, Dr. Rijsdijk estimates that it is 3,000 years old. More precise dating based on carbon isotopes is now under way.

Dr. Rijsdijk said that the fossils appeared to have formed in a forest lake. A big storm may have washed the animals and plants into the lake, where their bones settled into a single layer.

“Think of it like a snapshot,” Dr. Burney of Fordham said. “You set up a big camera and photograph the landscape at a particular instance. You’ve got the dodos and the other species, all captured in a moment.”

The scientists are now studying the material more carefully. Some are looking for ancient DNA, while others will analyze the dodo bones to get clues to their diet. “We may be really be able to shine a light on the dodo’s role in the ecosystem,” Dr. Rijsdijk said. The scientists will present early findings at the University of Oxford in September and will return to Mare aux Songes in 2007.

By understanding the Mauritius ecosystem before humans arrived, they hope to find clues to the dodo’s extinction. Dodos were easy to hunt, but hunting alone probably did not wipe them out. Recent research indicates that the early Dutch settlers rarely ate dodo meat. Nor did the deforestation of the island doom the dodo. Major forest clearing did not begin until after the dodo became extinct.

BTW, use Firefox and the bug me not extension to read the article if you don’t want to create an account there.

Dodos killed by natural disaster

Monday, July 3rd, 2006

From Reuters: Scientists say dodos killed by natural disaster. Scientists who unearthed a mass dodo grave in Mauritius say they have found evidence showing the birds were killed by a natural disaster long before humans arrived on the Indian Ocean island.

“There are indications that the fossil-rich layer represents the result of natural disaster wiping out a significant part of the Dodo-ecotope,” a statement by the researchers said.

While the latest find does not disprove the human theory, the scientists are convinced there was a mass dodo death, possibly caused by a cyclone or flood, pre-dating the arrival of humans, Christian Foo Kune, owner of the site, told Reuters.

“The fact that there are such a wide range of animals there, small and big ones, suggests that there was a sudden natural disaster,” Foo Kune said. “The mass grave also shows no domestic animals, so it is prior to the arrival of man.”

The bones were thought to be at least 500 years old, he added. “We could be talking about a cyclone or repeated cyclones, flooding or a sudden rise in (sea) water levels that trapped the animals there,” he said.

That’s an extract of the article, which is very interesting indeed. But who am I going to blame now?

Update: Reuters removed the article’s page, and I removed the broken link.

Scientists unearth keys to dodo’s past

Wednesday, June 28th, 2006

Dodo by Juliet Beentje

Scientists unearth keys to dodo’s past, from MSNBC. The same news of other day, because they are all via Reuters, but I liked the dodo image.

Update: I removed the link since “The page you are seeking has expired and is no longer available at msnbc.com.”

Distressed dodo and first impressions

Monday, June 26th, 2006

Fused vertebra of a dodo

From the Dodo Expedition Weblog: Distressed dodo and first impressions, by Ranjith Jayasena and Beth Shapiro.

The Mare aux Songes excavation has resulted in an enormous amount of finds. The many bones need to be washed, photographed and catalogued. Therefore a part of the team is staying at the base processing the finds while the others are busy to get themselves dirty in the field. Today Julian went through the collection of bones uncovered by Kenneth, Frans and Pieter in the Mare aux Songes last October. Apart from dodos and tortoises the faunal assemblage proved to contain several other (extinct) species. By analysing animal bones we get to know the different species that lived at the Mare aux Songes, as well as the age and health of these animals. Among last year’s finds were two fused vertebra of a dodo. Although it is not possible to say whether the bird got this as a result of a disease or old age, we can be sure that it must have suffered.

Dodo skeleton find in Mauritius

Monday, June 26th, 2006

Dr Hume

From BBC News Dodo skeleton find in Mauritius: Scientists say they have discovered part of the skeleton of a dodo, the large, flightless bird which became extinct more than 300 years ago.

“It’s a wonderful collection,” said Dr Julian Hume, a research associate with London’s Natural History Museum and a member of the largely Dutch-Mauritian team.

“The chances of a single (intact) bone being preserved [would be] a remarkable event; and here we have a whole collection of them,” the Reuters news agency quoted him as saying.

Dr Hume said previous bones had been plucked out in a haphazard way, with little attention given to adjacent dodo fossils or clues about the birds’ environment.

The find includes a complete hip and four leg bones (femur, fibula, tibiotarsus and hypotarsus). Numerous other dodo parts were also unearthed, such as skull fragments, beak bones, vertebrae, wing bones and toe bones.

The same news can also be read at ABC News with a different text or in your favourite journal, since I saw that this is in everywhere. Read also those “old” news, also from BBC: Scientists pinpoint dodo’s demise. Dodos for everybody!

PS.: Thanks to Chris and Jaime for having remembered my dodo blog and sent me the link.

Update: the ABC News link is no longer available, so I removed it.