Complete Book of Life from Aardvarks to Zorilla

The Encyclopedia of Life project will detail 1.8 million known plant and animal species in the format of an online archive. Each species will have its own page with descriptions, photographs, videos, and maps, compiled by experts.

It is hoped that the $100m USD (£50m GBP) archive will be complete in 10 years and that in addition to an educational tool, the archive will have value for conservation efforts.

The project will begin by harvesting information from existing databases, such as FishBase, which contains details of 29,900 extant fish species. Data input will begin with animals, then plants, fungi and microbes last. It is not clear when fossil species will be added.

Encyclopedia of Life began development January 2006 and is reminiscent of other ventures such as the Tree of Life, Catalogue of Life and Consortium for the Barcode of Life. The last was launched in 2005 and is attempting to identify all species through unique genetic markers (called ‘barcodes’) found in the mitochondria of cells. This project has so far identified more than 27,000 species.

Proponents claim the Encyclopedia of Life will be much more through and flexible in regards to structure compared to its predecessors and will include dynamic features such as live searches. Fast internet technology has meant that such a large-scale endeavor has only recently become possible.

It is unknown how many species currently live on our planet but estimate range form a modest 2 million to 100 million.

Life on Land: The evolution of five fingers and toes

Well it didn’t take long for avid readers to spot the oddity in Friday’s posted picture of the early tetrapod, Acanthostega. This strange animal did not have the ‘usual’ number of digits, instead it had eight. Having more than five fingers or toes is called polydactyly and is a rare condition.

Few examples of polydactyly occur in the animal kingdom today, the panda’s thumb though, is one classic example. The panda has five digits on its paw plus an opposable 'thumb' but this thumb is not a sixth digit like the others, but actually an unusual outgrowth of a wrist bone. Thus even the panda’s thumb is not truly an example of more than five digits.

So what about Acanthostega and his buddies? The Late Devonian was a busy time, plant life was diversifying and insect life was gaining ground on land. Tetrapods, were making their first steps on to land and living semi-aquatic lifestyles about 375 million years ago. These animals had many characteristics advantageous to aquatic life, such as streamlined bodies, webbed feet and tail fins. But they also had weight-bearing limbs with which they could lift themselves out of the water. Acanthostega had eight digits on its front and hind limbs and two other early tetrapods, Ichthyostega and Tulerpeton, also had more than five digits.

So how could these animals have had such a wide variety of limb structures when all of their descendants seem to have a variation upon the five digit structure? It is thought that pentadactyly evolved in an animal that was ancestral to all present day tetrapods (amphibians, reptiles, birds and mammals) and that this event event happened 340 million years ago in the Lower Carboniferous (about 35 million years after the first tetrapods evolved).

To be honest, we don#t understand how these animals could have been so experimental while their descendants were so conventional. And why 5 anyway? No one knows. And we have no examples to examine. There are few animals who have extra digits. The most common is the novelty polydactyl cat, but this species is the result of selective breeding of animals with a genetic anomaly.

In a general sense, we know that it easier to ‘lose’ a trait then to gain it, hence the large number of animals who have reduced digits. But the striking lack of polydactyl examples in the long history of tetrapods since the Devonian implies there may be an evolutionary constraint at work. For example, pleiotropy is the multiple effects of genes on more than one physical characteristic. Hand-Foot-Genital syndrome illustrates such a condition. This rare disorder malforms limbs and the urinary system because the same defective genes pattern both systems. So perhaps the constraint on tetrapod limb structure is part of a greater pattern.

My Research into Palaeozoic Communities

Yesterday I began writing a little bit about what I do, so if you want to catch up check out Part 1. My goal while I’m at Bristol is to compile a community-level study of tetrapod diversity and to compare it to Mike Benton’s global pattern of tetrapod diversity. I hope that my research will aid our understanding of some ‘big’ questions such as:
1) Is global diversity a reasonable measure of true biodiversity?
2) How did tetrapods diversify? Did they conquer new niches or expand into new habitats?
3) How did mass extinction events effect community structure?

But even more interestingly, this study has an application to our present situation. We are witnessing a biodiversity crisis right now and it is not clear whether it is simply a part of Earth’s natural cycle or massive impact by human presence (though to be honest I lean towards the latter). Studying past communities helps us understand more about our present situation.

The first part of my research covered the Palaeozoic, from the origin of tetrapods about 375 million years ago to about 250 million years ago. At this time there were no birds, no mammals and no dinosaurs. The landscape was dominated by large amphibians and the first reptiles. Amphibians at the time were not like frogs but more like very large salamanders, and the largest of these superficially resembled crocodiles (For example, see my post of Parotosuchus). This period of time ended with the largest mass extinction event, in Earth’s history, the Permo-Triassic event 251 million years ago, when over 90% of Earth’s species went extinct.

During the 125 million years though, a lot of changes took place. I realize this post has gotten long already so I will continue more next week starting with a look at the first tetrapods, who possessed a strange oddity that we rarely see today and one that has changed our understanding of the evolution of life on land. Can you spot this oddity in the image to the right?

Click to view a larger image at http://universe-review.ca/I10-72-Acanthostega.jpg

A little bit about my job…

I’m a palaeontologist at the University of Bristol, currently in the (yikes!) third year of my PhD. But what exactly DO I DO?!?!? Well I don’t fit into the stereotypes of Jurassic Park and Ross from Friends. I don’t spend most of my days in the hot Mongolian desert carefully brushing sand away to reveal amazing and perfectly intact dinosaur skeletons. Sometimes I wish I did though, because to be honest I spend most of my time in the office, counting.

Yes, counting, This is what I do, count animals form different parts of Earths’ past and from all over the world. But to what end? I’m a ‘Macroevolutionist’ so I like to think about the ‘Big picture’, which sounds grand but to be honest can be a bit tedious because big picture stuff often means gathering lots of data, compiling it, and producing graphs. To add a little excitement to my day sometimes I add colour to my graphs and occasionally throw in a pie chart just to be a little crazy.

Seriously though, my supervisor, Mike Benton, has spent a lot of his career counting and has come up with some pretty intriguing insights about biodiversity and Earth’s past. One of his biggest contributions has been the this graph, which is a count of the all of the tetrapods (amphibians, reptiles, mammals and birds) that we have found in the fossil record, from their origin, almost 400 million years ago to the present. As you can see the diversity of tetrapods has risen almost exponentially since their origin to the present day, punctuated occasionally by a mass extinction event, such as the Permo-Triassic event 250 million years ago, when over 90% of Earth’s species went extinct.

But the trouble with this graph is that counting the number of fossils we have from different times is Earth’s history reveals a similar pattern, so it is difficult to say whether Mike’s graph is a true reflection of diversity or simply an artifact of the rock record. This is where my research comes in. I am studying the diversity within communities through time, a study that is independent of these artifacts so I will see if community diversity is similar to global diversity and what the implications are. If you’re still with me and haven’t fallen asleep, tomorrow I will discuss some of early research, including (just for you Will:), Romer’s Gap.

Story of a Grizzly - Polar Bear Hybrid

The current issue of Nature celebrates Linnaeus’ 300^th birthday with a series of editorials, essays and features on the continuing work of taxonomists. One of the more provocative articles discusses the definition of species, including the status of the beloved polar bear,Ursus maritimus.

Polar bears are more closely related to some brown bears (Ursus arctos) then some brown bears are to each other. While the interrelationships of these species (and subspecies) is a surprise, it has long been known that the animals are closely related and has been evidenced (rarely) by the hybridization of the polar bear and the grizzly bear (Ursus arctos horribilis).

This hybrid, though extremely rare, has occurred in captivity and has long been storied in arctic legends. In 1864 biologist, Clinton Hart Merriam, described an animal killed at Rendezvous Lake, Northwest Territories, Canada as "buffy whitish with a golden brown muzzle". A century later, Clara Helgason remembers a bear shot by hunters on Kodiak Island during her childhood in 1943 as "a large, off-white bear with hair all over his paws".

The most recent sighting of the rare hybrid was made, unfortunately, after its death. On April 16, 2006, Jim Martell, a sport hunter from the United States, shot a grizzly–polar bear hybrid near on Banks Island, Northwest Territories, Canada. Martell had paid $50,000, for an official license and a guide to hunt polar bears in Canada’s arctic.


Martell shot what appeared, at a distance, to be a polar bear but officials noticed that beyond the thick, creamy white fur, typical of polar bears, the animal also had long claws; a humped shoulder, scoop-shaped snout and brown patches around its eyes. The hybrid was confirmed by a DNA test.

The government returned the carcass to Martell. Though the hybrid species has no conservational value (like white tigers), it is an amazing phenomenon and I am sad the hunter kept his prize. I think he should have been compensated and asked to donate the pelt to a museum where others could learn about the phenomenon.

Lastly, I will note that the US government is considering giving polar bears a ‘threatened’ status. The Canadian government has a different perspective as anecdotal evidence from aboriginals and official wildlife surveys indicate the polar bear population in Canada actually appears to be growing. This of course is a notion that doesn’t appeal fit well with proponents of climate change, but that is a debate for another posting.

Regardless of controversy surrounding these amazing animals I hate that the government advocates rich people throwing out $50,000 for the opportunity to shoot one of these creatures. It is one more example of how Canada continues to sell its natural resources and decimate its environment for a few greenbacks.

Marris, E. 2007. Linnaeus at 300: The species and the specious. Nature 446, 250-253.

Roach, J. May 16, 2006. Grizzly-polar bear hybrid found -- but what does it mean? National Geographic News.

Sometimes bad news….

This morning’s posting was a hopeful look at biodiversity so I am a little annoyed at having to post on an opposite story. In 2004 fleeting video footage caught a glimpse of ivory-billed woodpecker (Campephilus principalis) in an Arkansas swamp, for the first time since 1944. Birdwatchers and conservationists were elated by the news that the long-thought extinct bird is alive in North America, however recently, the woodpecker's existence has been questioned again.

Extensive searches have failed to find any more evidence of the animal’s existence and Dr. Martin Collinson of Aberdeen University has re-analysed the poor quality video. He has suggested that the mysterious bird may actually be a pileated woodpecker (Dryocopus pileatus) in flight. He cites the wing markings and the rate at which the creature flapped its wings as being more comparable to a pileated woodpecker than an ivory-billed woodpecker.

The Aberdeen researcher also argues that the missing bird's large size and colourful plumage (it is a dramatically coloured black and white bird with a red head) would surely have been spotted by now in the many follow-up surveys.

The 2004 video ignited hope that other extinct birds might be clinging to survival in isolated places and some still believe there is the lost bird will reappear. I hope they are right.

Sometimes good news….

This year did not start out well from a conservation perspective. On a macrocosmo scale, we faced the reality that the Baiji dolphin is likely gone forever after a 40-day search of the Yangtze River failed to locate a single member of the species. In 2006 the IUCN (International Union for Conservation of Nature) declared four species of French Polynesian birds as extinct and this year the United States Government realizes the need to classify the polar bear as a threatened species. We have a very rich variety of fauna in the world today, much of which is threatened by human expansion. Sometimes all we hear is bad news.

But today, some good (microcosmo) news: 60 years after the last sighting, a beetle thought to be extinct in the UK has re-emerged in South Devon. The short-necked oil beetle (Meloe brevicollis) was last seen in Chailey Common, Sussex in 1948 and was rediscovered by amateur entomologist, Bob Beckford, during a wildlife survey on National Trust land between Bolt Head and Bolt Tail.

The beetle gets its name from the highly toxic oil secretions it produces when threatened. Adult beetles lay about 1,000 eggs in burrowed soil, which hatch the next spring. The hatchlings crawl up vegetation and where they hitch a ride on the back of a mining bee. They are taken back to the hive, where they devour the bees’ eggs and the protein-rich pollen stores the bee intended as nourishment for its own larvae.

The National Trust says that natural habitat of the beetle and the bee has been decimated by intensive farming practices. The coastal strip of land where the oil beetle was discovered has been managed as ‘low intensity’ farmland, creating a habitat where the beetle could survive undisturbed.

This site will now be studied, monitored and managed to help ensure these creatures flourish.

"The discovery of a beetle that was thought to be extinct for nearly 60 years is an amazing story of survival, particularly for a species with such an interdependent lifecycle. It's great that this oil beetle, with its fascinating lifestyle, has survived against all the odds and is back in business on the south Devon coast."
-David Bullock, Head of Nature Conservation, National Trust

Image and original story from the BBC

Macrocosmos and Microcosmos: white tigers and the humble amoeba

This week pictures were released by Taman Safari Indonesia Animal Hospital & Zoo of two Sumatran tiger cubs and a pair of orangutan babies who have been sharing a home over the last month. All four were orphaned, rescued and are now being housed together at the animal hospital. The snapshots show gentle affection, playful behaviour and even a helpful orangutan feeding a tiger cub.

I am unsure what made the zoo decide to keep these animals together. Perhaps they are experimenting with bonding between species, or may be it was a more logistic matter of space. Regardless, the result is that the four have bonded and there are ethical dilemmas to consider in the near future. What if one of the animals gets aggressive and hurts the other? How will they react to separation if they continue to be as attached to each other as they are now? Holding animals in captivity means severely disrupting their relationship with their natural habitat and social structure. What are our responsibilities as conservationists?

I have long been of two minds about zoos. Like most people, I do not enjoy seeing animals in small cages and cringe when I see large animals display ‘stir crazy’ repetitive behaviour. But the greater good voice in my head says that without zoos we could not create awareness of biodiversity and fund many conservation programs. Of course safari parks are a way to ease the conscience over traditional zoos but despite their growing popularity, they have yet to resolve one of the most striking problems about conservation: a greater value is placed on the conservation of large, ‘sexy’ animals then small, ubiquitous species such as small mammals, amphibians, reptiles, insects, algae or microorganisms.

One example of this slanted perspective on biodiversity is white tigers. These spectacular animals are not a true breed but in fact the result of a rare, recessive genetic anomaly occurring in the more ordinary orange tiger (typically the Bengal Tiger subspecies) . Their fur is white or creamy, they have pink noses, usually blue eyes and black, smoky grey or chocolate-brown stripes or may lack stripes all together.

Until 1951, white tigers were a part of Indian folklore, then a rich Maharajah hunted and captured a white tiger cub and kept it in his palace. This tiger, Mohan, (the Enchanter) is thought to be the only white tiger ever caught in the wild. All white tigers in zoos now are the descendents of Mohan or other captive orange tigers whose recessive genes showed up through breeding programs. The novelty and excitement that such an animal generates means that now while less then 1% of the natural tiger population display the unusual phenotype, a significant number of captive tiger populations are white.

Since wild white tigers are so rare, the current captive breeding pools goes back to only a few individuals and there is so much pressure from zoos and collectors to produce more white tigers, that a host of inbred – related problems have begun to surface including strabismus (cross eyes), retinal degeneration, postural problems, clubbed feet, weakened immune systems and kidney abnormalities.

Zoos cater to the public’s demand of BIG! SEXY! FURRY! and FEROCIOUS! And so they over represent animals such as tigers, elephants, hippos and other macrocosmos. To get across the reality of biodiversity we have to make microcosmos interesting for people. Let’s be honest, does a kid runs up to a tank of water full of floating/swimming algae, amoebas and diatoms and get excited? No. Do children enjoy looking at sketches of insects and peering at them through a commplex dissecting microscope? No. So how do we bring microcosmos interesting? One of the best displays I have seen is at the Royal Tyrell Museum in Drumheller, Alberta. Their Burgess Shale gallery shows colourful large scale models of ‘swimming’ creatures in their marine environment. Visitors walk through the space which is dramatically lit and gives the real sense of being on a sea bed.

Media also plays a vital part. One of my favourite movies is Claude Nuridsany and Marie Pérennou's 1996 documentary Microcosmos. 15 years of research, 2 years of equipment design, and 3 years of shooting went into making this amazing venture into the hidden world of a French meadow. Especially memorable are a gross scene of slugs kissing and a humorous excerpt of a toiling dung beetle.

Large screens, high resolution graphics and even CGI help bring attention to small organisms but I don’t know if amoebas will ever have much of a ‘cool factor’. Anyway, next time I am at the zoo, I am going to spend a little extra time appreciating the small things.