Archive for the 'Animals' category

The new Encyclopedia of Life: Collections

Sep 05 2011 Published by under Animals, Endangered Species, Environment, Internet, Red Panda

I have to admit, I didn't use the Encyclopedia of Life very frequently in its first incarnation. I perused for media every now and then, or doubled checked the taxonomy for a species, but it was not a touchstone for research. The relaunch, however, gives users new functionality to make the experience more organized for personal and community use.

Like any good application, the startup/front page gives you just about everything you need. The mission statement is obvious, the search field is huge and the row of images tells you exactly what your searches will bring. The main site elements are listed below along with FAQ links, newsfeed tells you this is a busy place full of lots of other people. Facebook, Twitter, Tumblr, Flickr; Impression made. It's all familiar, accessible.

The main piece that I've grown to love is the collections. After you've created your account and start searching around for cute pictures of red pandas, you'll notice an Add to Collection button in the top right-hand corner of the page. Clicking the button displays a popup. Follow the prompts to create a new collection.

Collections allow you to create groups of organisms in EOL. Collections can be as subjective or scientific as you wish. Red panda could be included in a collection of the "Cutest Animals Ever" or a more natural category, maybe "Mammals of China." Once it's created, you can search for and add as many inhabitants of EOL as you wish by clicking the Add to Collection button and selecting one (or more) of your collections in the list. For the Cutest Animals Ever collection, you might want to add the echidna or the wolf spider. For the Mammals of China, you might want to add that other panda, whatever its name is.

I started a collection of monotypic taxa from the red panda, the sole species in the genus Ailurus. I searched for other monotypic taxa off the top of my head: the moose, the African civet cat, the Gingko. Then I started getting some responses from the community via the collection newsfeed. Katja said, "Don't forget the Aardvark!" Cyndy said the Western Osprey was a good candidate for the collection. Bob suggested that I add a description so that people visiting my collection knew exactly what "monotypic taxa" are. So I did:

This is how communities can grow out of collections of organisms, communities based on shared interests of one sort or another. In fact, there's functionality there to support those communities, just click the Create Community button next to your collection, add a description, invite some interested parties and start sharing.

EOL gets me thinking. It started with one of my favorite animals and quickly became a taxonomic scavenger hunt. I started researching: Just how many monotypic taxa are there? Why are they important? What does the classification say about these animals and their evolutionary history? As a writer, the answers become the building blocks for an essay. Usually there's nothing manipulable about those ideas; they spawn from reading papers, from the ideas of others. EOL provides a level of control that allows systems to be constructed that plead for further explanation.

Collection building can create new ideas, but it can also be useful for supplementing existing material. I've written about biomes and ecosystems frequently in the past, and it can be difficult to give readers a good idea of the extent or uniqueness of life in a particular region. I'm thinking about using collections in EOL when I can to create lists of organisms that constitute the ecosystem I describe so that readers can browse through the many unique organisms that live there. Excessive listing and description in prose structurally tedious; often its a choice between prose lists and long strings of bullets, which are ugly and usually scary for a casual reader.

EOL suddenly becomes a very interesting resource for science enthusiasts, educators and writers. I have some thoughts about how it could be used in more creative/artistic ways, but I'll hold off for a future post.

Go sign up and play around. It's Labor Day. The grill isn't ready just yet. EOL is a lot of fun.

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Forest fragmentation and the isolation of the giant panda (a goodbye to Tai Shan and Mei Lan)

Feb 03 2010 Published by under Animals, Conservation, Ecology, Environment, Research Blogging

ResearchBlogging.orgTwo of the cities I’ve called home in the past 10 years – DC and Atlanta – are each sending a panda home to China tomorrow. Mei Lan and Tai Shan were both born in captivity and both a huge boon for conservation and science education on the east coast. I watched Tai Shan grow up along with other zoo goers in the DC area.

They’re returning to their ancestral home in China, where wild pandas are still endangered. Fossil records show us that giant pandas had a much wider range in Asia, inhabiting subtropical and warm temperate forests. Now, mostly because of human encroachment, they are restricted to 24 isolated populations in China’s fragmented mountain forests where bamboo dominates the understory.

In recent surveys, researchers have shown that the number of individual pandas has increased due to conservation efforts in the country, but the populations remain disparate. A recent study published in the Journal of Biogeography takes a look at how exactly these pandas are distributed in the forests of Southwest China, in relation to the level of fragmentation.

Forest fragmentation is a term we read a lot in newspapers and magazines listing the numerous causes of a population decline or a biological invasion, but it’s rarely fleshed out, so I’m going to take the opportunity to briefly describe its most important aspects.

You’re standing on a rock at the edge of a large stream or small river. A forest stretches from the banks of this stream to the faint peaks of mountains far in the distance. You turn around, looking across the stream to the other bank. There’s a stone like the one you’re standing on, and beyond that an identical forest running seamlessly from river to mountains in the other direction. Where the forest ends, at the bank, it changes from one ecosystem to another. In the river itself, another ecosystem, with microhabitats. On the other bank, a replica, then the forest again.

Now imagine you’re standing in a gravel patch on the side of a highway. There is a forest in front of you with no shrubby transitional area. On the other side, a replica: a gravel patch and a wall of trees extending to the mountains in the distance, or so you assume. You see the difference in the split. One is natural and supports a diversity of dovetailing ecosystems, the other is anthropogenic, effectively splitting one forest “patch” into two patches.

As these forest patches are further split, metapopulations form: smaller, per-patch assemblages of the populations found in the once contiguous forest patch. As land is developed, the patches shrink, becoming more and more isolated until migration and dispersal between them becomes strained due to a lack of food and shelter in the developed land. In the process of development, a higher ratio of forest edge to core is created, a drier, sunnier habitat that supports a different network of organisms. The extension of the forest patch edge also means more access for predators and parasites living outside.

Not surprisingly, the researchers found that dense forest (defined as forests with canopy cover > 30%) is “essential” for giant panda survival in the wild. The highest densities of pandas were found in the Qinling Mountains, which also happened to be an area with low relative fragmentation. Broken down, the most important factors for pandas turned out to be patch area, edge density (distance of edge per unit area) and patch “clumpiness” or how close patches are from one another.

Large mammals like the giant panda are particularly sensitive to fragmentation due to their need for space within a preferred habitat, the dense forest. It’s not just territorial; it has a lot to do with biodiversity. The size of these patches determines the diversity of the forest, which creates these smaller habitats like core or dense forest. In this current situation, where forest has been significantly reduced, pandas are forced to transverse long stretches of alien landscapes, which requires more energy despite the lack of food and exposes them to human influences.

Instead of establishing new reserves for other isolated populations, the authors recommend that future conservation efforts should be focused on creating corridors between the disparate patches. It’s great that the conservation efforts to bolster and protect populations are starting to work and the number of individuals is increasing, but the population needs to be considered as a whole. That means trying to reconnect forest patches and expanding the gene pool.

So as we say goodbye to Tai Shan and Mei Lan, it’s important to recognize just why they’re here in the first place. They’re ambassadors for conservation, for the reestablishment of their species in the wild, not in zoos.

The last time I saw Tai Shan, he was doing this:

It made me smile. The interest he generated, that oblivious little panda cub, just by doing what young mammals do – eating, sleeping, playing, sleeping some more – is remarkable. The crowds that lined up in front of that panda enclosure were enormous; so big, in fact, that they had to expand the area to compensate. Dads of every nationality held their squirming little ones on sweaty shoulders during the summer. In the fall, hundreds of school kids – in uniform and out – would pack in for the keeper’s lecture. And in the winter, after the New Year, Heather and I went to the zoo one weekday afternoon between semesters and had Tai Shan completely to ourselves for almost an hour. You can’t help but vicariously reach out to that little life, stumbling along with him as he paws and climbs and sniffs. It’s our proper place in stewardship. From a distance, we’re touched by the clear, oblivious innocence of nature.

Wang, T., Ye, X., Skidmore, A., & Toxopeus, A. (2010). Characterizing the spatial distribution of giant pandas (

) in fragmented forest landscapes
Journal of Biogeography DOI: 10.1111/j.1365-2699.2009.02259.x

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>Climate change drying up streams, reducing the reproductive success of bats in the Rockies

Jan 28 2010 Published by under Animals, Conservation, Ecology, Environment, Research Blogging


From left to right: fringed myotis (Myotis thysanodes), the big brown bat (Eptesicus fuscus) and the long-eared myotis (Myotis evotis).

ResearchBlogging.orgWith the widespread effects of the changing climate on biological communities and landscapes across the world, it has become increasingly important for ecologists to identify indicator species among these ecosystems that can indirectly relate information about environmental changes that are not apparent or easily accessible. So it is in the west, the Rocky Mountains and in particular the Colorado River Basin, where temperatures have increased more than anywhere else in the contiguous United States, an average 1.2° C higher than the 20th century averages. The biggest increases in temperature happens at the highest elevations, which is

With warming temperatures comes less precipitation and less snowpack, which means during the summer months, the breeding season for most species, there is significant reductions of stream discharge, which has reduced the flow of the Colorado River. Thirty million people rely on the water provided by the Colorado River, and the Basin is foundational to all life in such a dry environment. Bats, as this article in Ecology explains, are particularly sensitive to these changes and, due to their enormous numbers, are integral to food webs as predator and prey. They may be that indicator ecologists are looking for.

Using capture and environmental data from over 12 years - 1996 to 2008 - Rick Adams from the University of Colorado has demonstrated dramatic correlations between the reduced availability of water and declines in the reproductive success of certain species of bats in the west. Bats are particularly sensitive to evaporative loss because of their small size, large surface area to volume ratio and uninsulated wings. Reproductive females are particularly sensitive considering that 76 percent of their milk is water. Lactating fringed myotis bats have been demonstrated to drink 13 times more often than non-reproductive females from nearby sources like streams or pools.

The study area was in the foothills of the Rockies, between 1650 m and 2250 m, a mix of montane meadows, shrubland, pine woods, riparian woodland and mixed coniferous forest, the habitats of nine species of bats; data was collected on the five most common: small-footed myotis (M. ciliolabrum), little brown myotis (Myotis lucifugus), big brown bat (Eptesicus fuscus), long-eared myotis (M. evotis), and fringed myotis (M. thysanodes). The 2,329 bats captured were put into one of four categories: Non-reproductive, Pregnant, Lactating or Post-lactating.

The reproductive output of these bats has declined, especially when stream discharge dipped below 7 cubic meters per second. During the hottest and driest years, 2007 and 2008, Adams captured more non-reproductive females. Among two species, M. thysanodes and M. lucifugus, the percentage of non-reproductive females was remarkably high, 56 percent and 64 percent respectively.

Both of these species use maternity sites having south or southeast aspects that promote highest solar gains throughout the diurnal roosting period (Adams and Thibault 2006; Adams and Hayes 2008), maintaining internal temperatures between 27° C and 36° C (Adams unpubl. data). Such microenvironmental conditions within roost sites promote high evaporative water loss and consequently a greater need for water intake, especially during the lactation period.

The other myotis species are more likely to roost in cooler, more humid microclimes, closer to the ground.

So if bats - mammals with high mobility* - are facing difficulties from a reduction of water availability, what about other animals more restricted to certain areas? How is this aspect of climate change affecting them? Bats, Adams says, are good bioindicators, organisms that can help scientists predict similar, indirect effects of climate change in other regional animal populations.

Current predictions from the IPCC tell us that this is just the beginning; it's "very likely" (90 percent confidence) that ecosystems will be significantly affected if the warming trend continues. In the next century, due to continued average temperature increases and an increase in the frequency of heat waves and drought, the Colorado River is facing a potential 8 - 11 percent reduction of flow. This will certainly exacerbate the bats' reproductive problems, but perhaps the continuance will afford ecologists the opportunity to transpose data to study similar problems among other animals and propose meaningful, sensible solutions - even if they are bandaids, like providing artificial water sources for vulnerable populations, temporary but viable, buying much needed time for more comprehensive applications.

*Bats are mobile, but they stick to their traditional maternity sites, still focused in a local area.


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>Dinosaurs and the Mystery of Body Temperature III: Intertial Homeothermy

Jan 28 2007 Published by under Animals, Evolution, Links, Paleontology, Physiology

>Body size is an important factor in the debate over whether dinosaurs were cold or warm blooded (or something in between). When you have a land animal 42 feet long weighing nearly as much as a blue whale, temperature models tend to break down. If the dinosaurs were ectotherms, relying on the environment for heat, they may lack the surface area to sufficiently heat the blood pumping directly beneath the skin. If dinosaurs are endotherms, and internally heated by its own metabolism, it may not have enough surface area to expel excess heat from the depths of its massive body.

The following chart shows this principle a little more clearly.

As you can see, the second two cubes have the exact same volume (body size), but the surface areas are vastly different. Large animals like dinosaurs and blue whales are like the middle cube with the smaller ratio; it becomes difficult to use surface area to heat/cool its insides. Also, the more massive an animal is, the more heat it produces/requires, generally speaking.

The reason blue whales get away with being the most massive animal to ever live (so far) is that temperature exchange with their environment is rapid. The ambient temperature of the ocean is on average much lower than ambient temperatures on land, allowing the whale to circulate heat through the thinner parts of its body and allowing the cold water to carry away the excess. Plus, the whale's 100 tons is spread out along 100 feet of body as well.

You can see how a creature on land weighing as much as the blue whale, compacted into 40 or 50 feet and lacking the might present a particular problem for scientists to figure out, especially in the absence of direct evidence.

But, the creature did exist. We're just now picking up the pieces, so to speak.

And recently, scientists put those pieces to good use. By simulating the ontogenetic development of eight different dinos using data from recent bone analyses, they were able to determine that the internal temperature of dinos depended on size. Smaller dinosaurs maintained a lower body temperature and probably grew at a rate consistent with extant reptiles, while the larger dinos maintained a higher body temperature, like today's birds and mammals.

The largest animal studied, Sauroposeidon proteles, was estimated to have an internal temperature of 48 degrees Celsius (120 degrees Fahrenheit), a few degrees higher than what was thought to be the upper limit of temperature tolerance for animals. Because of this extremity, the authors believe that temperature may have been the ultimate cap on body size.

Ultimately, this study was transposing a state called "inertial homeothermy," which is observed in ectotherms like crocodiles and the Galapagos tortoise that can maintain their internal temperatures by adjusting their internal physiological conditions, much like endotherms. The researchers performed the same tests on crocodiles of similar size (when they could; there are no crocs alive today to compare with the larger dinos):

Perhaps, if time allows in the near future, I'll detail a bit more about all the thermies: poikilo, homeo, hetero, ecto and endo.

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>Dinosaurs and the Mystery of Body Temperature II: The Evolution of Endothermy

Jan 19 2007 Published by under Animals, Birds, Evolution, Links, Paleontology, Physiology

>There's a fairly significant problem with the evolution of endothermy from ectothermy, a paradox that has no satisfactory conclusion as of yet: How could well-insulated animals with high metabolic rates producing lots of heat from within their bodies evolve from animals with low metabolic rates and poor insulation, expertly absorbing heat from the surrounding environment?

If these characteristics evolved independently what purpose would they serve? An ectotherm has no use for insulation like feathers or hair since heat exchange needs to be rapid with its surroundings, just as it has no use for a heat producing high metabolism without the necessary insulation.

Raymond Cowles' experiment showed that by putting little fur coats on lizards wasn't keeping heat in, it was keeping heat out. The lizards couldn't warm up.

That's the paradox, the catch-22. The ticket out, however, is the exaptation: An adaptation of a structure that becomes useful for one biological purpose that originally evolved for another.

Feathers are are thought to be derived from the long scales of ancient archosaurs. These reptiles could lift their scales and expose their skin directly to the source of heat, or orient them so that they could block heat absorption. Just as the marine iguanas of the Galapagos Islands are able to trap a layer of air within their scales, these reptiles are thought to have done the same, retaining more metabolic heat, leading to a more active life.

Another theory concentrates on our reptilian ancestors from the synapsid lineage. The synapsids were steadily becoming more active (illustrated by changes in bone structure), and those morphological changes could have been accompanied by higher metabolic rates, leading to more heat in the body. The more hair on the body, the better heat retention.

So which came first, the dino or the egg?

It's apparent that endothermy evolved at least twice; once beginning with an exaptational insulator in the case of birds, and once beginning with exaptational skeletal changes and a needed increase in activity for foraging, in the case of mammals.

Largely, however, the jury is still out. (I heard that there is also evidence that pterosaurs might have been endothermic, leading to a third origin of endothermy; please link research if you know of any.)

Its important to realize that there are in-between states of thermoregulation, and the progression from ectothermy to endothermy (and back again, in some cases) took place in baby steps across millennia. Time and again we're shown that organisms tend not to fit our definitions and molds. It's not like flipping a switch.

More on dinos and thermoregulation for part III.

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Why Spiders Aren't Insects IV: Molecular Homology

Photo by: Gerald Yuvailos

This is the fourth part in an ongoing series discussing the distinction and evolution of spiders and other arthropods.
Part I, part II and part III have led up to this point:

In the last post of this series, we established that spiders descended from marine arthropods called the eurypterids, distinct and separate from insects, appearing in the fossil record in the late Silurian/early Devonian, about 425 million years ago.

The cladogram we used to analyze the spider's history was based on the organism's morphological characteristics, that is, visible structures like chelicerae and book lungs that can be tied to other organisms that possess the same structures. Limulus (the extant horseshoe crab) has both of these structures and predates the spiders, placing them further back in the chelicerates' evolutionary history.

Homologous bones from human (I), dog (II), pig (III), cow (IV), tapir (V) and horse (VI):
r — Radius, u — Ulna, a — Scaphoid, b — Lunare, c — Triquetrum, d — Trapezium,
e — Trapezoid, f — Capitatum, g — Hamatum, p — Pisiforme

Paleontologists call this comparison of physical characteristics homology (coined by Richard Owen an anatomist and, ironically an opponent of Darwin). The mouth parts of a spider are homologous to the mouth parts of Limulus because of the cherlicae's exact form and function. This is a different designation than analogy; analogous structures may function in the same way, but they are different in form because of their different lineage. For this reason, scientists call analogy an artificial classification system.

A good example of analogous structures are wings from bat and bird. They perform the same function in varying degrees, but they have evolved very different forms. A bat's wing is basically a modified mammal hand, while the bird wing is a modified tetrapod arm.

Homology is essential in building an organism's phylogeny (evolutionary history). More recently, geneticists have employed this classification technique to analyze and find similarities among the less visible traits in life, RNA (ribonucleic acid) and the building blocks of proteins, amino acids.

Think of these cellular chemicals this way: If DNA is the blueprint of life, RNA is the builder and its materials are amino acids. When these amino acids are placed in the correct sequence by RNA, they become proteins, the framework of our body. And, since the genetic code for protein constructions is nearly universal*, geneticists can compare entire swaths of RNA from one organism to those of another and find homology at the molecular level.

Here's an example (sequences are greatly abbreviated for the sake of our sanity):

Organism 1: ACGC-CCCCC
Organism 2: ACGC-CCCUC
Organism 3: ACGU-CUCUC

Basically, from noting the differences in each RNA sequence, and determining the homologous sequences (such as the ACGU sequence above), a cladogram can be constructed that shows common ancestry without the murky distinctions that sometimes cloud the comparison of bones to bones, or mouth parts to mouth parts.

The problem with this molecular system of analysis is that it often provides vastly different cladograms than the ones crafted through morphological analysis. This is not necessarily the case between the spiders and and Limulus, the molecular evidence supports the fossil record's interpretation of ancestry, but it calls into question the descent of insects from chelicerates like spiders.

In short, the molecular evidence agrees with the morphological evidence: spiders are more closely related to horseshoe crabs than insects. But where and when did the insects arise?

Next time we'll tackle the more recent movements to elucidate the phylogeny of arthropods, including a discussion on the significance Hox genes and evolutionary-developmental biology (evo-devo).

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Why Spiders Aren't Insects III: The Evolutionary Advantages of Mass Extinction

So far we have established that spiders are distinct from insects for two reasons: physiology (mouth parts, body plan, respiratory structures) and more importantly, evolutionary history (or phylogeny, as scientists call it).

But where did spider's come from? How did they crawl out of the water as euryterids and speciate (become a distinct organism that cannot interbreed)?

The answer, like many in invertebrate paleontology, is cloudy. Organisms without hard, thick shells rarely become fossilized. In fact, for any organism's parts to become fossilized, even vertebrates, is a profound rarity, as Bill Bryson illustrates in A Short History of Nearly Everything:

Only about one bone in a billion, it is thought, ever becomes fossilized. If that is so, it means that the complete fossil legacy of all the Americans alive today - that's 270 million people with 206 bones each - will only be about fifty bones, one quarter of a complete skeleton.

Needless to say, invertebrate paleontologists are having a heck of a time piecing things together from such a paltry fossil record. But that doesn't mean there's no evidence.

According to morphological and geological evidence, and therefore directly observable comparison, spiders and their brethren descended from the eurypterids, many of which were sea-going creatures. The eurypterids arose in the Ordovician, a period that began with the decimation of perhaps 60% of all marine life, and consequently ended with another more devastating cataclysm, which which some paleontologists rank as the second most destructive extinction event in the history of the world (by extinction of family). This has become known, quite appropriately, as the end-Ordovician event.

Mass extinctions make room for the evolution of unique characteristics as dictated by an organism's environment, and the environment changed drastically for the eurypterids at the end of the Ordovician. Glaciers began to creep down from the upper latitude, as the greenhouse gas carbon dioxide was depleted from the atmosphere, reducing the Earth's ability to trap the sun's heat energy. As the glaciers encroached, sea levels dropped and global temperatures cooled. This rapid progression decimated habitats, and destroyed a species' equilibrium with its environment.

But the end-Ordovician event was comprised of two parts: glaciation and then a period melting, an interglacial. Temperatures warmed once more, glaciers melted, flooding the land, and raising sea levels once more. The world had completely lost almost 50 percent of the families of life, but the ancestors of the spiders had survived. The Silurian period had begun, and new ecological niches were available for exploitation, a habitat opportunity that eventually would produce the spider.

That's about how it stands from a morphological perspective. But more recently scientists have been delving into molecular evidence and crafting very different explanations of not only the rise of the spider, but the vast diversification of arthropods in general.

Next time we'll address the new cladograms produce by this molecular evidence, and what ramifications it might have in interpreting the diaspora of the most abundant creatures on the planet.

*Interestingly enough, we are in the middle of an interglacial right now, the Holocene. Much like the success of the spider, our current interglacial, which began about 16,000 years ago, may have contributed to the ultimate "success" of Homo sapiens.


Pechenik, J. A. (2000). Biology of the Invertebrates. : McGraw Hill Companies.

Gradstein, Felix, James Ogg, and Alan Smith, eds., 2004. A Geologic Time Scale 2004 (Cambridge University Press)

Baez, J. (2005). Temperature. Retrieved July 18, 2006, from

Webby, Barry D. and Mary L. Droser, eds., 2004. The Great Ordovician Biodiversification Event

University of Bristol. (2004). Fossil chelicerates and evolution. Retrieved July 18, 2006, from

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