iBiome

infinite blue

i've been on the road the last few weeks, working in the middle east and the Philippines.  While in Manila I was able to take a short side trip to Eagle Point, Batangas, for a bit of scuba diving. There's something for me therapeutic about turning away from the reef, and looking out into the deep endless depth. 

A new theory emerges for where some fish became 4-limbed creatures

"These transitional fossils were not associated with drying ponds or deserts, but consistently were found with humid woodland soils," he said. "Remains of drying ponds and desert soils also are known and are littered with fossil fish, but none of our distant ancestors. Judging from where their fossils were found, transitional forms between fish and amphibians lived in wooded floodplains. Our distant ancestors were not so much foolhardy, as opportunistic, taking advantage of floodplains and lakes choked with roots and logs for the first time in geological history."

Limbs proved handy for negotiating woody obstacles, and flexible necks allowed for feeding in shallow water, Retallack said. By this new woodland hypothesis, the limbs and necks, which distinguish salamanders from fish, did not arise from reckless adventure in deserts, but rather were nurtured by a newly evolved habitat of humid, wooded floodplains.

The findings, he said, dampen both the desert hypothesis of Romer and a newer inter-tidal theory put forth by Grzegorz Niedbwiedzki and colleagues at the University of Warsaw. In 2010, they published their discovery of eight-foot-long, 395-million-year-old tetrapods in ancient lagoonal mud in southeastern Poland, where Retallack also has been studying fossil soils with Polish colleague Marek Narkeiwicz.

via www.eurekalert.org

This evolutionary pathway can be imagined when you consider floodplains such as Tonle Sap, where during the monsoon the river reverses flow and the fish breed and thrive among a submerged forest.

a colony of bees in the garden

Last weekend we were treated to an unusual wildlife encounter. A colony of bees, likely in the process of locating and founding a new hive, settled in our garden on Saturday afternoon.  After trying out a branch in our plum tree, they dropped to the ground and settled for the next 24 hours or so.  Individual bees, perhaps scouts, shuttled in and out of the cluster until sunset and then again throughout Sunday morning.  Finally on Sunday evening they rose in one great cloud (well, they did leave some stragglers) and made their way to Pacific Spirit Park.   

It's great to see honey bees around and, it seems, in good health.

Colony Collapse Disorder

One of the great triumphs of civilization, (and one that may just help put an end to us) is that most of us in the developed, urban world can afford to ignore the barely visible cloud of ecosystem functions and services that we float comfortably on.  Barely conscious of the fragility of some of these essential systems, we are slow to grasp the importance of what one might consider "the little things".  Listening to Bill Maher's Real Time last night I first heard of Colony Collapse Disorder and the apparent loss of 50% (!) of honeybee hives in North America and Europe.  This made the news as it was speculated that cell phones are a contributing factor. 

Grrrlscientist (Pathogens Causing HoneyBee Deaths?) notes another take on the phenomenon i.e. that it may be caused by a pathogen.  Regardless of the cause, the loss of substantial numbers of a key pollinating insect could have absolutely enormous consequences for our food supply.  This is spooky:

During the previous year, bee keepers and other experts have observed tremendous declines in honeybee populations -- often entire colonies disappear suddenly and without warning, a situation referred to as "collapse" so scientists refer this phenomenon as "Colony Collapse Disorder" or CCD. Thus far, approximately 50 percent of bee hives have collapsed in this manner. As a result, experts fear that this loss of honeybees will have an enormous horticultural and economic impact around the world, leaving important food crops such as fruits, vegetables, and almonds unpollinated, so they are working hard to find the cause of this mysterious syndrome, and this cutting-edge technology might have provided them with an answer.

Microarrays and Climate Change

From  Technology Review, new applications of genomics tools, in this case microarray technology, to model the effects of climate change on marine species at the gene expression level:

Using novel genomic technology, marine biologists have found troubling clues that marine life could be extremely vulnerable to climate change. By mimicking future ocean climes and using gene chips to detect how marine organisms respond, the researchers can evaluate how well different organisms deal with environmental stress. The findings, while still preliminary and incomplete, are worrisome...

...So far, the team has focused its attention on a set of proteins, known as heat-shock proteins, which kick in when an animal is under stress. Almost all animals carry copies of these proteins, which can repair other proteins that have been bent out of shape by heat and additional environmental stresses. According to early results from gene-chip studies, sea-urchin larvae raised at current carbon levels activate their heat-shock proteins when faced with warming water temperatures. But larvae raised at the best-case-scenario carbon level no longer activate these genes under stress and therefore can't respond to a warming climate. "I don't want to say we will lose all sea urchins," says Hoffman. "But there will be some part of the population that can't develop."...

...Although it's hard to predict exactly how that loss will affect the environment, it's likely to change the structure of the entire ecosystem. Without algae-eating urchins, "you might predict that algae will become dominant in a particular area, which then might affect availability of fish that live there, which could affect the fishing industry or even tourism," Hoffman says.

While illuminating some of the useful applications of genomics to conservation, I find this article a bit alarmist.  As pointed out by a commenter on the article, sea urchins have faced warmer oceans in the past and survived.  There will be transition and loss, and a new equilibrium. The key point for we humans is whether the transition and new equilibrium significantly affects us, and how.

Biodiversity Podcast

via: Evolving Thoughts.  EcoGeeks on Biodiversity

DNA and Ivory

This article in the Globe and Mail (Genetic maps help unravel black market in ivory) underscores the promise of genomics tools for compliance and enforcement of conservation laws. 

Dr. Wasser was asked to help in 2002, when the authorities in Singapore seized a huge shipment of contraband ivory. Investigators from a number of countries wanted to know where it had come from, and he had developed a technique for matching the genetic material found in tusks to the DNA found in feces of elephants, allowing him to pinpoint where the tusks came from.

There were 532 tusks in the shipment, plus more than 40,000 hunks of ivory already cut up to make the ivory seals. Between 3,000 and 6,500 elephants were likely killed to get that much ivory, the scientists say.

The DNA showed the elephants came from central Zambia, a country that has not been given permission to sell its ivory stockpiles internationally. The government wanted to sell ivory taken from animals killed prior to 1989, and said that only 135 elephants had been illegally killed over the past 10 years.

Through genetic maps and the identification of biomarkers for specific populations, authorities will increasingly be able to determine the provenance of a given piece of ivory, can of abalone, or sockeye fillet.  A quick and reliable test for biomarkers of threatened species will tighten the screws on the middlemen who trade with dodgy sources, and that is a good thing. 

The original PNAS article is here.

Strange New Creatures Found in Antarctica

Link: LiveScience.com

Following ice shelf collapses in Antarctica, researchers have gained access to sea bed areas previously accessible only through holes drilled through 100 m - thick ice. Among the new creatures discovered is the Antarctic octopus (Paraledone turqueti) (below- Credit: E. Jorgensen, NOAA 2007): 

"One of the main aims of the expedition was to survey both indigenous life-forms and creatures that had moved in after the collapse to take advantage of the newly opened environment.

Gutt said that 95 percent of the animals the expedition found were probably indigenous and just 5 percent had moved in after the ice shelves collapsed, but even that small percentage indicated a shift in biodiversity and species composition in the area which will probably continue.

“Life at the sea floor obviously reacts very slowly to this very climactic change in the environmental conditions," Gutt said. “[It] needs hundreds to thousands of years until a new community has fully developed, if this will happen at all.”

One creature new to the neighborhood was the fast-growing, gelatinous sea squirt, which the scientists found in several dense patches."

For Peat's sake

Peat forests are a vital component of Borneo's ecology and act as both carbon sink and habitat for a diversity of plants and wildlife.  This item from the BBC Smoking out the world's lungs highlights current threats to Borneo's peatlands, which include logging and agricultural clearing:

According to the conservation organisation Wetlands International, 48% of the country's peatland forest has been deforested, and most of the rest degraded by illegal logging. And that has caused some major problems.

Marcel Silvius, a senior programme manager for Wetlands International, believes we are looking at one of the biggest environmental disasters of our age.

"From the drainage of its peatlands alone," he told me, "Indonesia is producing 632 million tonnes of carbon dioxide a year.

"But from its annual forest fires, it produces another 1,400 million tonnes. That's a total of 2,000 million tonnes of carbon dioxide a year. The Netherlands emits 80 million."

Indonesia's annual forest fires are a major problem, and have been increasing over recent years. 

Sometimes they are caused by companies wanting a fast, cheap way of clearing the land for planting.

Sometimes, though, it is local villagers, eking out a living from small patches of land hewn out of the forest.

A Visit by the Great Hornbill

YC Wee documents a Great Hornbill at large near Bukit Timah in Singapore.  Likely an escapee from Jurong Bird Park, it would be more at home in the forests of borneo or penninsular malaysia than hyper-urban Singapore.  A magnificent sight on one's back balcony.