New Whipray Species Identified by Its DNA

July 29, 2013 — Biologists have analysed tissue samples of 115 spotted whiprays of the Himantura genus, collected in various parts of the Indio-Pacific region. By means of genetic markers -- as opposed to morphological criteria only -- the scientists were able to describe these leopard-skin whiprays in detail and demonstrate that they are isolated from each other in terms of reproduction. They have also discovered a new species that they call Himantura tutul, which belongs to a genetic line that is totally distinct from the three other species that are known in the same group:H. leoparda, H. uarnak and H. undulata. They frequent the same costal habitats but occupy different ecological niches.

Biologists have discovered a new species of whipray that they call Himantura tutul, which belongs to a genetic line that is totally distinct from the three other species that are known in the same group: H. leoparda, H. uarnak and H. undulata. They frequent the same costal habitats but occupy different ecological niches. (Credit: © IRD / P. Laboute)

Distinguish in order to protect

These studies should help to assess the state of these whipray populations and improve their conservation. Knowing the biological characteristics of each species will for instance help to redefine a minimum size for fishing purposes to avoid the catching of juveniles that belong to the larger species. Determining their geographical distribution and habitats will also make it possible to protect the breeding and nursery habitats of each species.

Economical and ecological interest

Ocellated whiprays can grow over 1.50 metres wide. These large animals start breeding fairly late, at the age of 5 or 10 years, and only in small numbers. Their populations are therefore very vulnerable. Fished for food and especially for their skin that is sold to tanneries in South-East Asia, they are threatened almost throughout the tropical Indo-West Pacific. Their overfishing will in time jeopardise a whole segment of the economy in Indonesia, which is the largest shark and whipray exploiter with 30% of all catches worldwide. In less than twenty years, the amount fished in the Java Sea has been divided by ten! As high-level predators, whiprays also play an important role in regulating ecosystems. Their extinction will threaten the functioning of coastal marine environments.

The International Union for Conservation of Nature (IUCN) estimates that 36% of the 650 ray species known in the world are at risk of becoming extinct, including leopard whiprays that are classified as "vulnerable." A better identification of these singular animals is the first vital step towards their conservation.

Did you know?

Ocellated whiprays have one or two venom glands at the base of their tail to protect them against their natural predators, namely sharks and killer whales. Their sting is painful and potentially infectious, with serious consequences if not treated correctly.

Cockatoos Know What Is Going On Behind Barriers

July 29, 2013 — How do you know that the cookies are still there even though they have been placed out of your sight into the drawer? How do you know when and where a car that has driven into a tunnel will reappear? The ability to represent and to track the trajectory of objects, which are temporally out of sight, is highly important in many aspects but is also cognitively demanding. Alice Auersperg and her team from the University of Vienna and Oxford show that "object permanence" abilities in a cockatoo rivals that of apes and four-year-old humans.

The researchers published their findings in the journal Journal of Comparative Psychology.

For investigating spatial memory and tracking in animals and human infants a number of setups have been habitually used. These can roughly be subdivided depending on what is being moved: a desired object (food reward), the hiding places for this object or the test animal itself: In the original invisible displacement tasks, designed by French psychologist Jean Piaget in the 50s, the reward is moved underneath a small cup behind one or more bigger screens and its contents is shown in between visits: if the cup is empty we know that the reward must be behind the last screen visited. Humans solve this task after about two years of age, whereas in primates only the great apes show convincing results.

Likely to be even more challenging in terms of attention, are "Transposition" tasks: the reward is hidden underneath one of several equal cups, which are interchanged one or more times. Human children struggle with this task type more than with the previous and do not solve it reliably before the age of three to four years whereas adult apes solve it but have more trouble with double than single swaps.

In "Rotation" tasks several equal cups, one bearing a reward are aligned in parallel on a rotatable platform, which is rotated at different angles. "Translocation" tasks are similar except that the cups are not rotated but the test animal is carried around the arrangement and released at different angles to the cup alignment. Children find Translocation tasks easier than Rotation tasks and solve them at two to three years of age.

A team of international Scientists tested eight Goffin cockatoos (Cacatua goffini), a conspicuously inquisitive and playful species on visible as well as invisible Piagetian object displacements and derivations of spatial transposition, rotation and translocation tasks. 

Birgit Szabo, one of the experimenters from the University of Vienna, says: "The majority of our eight birds readily and spontaneously solved Transposition, Rotation and Translocation tasks whereas only two out of eight choose immediately and reliably the correct location in the original Piagetian invisible displacement task in which a smaller cup is visiting two of three bigger screens."

Alice Auersperg, the manager of the Goffin Lab who was also one of the experimenters, explains: "Interestingly and just opposite to human toddlers our cockatoos had more problems solving the Piagetian invisible displacements than the transposition task with which children struggle until the age of four. Transpositions are highly demanding in terms of attention since two occluding objects are moved simultaneously. Nevertheless, in contrast to apes, which find single swaps easier than double the cockatoos perform equally in both conditions."

Similarly, Goffins had little complications with Rotations and Translocation tasks and some of them solved them at four different angles. Again, in contrast to children, which find Translocations easier than Rotations, the cockatoos showed no significant differences between the two tasks. 

Auguste von Bayern from the University of Oxford adds: " We assume that the ability to fly and prey upon or being preyed upon from the air is likely to require pronounced spatial rotation abilities and may be a candidate trait influencing the animals' performance in rotation and translocation tasks."

Thomas Bugnayer from the University of Vienna concludes: "Finding that Goffins solve transposition, rotation and translocation tasks, which are likely to pose a large cognitive load on working memory, was surprising and calls for more comparative data in order to better understand the relevance of such accurate tracking abilities in terms of ecology and sociality."

 

Borneo's Orangutans Are Coming Down from the Trees; Behavior May Show Adaptation to Habitat Change

July 29, 2013 — Orangutans might be the king of the swingers, but primatologists in Borneo have found that the great apes spend a surprising amount of time walking on the ground. The research, published in theAmerican Journal of Primatology found that it is common for orangutans to come down from the trees to forage or to travel, a discovery which may have implications for conservation efforts.

An expedition led by Brent Loken from Simon Fraser University and Dr. Stephanie Spehar from the University of Wisconsin Oshkosh, travelled to the East Kalimantan region of Borneo. The region's Wehea Forest is a known biodiversity hotspot for primates, including the Bornean orangutan subspecies, Pongo pygmaeus morio, the least studied of orangutan subspecies.

"Orangutans are elusive and one reason why recorded evidence of orangutans on the ground is so rare is that the presence of observers inhibits this behaviour," said Loken. "However, with camera traps we are offered a behind the scenes glimpse at orangutan behaviour."

The team positioned ground-based cameras across a 38-square-kilometre region of the forest and succeeded in capturing the first evidence of orangutans regularly coming down from the trees. The amount of time orangutans spent on the forest floor was found to be comparable to the ground-dwelling pig-tailed macaque, Macaca nemestrina, which is equally abundant in Wehea Forest. Over 8-months orangutans were photographed 110 times, while the macaques were photographed 113 times.

The reason orangutans come down from the trees remains a mystery. However, while the absence of large predators may make it safer to walk on the forest floor, a more pressing influence is the rapid and unprecedented loss of Borneo's orangutan habitat.

"Borneo is a network of timber plantations, agro-forestry areas and mines, with patches of natural forest," said Loken. "The transformation of the landscape could be forcing orangutans to change their habitat and their behaviour."

This research helps to reveal how orangutans can adapt to their changing landscape; however, this does not suggest they can just walk to new territory if their habitat is destroyed. The orangutan subspecies P. p. morio may be adapted to life in more resource scarce forests, having evolved larger jaws which allow them to consume more tree bark and less fruit but they are still dependent on natural forests for their long term survival.

"While we're learning that orangutans may be more behaviourally flexible than we thought and that some populations may frequently come to the ground to travel, they still need forests to survive," said Dr. Spehar. "Even in forest plantation landscapes they rely heavily on patches of natural forest for food resources and nesting sites."

Wehea Forest is one of the only places in Borneo where ten primates species, including five species found only in Borneo, overlap in their ranges. Since Wehea Forest is a biodiversity hotspot, paperwork have been submitted to legally change the status of Wehea Forest from "production forest" to "protected forest." However, given that 78% of wild orangutans live outside of protected areas, it is critical that all of Borneo's remaining forests are either protected or sustainably managed.

"We do not know how long this may take, but protecting Wehea Forest and Borneo's remaining forests is vital to the long term survival of the orangutans," concluded Loken. "Fortunately 60% of Wehea Forest falls under Indonesia's logging moratorium, which helps give legal protection to a large part of the forest for a few more years."

 

Mechanism Behind Squids' and Octopuses' Ability to Change Color Revealed

uly 25, 2013 — Color in living organisms can be formed two ways: pigmentation or anatomical structure. Structural colors arise from the physical interaction of light with biological nanostructures. A wide range of organisms possess this ability, but the biological mechanisms underlying the process have been poorly understood.

Two years ago, an interdisciplinary team from UC Santa Barbara discovered the mechanism by which a neurotransmitter dramatically changes color in the common market squid, Doryteuthis opalescens. That neurotransmitter, acetylcholine, sets in motion a cascade of events that culminate in the addition of phosphate groups to a family of unique proteins called reflectins. This process allows the proteins to condense, driving the animal's color-changing process.

Now the researchers have delved deeper to uncover the mechanism responsible for the dramatic changes in color used by such creatures as squids and octopuses. The findings -- published in the Proceedings of the National Academy of Science, in a paper by molecular biology graduate student and lead author Daniel DeMartini and co-authors Daniel V. Krogstad and Daniel E. Morse -- are featured in the current issue of The Scientist.

Structural colors rely exclusively on the density and shape of the material rather than its chemical properties. The latest research from the UCSB team shows that specialized cells in the squid skin called iridocytes contain deep pleats or invaginations of the cell membrane extending deep into the body of the cell. This creates layers or lamellae that operate as a tunable Bragg reflector. Bragg reflectors are named after the British father and son team who more than a century ago discovered how periodic structures reflect light in a very regular and predicable manner.

"We know cephalopods use their tunable iridescence for camouflage so that they can control their transparency or in some cases match the background," said co-author Daniel E. Morse, Wilcox Professor of Biotechnology in the Department of Molecular, Cellular and Developmental Biology and director of the Marine Biotechnology Center/Marine Science Institute at UCSB.

"They also use it to create confusing patterns that disrupt visual recognition by a predator and to coordinate interactions, especially mating, where they change from one appearance to another," he added. "Some of the cuttlefish, for example, can go from bright red, which means stay away, to zebra-striped, which is an invitation for mating."

The researchers created antibodies to bind specifically to the reflectin proteins, which revealed that the reflectins are located exclusively inside the lamellae formed by the folds in the cell membrane. They showed that the cascade of events culminating in the condensation of the reflectins causes the osmotic pressure inside the lamellae to change drastically due to the expulsion of water, which shrinks and dehydrates the lamellae and reduces their thickness and spacing. The movement of water was demonstrated directly using deuterium-labeled heavy water.

When the acetylcholine neurotransmitter is washed away and the cell can recover, the lamellae imbibe water, rehydrating and allowing them to swell to their original thickness. This reversible dehydration and rehydration, shrinking and swelling, changes the thickness and spacing, which, in turn, changes the wavelength of the light that's reflected, thus "tuning" the color change over the entire visible spectrum.

"This effect of the condensation on the reflectins simultaneously increases the refractive index inside the lamellae," explained Morse. "Initially, before the proteins are consolidated, the refractive index -- you can think of it as the density -- inside the lamellae and outside, which is really the outside water environment, is the same. There's no optical difference so there's no reflection. But when the proteins consolidate, this increases the refractive index so the contrast between the inside and outside suddenly increases, causing the stack of lamellae to become reflective, while at the same time they dehydrate and shrink, which causes color changes. The animal can control the extent to which this happens -- it can pick the color -- and it's also reversible. The precision of this tuning by regulating the nanoscale dimensions of the lamellae is amazing."

Another paper by the same team of researchers, published in Journal of the Royal Society Interface, with optical physicist Amitabh Ghoshal as the lead author, conducted a mathematical analysis of the color change and confirmed that the changes in refractive index perfectly correspond to the measurements made with live cells.

A third paper, in press at Journal of Experimental Biology, reports the team's discovery that female market squid show a set of stripes that can be brightly activated and may function during mating to allow the female to mimic the appearance of the male, thereby reducing the number of mating encounters and aggressive contacts from males. The most significant finding in this study is the discovery of a pair of stripes that switch from being completely transparent to bright white.

"This is the first time that switchable white cells based on the reflectin proteins have been discovered," Morse noted. "The facts that these cells are switchable by the neurotransmitter acetylcholine, that they contain some of the same reflectin proteins, and that the reflectins are induced to condense to increase the refractive index and trigger the change in reflectance all suggest that they operate by a molecular mechanism fundamentally related to that controlling the tunable color."

Could these findings one day have practical applications? "In telecommunications we're moving to more rapid communication carried by light," said Morse. "We already use optical cables and photonic switches in some of our telecommunications devices. The question is -- and it's a question at this point -- can we learn from these novel biophotonic mechanisms that have evolved over millions of years of natural selection new approaches to making tunable and switchable photonic materials to more efficiently encode, transmit, and decode information via light?"

In fact, the UCSB researchers are collaborating with Raytheon Vision Systems in Goleta to investigate applications of their discoveries in the development of tunable filters and switchable shutters for infrared cameras. Down the road, there may also be possible applications for synthetic camouflage.

Other members of the UCSB interdisciplinary research team involved in these discoveries include Elizabeth Eck, Erica Pandolfi, Aaron T. Weaver, and Mary Baum.

This research was supported by the Office of Naval Research via a Multidisciplinary University Research Initiative award and an Army Research Office grant through UCSB's Institute for Collaborative Biotechnologies. As well, use was made of UCSB Materials Research Laboratory central facilities and equipment, which are supported by a grant from the National Science Foundation.

Using Earthquake Sensors to Track Endangered Whales

May 13, 2013 — The fin whale is the second-largest animal ever to live on Earth. It is also, paradoxically, one of the least understood. The animal's huge size and global range make its movements and behavior hard to study.

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A carcass that washed up on a Seattle-area beach this spring provided a reminder that sleek fin whales, nicknamed "greyhounds of the sea," are vulnerable to collision when they strike fast-moving ships. Knowing their swimming behaviors could help vessels avoid the animals. Understanding where and what they eat could also help support the fin whale's slowly rebounding populations.

University of Washington oceanographers are addressing such questions using a growing number of seafloor seismometers, devices that record vibrations. A series of three papers published this winter in the Journal of the Acoustical Society of America interprets whale calls found in earthquake sensor data, an inexpensive and non-invasive way to monitor the whales. The studies are the first to match whale calls with fine-scale swimming behavior, providing new hints at the animals' movement and communication patterns.

The research began a decade ago as a project to monitor tremors on the Juan de Fuca Ridge, a seismically active zone more than a mile deep off the Washington coast. That was the first time UW researchers had collected an entire year's worth of seafloor seismic data.

"Over the winter months we recorded a lot of earthquakes, but we also had an awful lot of fin-whale calls," said principal investigator William Wilcock, a UW professor of oceanography. At first the fin whale calls, which at 17 to 35 vibrations per second overlap with the seismic data, "were kind of just a nuisance," he said.

In 2008 Wilcock got funding from the Office of Naval Research to study the previously discarded whale calls.

Dax Soule, a UW doctoral student in oceanography, compared the calls recorded by eight different seismometers. Previous studies have done this for just two or three animals at a time, but the UW group automated the work to analyze more than 300,000 whale calls. The method is similar to how a smartphone's GPS measures a person's location by comparing paths to different satellites. Researchers looked at the fin whale's call at the eight seismometers to calculate a position. That technique let them follow the animal's path through the instrument grid and within 10 miles of its boundaries.

Soule created 154 individual fin whale paths and discovered three categories of vocalizing whales that swam south in winter and early spring of 2003. He also found a category of rogue whales that traveled north in the early fall, moving faster than the other groups while emitting a slightly higher-pitched call.

"One idea is that these are juvenile males that don't have any reason to head south for the breeding season," Soule said. "We can't say for sure because so little is known about fin whales. To give you an idea, people don't even know how or why they make their sound."

The fin whale's call is not melodic, but that's a plus for this approach. The second-long chirp emitted roughly every 25 seconds is consistently loud and at the lower threshold of human hearing, so within range of earthquake monitoring instruments. These loud, repetitive bleeps are ideally suited for computer analysis.

Michelle Weirathmueller, a UW doctoral student in oceanography, used Soule's triangulations to determine the loudness of the call. She found the fin whale's call is surprisingly consistent at 190 decibels, which translates to 130 decibels in air -- about as loud as a jet engine.

Knowing the consistent amplitude of the fin whale's song will help Weirathmueller track whales with more widely spaced seismometer networks, in which a call is recorded by only one instrument at a time. Those include the Neptune Canada project, the U.S. cabled observatory component of the Ocean Observatories Initiative, and the huge 70-seismometer Cascadia Initiative array that's begun to detect tremors off the Pacific Northwest coast.

"We'd like to know where the fin whales are at any given time and how their presence might be linked to food availability, ocean conditions and seafloor geology," Weirathmueller said. "This is an incredibly rich dataset that can start to pull together the information we need to link the fin whales with their deep-ocean environments."

Seabird Bones Reveal Changes in Open-Ocean Food Chain

May 13, 2013 — Remains of endangered Hawaiian petrels -- both ancient and modern -- show how drastically today's open seas fish menu has changed.

A research team, led by Michigan State University and Smithsonian Institution scientists, analyzed the bones of Hawaiian petrels -- birds that spend the majority of their lives foraging the open waters of the Pacific. They found that the substantial change in petrels' eating habits, eating prey that are lower rather than higher in the food chain, coincides with the growth of industrialized fishing.

The birds' dramatic shift in diet, shown in the current issue of the Proceedings of the National Academy of Sciences, leaves scientists pondering the fate of petrels as well as wondering how many other species face similar challenges.

"Our bone record is alarming because it suggests that open-ocean food webs are changing on a large scale due to human influence," said Peggy Ostrom, co-author and MSU zoologist. "Our study is among the first to address one of the great mysteries of biological oceanography -- whether fishing has gone beyond an influence on targeted species to affect nontarget species and potentially, entire food webs in the open ocean."

Hawaiian petrels' diet is recorded in the chemistry of their bones. By studying the bones' ratio of nitrogen-15 and nitrogen-14 isotopes, researchers can tell at what level in the food chain the birds are feasting; generally, the larger the isotope ratio, the bigger the prey (fish, squid and crustaceans).

Between 4,000 and 100 years ago, petrels had high isotope ratios, indicating they ate bigger prey. After the onset of industrial fishing, which began extending past the continental shelves around 1950, the isotope ratios declined, indicating a species-wide shift to a diet of smaller fish and other prey.

Much research has focused on the impact of fishing near the coasts. In contrast, the open ocean covers nearly half of Earth's surface. But due to a lack of historical records, fishing's impact on most open-ocean animal populations is completely unknown, said lead author Anne Wiley, formerly an MSU doctoral student and now a Smithsonian postdoctoral researcher.

"Hawaiian petrels spend the majority of their lives foraging over vast expanses of open ocean," she said. "In their search for food, they've done what scientists can only dream of. For thousands of years, they've captured a variety of fish, squid and crustaceans from a large portion of the North Pacific Ocean, and a record of their diet is preserved in their bones."

Addressing fishery impact through a chronology of bones is remarkable. Most marine animals die at sea, where their bones are buried on the ocean bottom. But after three decades of fossil collection in the Hawaiian Islands -- the breeding grounds of the Hawaiian petrel -- co-author Helen James of the Smithsonian Institution and her colleagues have amassed a collection of more than 17,000 ancient Hawaiian petrel bones.

"The petrels breed in burrows and caves where, if they die, their bones are likely to be preserved for a long time," James said. "It's fortuitous to find such a rich bone record for a rare oceanic predator."

Further studies are needed to explore how the shift down the food chain is affecting Hawaiian petrels. For a coastal seabird, however, a similar shift in diet has been associated with decreases in population -- bad news for a federally protected bird.

Since petrels exploit fishing grounds from the equator to near the Aleutian Islands -- an area larger than the continental United States -- their foraging habits are quite telling. If petrels, signal flares for open-ocean food webs, have had a species-wide change in feeding habits, how many other predators around the world has fishing impacted? And what role do consumers play?

"What you choose to put on your dinner plate -- that's your connection with the endangered Hawaiian petrel, and with many other marine species," Wiley said.

The research was funded by the National Science Foundation, MSU and the Smithsonian Institution.

Biologists Race to Save Nearly Extinct Florida Bird

19 April 2013 - Even though the project didn't snag a hoped-for grant, federal officials said Thursday they have decided to proceed with plans to collect eggs from the nests of one of the most endangered species in North America — the Florida grasshopper sparrow — in hopes of preventing its extinction.

Researchers fear the small, elusive bird, now clinging to survival in three Central Florida parklands, could vanish within a few years.

U.S. Fish and Wildlife Service officials said the captive-breeding program will consist of volunteers and staff from their agency, the state Fish and Wildlife Conservation Commission and the state Park Service. Teams will attempt to collect eggs through early summer, taking them to the Rare Species Conservatory Foundation in Loxahatchee.

Hatchlings will be kept in captivity in a years-long effort to establish a population of birds that eventually could help bolster the health of sparrows still existing in the wild — or serve as pioneers in re-establishing a wild population should the current one go extinct.

Several university and private researchers have criticized the federal agency, harshly in some cases, for giving the sparrows a low priority as their numbers dipped alarmingly and inexplicably in recent years. The birds rely on vast, treeless prairies, but much of that habitat has been paved by development or plowed under by agriculture.

Researchers are vexed by the birds' decline in part because the public lands where they still exist, including Three Lakes Wildlife Management Area and Kissimmee Prairie Preserve State Park, have been intensively managed to suit the sparrows' needs. Invading fire ants are suspected to play a role in the decline.

The Fish and Wildlife Service said it will cobble together dollars from various sources to support further research and the captive-breeding work.