With Environmental DNA, Small Water Samples Can Find Really Big Animals

By WILDLIFE CONSERVATION SOCIETY MARCH 27, 2022

Humpback whales now swim within sight of New York City. Credit: Julie Larsen Maher

Scientists say environmental DNA can detect whales and dolphins in New York waters.

• Results are some of the most promising to date in the open Ocean
• Massive renewable energy projects coming to the New York Bight could impact whales and dolphins

A team of scientists used an emerging genetic tool that analyzes DNA in water samples to detect whales and dolphins in New York waters.

Called environmental DNA or eDNA, the technique searches for trace amounts of genetic material left behind by wildlife.

The scientists, from California State University, CUNY, Wildlife Conservation Society (WCS), and Columbia University, published their results in the journal Frontiers.

The scientists say that eDNA can be used to complement other methods to locate whales and dolphins such as visual observations and acoustic monitoring, and their eDNA detections are some of the most promising to date for detecting whales and dolphins from seawater in the open ocean.

Said the study’s lead author Dr. Elizabeth Alter of California State University: “Determining how cetaceans and other threatened marine animals use coastal habitats is critical to their effective conservation. By generating eDNA data in parallel with survey data, it will be possible to gain a clearer understanding of how this tool can be used in management and conservation contexts to monitor species of conservation concern over large marine ecosystems.”

In addition to finding whales and dolphins, the technique detected baitfish present in the area preyed on by whales and dolphins. The authors say the technique could eventually be used to identify individual animals.

Said Dr. Howard C. Rosenbaum, Director of WCS’s Ocean Giants Program/Senior Scientist NY Aquarium and a co-author of the study: “Innovation and application of new techniques, such as the possibility of using eDNA, that leads to having better information about distribution of whales, dolphins and their prey is so important today, especially where potential impacts in these habitats may be increasing human activities.”

The authors say that eDNA drops to lower levels over time and that additional research is needed to better understand how factors such as behavior and oceanographic conditions contribute to the longevity of eDNA signals.

Though there are some signs of promising recovery for many whale species and populations, whales continue to face a range of modern day threats ranging from ship strikes, to entanglement with nets, to ocean noise.

The Biden-Harris administration, New York State and other states on the eastern seaboard are scaling up massive renewable energy projects to meet energy demands and help address climate change, including a wind energy auction for more than 488,000 acres in the New York Bight. There are many potential impacts from these developments to whales that the environmental community, industry, and state/federal authorities are aiming to address. WCS has been involved at state and national level dialogues as well as developing best practice guidance through the IUCN.

The use of emerging and novel techniques such as eDNA as demonstrated by the results of the current study in the NY Bight and other approaches can offer new insights as to whale presence and their prey in and around lease areas as offshore wind scales up along the eastern seaboard.  More broadly, WCS increasingly uses eDNA in its conservation work, detecting critically endangered wildlife such as Swinhoe’s softshell turtle, in the Bolivian Amazon, and in some of the most rugged areas on the planet including Mt. Everest.

Reference: “Using Environmental DNA to Detect Whales and Dolphins in the New York Bight” by S. Elizabeth Alter, Carissa D. King, Emily Chou, Sam Chew Chin, Melinda Rekdahl and Howard C. Rosenbaum, 11 February 2022, Frontiers in Conservation Science.
DOI: 10.3389/fcosc.2022.820377

DNA Testing Exposes Tactics of International Criminal Networks Trafficking Elephant Ivory Out of Africa

By UNIVERSITY OF WASHINGTON MARCH 27, 2022

These maps illustrate shifts in smuggling operations over time to different African ports. Each solid dot represents an ivory seizure in that country. Blue lines indicate that two seizures are connected by genetic matches among tusks, physical evidence or both. Initially, savannah elephant ivory shipments were smuggled through Tanzania, Zambia and Malawi, but shifted to Kenya in 2010-2012 and Uganda in 2013-2015. Next, operations shifted to the Democratic Republic of the Congo and Angola in 2016-2019. Forest elephant ivory shipments shifted from Togo in 2013-2014 to Nigeria in 2016-2019, and showed connections to seizures in Central Africa. Credit: Wasser et al. 2022, Nature Human Behaviour

A team led by scientists at the University of Washington and special agents with the U.S. Department of Homeland Security has used genetic testing of ivory shipments seized by law enforcement to uncover the international criminal networks behind ivory trafficking out of Africa. The genetic connections across shipments that they’ve uncovered exposes an even higher degree of organization among ivory smuggling networks than previously known.

The paper, published recently in the journal Nature Human Behaviour, incorporates results from DNA testing of more than 4,000 African elephant tusks from 49 different ivory seizures made in 12 African nations over a 17-year period.

Tusks from an ivory seizure in 2015 in Singapore after they have been sorted into pairs by the process developed by Wasser and his team. Credit: Center for Environmental Forensic Science/University of Washington

Exposing the connections among separate ivory seizures — made at African and Asian ports sometimes thousands of miles apart — will likely boost evidence against the criminals arrested for elephant poaching and ivory smuggling, and strengthen prosecutions of the responsible transnational criminal organizations, according to lead author Samuel Wasser, a UW professor of biology and director of the Center for Environmental Forensic Science, whose group developed the genetic tools behind this work.

“These methods are showing us that a handful of networks are behind a majority of smuggled ivory, and that the connections between these networks are deeper than even our previous research showed,” said Wasser.

Tusks from an ivory seizure in 2017 in Hong Kong. Credit: WildAid

Illegal ivory trade — along with habitat loss, climate change and other factors — has decimated the two elephant species in Africa. Although ivory seizures by authorities come from elephants that have already been slaughtered, the tusks can provide valuable information by illuminating the poaching, shipment activities and connectivity of traffickers.

Previous work by Wasser and his collaborators — published in 2018 in the journal Science Advances — identified tusks from the same elephant that were separated and smuggled in different shipments prior to being seized by law enforcement. Finding both tusks from the same individual linked those seizures to the same trafficking networks. Those efforts indicated that, from 2011 to 2014, cartels tended to smuggle ivory out of three African ports: Mombasa, Kenya; Entebbe, Uganda; and Lomé, Togo.

African elephants examine a bone from a fellow elephant. Credit: Karl Ammann

In this new endeavor, Wasser and his colleagues expanded their DNA analysis and testing regimen to also identify tusks of elephants that were close relatives — parents and offspring, full siblings and half-siblings. Adding close relatives expands the scope of the effort, Wasser said.

“If you’re trying to match one tusk to its pair, you have a low chance of a match. But identifying close relatives is going to be a much more common event, and can link more ivory seizures to the same smuggling networks,” said Wasser.

The team tested this expanded protocol on 4,320 tusks — from both forest elephants, Loxodonta cyclotis, and savannah elephants, Loxodonta africana — from 49 separate large shipments totaling 111 metric tons of ivory, all seized from 2002 to 2019. Results showed that a majority of these shipments could be linked based on matching tusks either from the same individual or from close relatives.

Wasser (left) and his team sort tusks from a seizure in Singapore in 2015 and use saws to cut away ivory samples for subsequent DNA extraction and genetic analysis. Credit: Kate Brooks

“Identifying close relatives indicates that poachers are likely going back to the same populations repeatedly — year after year — and tusks are then acquired and smuggled out of Africa on container ships by the same criminal network,” said Wasser. “This criminal strategy makes it much harder for authorities to track and seize these shipments because of the immense pressure they are under to move large volumes of containers quickly through ports,” said Wasser.

The genetic data show that a handful of interconnected smuggling networks are likely behind most large ivory shipments, most often exported from ports in Kenya, Uganda and Nigeria. By expanding the analysis to identify tusks from close relatives, the team could also link seizures from a dozen countries in Central and West Africa, stretching from Ivory Coast on the Atlantic Ocean to Mozambique on the Indian Ocean.

Tusks from a seizure in Malaysia in 2012. Credit: Malaysia Department of National Parks

The larger analysis also can track how smuggling networks shifted their operations to different ports over time: from Tanzania in the early 2000s; then to Kenya and Uganda; and, most recently, to Angola and the Democratic Republic of the Congo. In West Africa, a temporal shift occurred from Togo to Nigeria.

“By linking individual seizures, we’re laying out whole smuggling networks that are trying to get these tusks off the continent,” said Wasser.

Wasser (left) and his team sample ivory from tusks in Malaysia in 2014. Credit: Malaysia Department of National Parks

The criminals behind one ivory seizure would have been prosecuted solely for that seizure. But the genetic evidence by Wasser and his team could strengthen investigations and prosecutions by linking responsible transnational criminal organizations to multiple seizures — leading to more severe penalties.

Reference: “Elephant genotypes reveal the size and connectivity of transnational ivory traffickers” by Samuel K. Wasser, Charles J. Wolock, Mary K. Kuhner, John E. Brown III, Chris Morris, Ryan J. Horwitz, Anna Wong, Charlene J. Fernandez, Moses Y. Otiende, Yves Hoareau, Zofia A. Kaliszewska, Eunjin Jeon, Kin-Lan Han and Bruce S. Weir, 14 February 2022, Nature Human Behaviour.
DOI: 10.1038/s41562-021-01267-6

Co-authors are Charles Wolock, a UW doctoral student in biostatistics; John Brown III with the U.S. Department of Homeland Security; UW biology research scientists Mary Kuhner, Yves Hoareau, Eunjin Jeon and Zofia Kaliszewska; Kin-Lan Han, a former UW researcher who is currently a geneticist with the U.S. Fish and Wildlife Service; Chris Morris with SeeJ-Africa in Nairobi, Kenya; Ryan Horwitz, who was at the University of Michigan and is now a UW research scientist; Anna Wong and Charlene J. Fernandez with the National Parks Board of Singapore; and Moses Otiende with the Kenya Wildlife Service.

The research was funded by the Paul and Yaffe Maritz Family Foundation, the Wildlife Conservation Network, the Elephant Crisis Fund, the U.N. Development Program, the Paul G. Allen Family Foundation, the Woodtiger Fund, the Wildcat Foundation, the U.S. Department of State, U.S. Department of Homeland Security, HSI, the World Bank, the U.N. Office on Drugs and Crime, the National Institute of Justice and the National Institutes of Health.

Grant numbers: 2020-DQ-BX-0022, GM075091

How the MIT Mini Cheetah Robot Learns To Run Entirely by Trial and Error

By RACHEL GORDON, MIT CSAIL MARCH 29, 2022

MIT’s mini cheetah, using a model-free reinforcement learning system, broke the record for the fastest run recorded. Credit: Photo courtesy of MIT CSAIL.

CSAIL scientists came up with a learning pipeline for the four-legged robot that learns to run entirely by trial and error in simulation.

It’s been roughly 23 years since one of the first robotic animals trotted on the scene, defying classical notions of our cuddly four-legged friends. Since then, a barrage of the walking, dancing, and door-opening machines have commanded their presence, a sleek mixture of batteries, sensors, metal, and motors. Missing from the list of cardio activities was one both loved and loathed by humans (depending on whom you ask), and which proved slightly trickier for the bots: learning to run.

Researchers from MIT’s Improbable AI Lab, part of the Computer Science and Artificial Intelligence Laboratory (CSAIL) and directed by MIT Assistant Professor Pulkit Agrawal, as well as the Institute of AI and Fundamental Interactions (IAIFI) have been working on fast-paced strides for a robotic mini cheetah — and their model-free reinforcement learning system broke the record for the fastest run recorded. Here, MIT PhD student Gabriel Margolis and IAIFI postdoc Ge Yang discuss just how fast the cheetah can run.

Q: We’ve seen videos of robots running before. Why is running harder than walking?

A: Achieving fast running requires pushing the hardware to its limits, for example by operating near the maximum torque output of motors. In such conditions, the robot dynamics are hard to analytically model. The robot needs to respond quickly to changes in the environment, such as the moment it encounters ice while running on grass. If the robot is walking, it is moving slowly and the presence of snow is not typically an issue. Imagine if you were walking slowly, but carefully: you can traverse almost any terrain. Today’s robots face an analogous problem. The problem is that moving on all terrains as if you were walking on ice is very inefficient, but is common among today’s robots. Humans run fast on grass and slow down on ice — we adapt. Giving robots a similar capability to adapt requires quick identification of terrain changes and quickly adapting to prevent the robot from falling over. In summary, because it’s impractical to build analytical (human-designed) models of all possible terrains in advance, and the robot’s dynamics become more complex at high-velocities, high-speed running is more challenging than walking.

The MIT mini cheetah learns to run faster than ever, using a learning pipeline that’s entirely trial and error in simulation.

Q: Previous agile running controllers for the MIT Cheetah 3 and mini cheetah, as well as for Boston Dynamics’ robots, are “analytically designed,” relying on human engineers to analyze the physics of locomotion, formulate efficient abstractions, and implement a specialized hierarchy of controllers to make the robot balance and run. You use a “learn-by-experience model” for running instead of programming it. Why?

A: Programming how a robot should act in every possible situation is simply very hard. The process is tedious, because if a robot were to fail on a particular terrain, a human engineer would need to identify the cause of failure and manually adapt the robot controller, and this process can require substantial human time. Learning by trial and error removes the need for a human to specify precisely how the robot should behave in every situation. This would work if: (1) the robot can experience an extremely wide range of terrains; and (2) the robot can automatically improve its behavior with experience.

Thanks to modern simulation tools, our robot can accumulate 100 days’ worth of experience on diverse terrains in just three hours of actual time. We developed an approach by which the robot’s behavior improves from simulated experience, and our approach critically also enables successful deployment of those learned behaviors in the real world. The intuition behind why the robot’s running skills work well in the real world is: Of all the environments it sees in this simulator, some will teach the robot skills that are useful in the real world. When operating in the real world, our controller identifies and executes the relevant skills in real-time.

Q: Can this approach be scaled beyond the mini cheetah? What excites you about its future applications?

A: At the heart of artificial intelligence research is the trade-off between what the human needs to build in (nature) and what the machine can learn on its own (nurture). The traditional paradigm in robotics is that humans tell the robot both what task to do and how to do it. The problem is that such a framework is not scalable, because it would take immense human engineering effort to manually program a robot with the skills to operate in many diverse environments. A more practical way to build a robot with many diverse skills is to tell the robot what to do and let it figure out the how. Our system is an example of this. In our lab, we’ve begun to apply this paradigm to other robotic systems, including hands that can pick up and manipulate many different objects.

This work was supported by the DARPA Machine Common Sense Program, the MIT Biomimetic Robotics Lab, NAVER LABS, and in part by the National Science Foundation AI Institute for Artificial Intelligence Fundamental Interactions, United States Air Force-MIT AI Accelerator, and MIT-IBM Watson AI Lab. The research was conducted by the Improbable AI Lab.

Hundreds of “Hidden” New Mammal Species Waiting To Be Found

By OHIO STATE UNIVERSITY MARCH 29, 2022

Elephant shew.

Research suggests where these species may be “hidden.”

At least hundreds of so-far unidentified species of mammals are hiding in plain sight around the world, a new study suggests.

Researchers found that most of these hidden mammals are small bodied, many of them bats, rodents, shrews, and moles.

These unknown mammals are hidden in plain sight partly because most are small and look so much like known animals that biologists have not been able to recognize they are actually a different species, said study co-author Bryan Carstens, a professor of evolution, ecology and organismal biology at The Ohio State University.

“Small, subtle differences in appearance are harder to notice when you’re looking at a tiny animal that weighs 10 grams than when you’re looking at something that is human-sized,” Carstens said.

“You can’t tell they are different species unless you do a genetic analysis.”

The study was published on March 28, 2022, in the journal Proceedings of the National Academy of Sciences.

Small mammals, like this bicolored shrew, are more likely than larger animals to be ‘hiding’ new species. Credit: Werner Korschinsky, via Wikimedia Commons

The team, led by Ohio State graduate student Danielle Parsons, used a supercomputer and machine-learning techniques to analyze millions of publicly available gene sequences from 4,310 mammal species, as well as data on where the animals live, their environment, life history, and other relevant information.

This allowed them to build a predictive model to identify the taxa of mammals that are likely to contain hidden species.

“Based on our analysis, a conservative estimate would be that there are hundreds of species of mammals worldwide that have yet to be identified,” Carstens said.

That finding, in itself, would not be surprising to biologists, he said. Only an estimated 1 to 10% of Earth’s species have been formally described by researchers.

“What we did that was new was predict where these new species are most likely to be found,” Carstens said.

Results showed unidentified species are most likely to be found in the families of small-bodied animals, such as bats and rodents.

The researchers’ model also predicted hidden species would most likely be found in species that have wider geographic ranges with higher variability in temperature and precipitation.

Many of the hidden species are also likely to occur in tropical rain forests, which is not surprising because that’s where most mammal species occur.

But many unidentified species are also likely living here in the United States, Carstens said. His lab has identified some of them. For example, in 2018, Carstens and his then-graduate student Ariadna Morales published a paper showing that the little brown bat, found in much of North America, is actually five different species.

That study also showed a key reason why it is important to identify new species. One of the newly delimited bats had a very narrow range where it lived, just around the Great Basin in Nevada – making its protection especially critical.

“That knowledge is important to people who are doing conservation work. We can’t protect a species if we don’t know that it exists. As soon as we name something as a species, that matters in a lot of legal and other ways,” Carstens said.

Based on the results of this study, Carstens estimates that somewhere near 80% of mammal species worldwide have been identified.

“The shocking thing is that mammals are very well described compared to beetles or ants or other types of animals,” he said.

“We know a lot more about mammals than many other animals because they tend to be larger and are more closely related to humans, which makes them more interesting to us.”

Reference: “Analysis of biodiversity data suggests that mammal species are hidden in predictable places” by Danielle J. Parsons, Tara A. Pelletier, Jamin G. Wieringa, Drew J. Duckett and Bryan C. Carstens, 28 March 2022, Proceedings of the National Academy of Sciences.
DOI: 10.1073/pnas.2103400119

The study was supported by the National Science Foundation and the Ohio Supercomputer Center.

Other co-authors were Tara Pelletier, assistant professor of biology at Radford University; and Jamin Wieringa and Drew Duckett, graduate students at Ohio State.

CRISPR CRITTER

Here CRISPR Kitty? Progress in Developing a Hypoallergenic Cat

By GENETIC ENGINEERING NEWS MARCH 28, 2022

Researchers at InBio (formerly Indoor Biotechnologies), a biotech company in Virginia, report progress en route to developing a hypoallergenic cat – or at least treating patients with allergies to the domestic cat – in a new article published online in The CRISPR Journal.

Journal dedicated to outstanding research and commentary on all aspects of CRISPR and gene editing research. Credit: Mary Ann Publications, Inc., publishers

About 15 percent of the population suffer allergies to domestic cats, which researchers have previously shown is largely attributable to what the Atlantic called “a pernicious little protein” — an allergen called Fel d 1 that is shed by all cats. In the new study, Nicole Brackett and colleagues at InBio performed a bioinformatics analysis of the Fel d 1 gene from 50 domestic cats to pinpoint conserved coding regions suitable for CRISPR editing. Further comparisons to genes in eight exotic felid species revealed a high degree of variation, suggesting that Fel d 1 is nonessential for cats. The researchers used CRISPR-Cas9 to disrupt Fel d 1 with high efficiency.

“Our data indicate that Fel d 1 is both a rational and viable candidate for gene deletion, which may profoundly benefit cat allergy sufferers by removing the major allergen at the source,” the authors write. The study paves the way for further experiments exploring the use of CRISPR as a potential genetic therapy to muzzle the release of cat allergens.

Reference: 28 March 2022, The CRISPR Journal.

Sentinel-6: International Sea Level Satellite Takes Over

By JET PROPULSION LABORATORY MARCH 27, 2022

This animation shows the radar pulse from the Sentinel-6 Michael Freilich satellite’s altimeter bouncing off the sea surface in order to measure the height of the ocean. Credit: NASA/JPL-Caltech

Sentinel-6 Michael Freilich, the newest addition to a long line of ocean-monitoring satellites, becomes the reference satellite for sea level measurements.

On March 22, the newest U.S.-European sea level satellite, named Sentinel-6 Michael Freilich, became the official reference satellite for global sea level measurements. This means that sea surface height data collected by other satellites will be compared to the information produced by Sentinel-6 Michael Freilich to ensure their accuracy.

Launched from Vandenberg Air Force Base in November 2020, the satellite is continuing a nearly 30-year legacy started by the TOPEX/Poseidon satellite, which began its mission to measure sea surface height in the early 1990s. A series of successor satellites have carried on the effort since then, with Sentinel-6 Michael Freilich being the most recent. Its twin, Sentinel-6B, is slated to launch in 2025.

“These missions, of which Sentinel-6 Michael Freilich is the latest, are the gold standard when it comes to sea level measurements, which are critical for understanding and monitoring climate change,” said Josh Willis, Sentinel-6 Michael Freilich project scientist at NASA’s Jet Propulsion Laboratory in Southern California.

Meltwater from Greenland glaciers like the one pictured can contribute significantly to sea level rise. Sentinel-6 Michael Freilich monitors the height of Earth’s oceans so that researchers can better understand the amount and rate of sea level rise. Credit: NASA Earth Observatory using Landsat data from USGS

Long-term records of sea level height are key to monitoring how much, and how fast, the oceans are rising in a warming climate. “We can’t lose track of how much sea level has gone up because if we do, it’s hard to predict what’s going to happen in the decades to come,” Willis added.

“The unprecedented accuracy of the sea level measurements provided by this mission ensures not only the continuity of a 30-year data record, but allows improving our understanding of climate change and the impact of rising seas on coastal areas and communities,” said Julia Figa Saldana, ocean altimetry program manager at the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT).

Sentinel-6 Michael Freilich. Credit: NASA

After Sentinel-6 Michael Freilich launched, it settled into orbit flying 30 seconds behind its predecessor, Jason-3. Science and engineering teams have spent the time since launch making sure Sentinel-6 Michael Freilich was collecting the intended data and that the information was accurate. Some of the initial data was made available last year for use in tasks like weather forecasting. And after further validation, the scientists agreed that Sentinel-6 Michael Freilich should become the reference satellite for sea level measurements.

Later this year, teams will move Jason-3 into what’s called an interleaved orbit. From that new position, the ground track – or the strip of Earth that Jason-3’s instruments see as the satellite travels around the planet – will run in between the ground tracks of successive orbits for Sentinel-6 Michael Freilich. Jason-3 will keep measuring sea level height from the interleaved orbit, although it will no longer serve as the official reference sea level satellite. But by continuing to collect sea level data, Jason-3 will essentially double the number of measurements seen by each pass of Sentinel-6 Michael Freilich, helping to greatly increase the spatial resolution of sea level measurements provided by both satellites.

More About the Mission

Sentinel-6 Michael Freilich, named after former NASA Earth Science Division Director Michael Freilich, is one of two satellites that compose the Copernicus Sentinel-6/Jason-CS (Continuity of Service) mission.

Sentinel-6/Jason-CS was jointly developed by ESA (European Space Agency), EUMETSAT, NASA, and NOAA, with funding support from the European Commission and technical support on performance from CNES (France’s National Centre for Space Studies). Spacecraft monitoring and control, as well as the processing of all the altimeter science data, is carried out by EUMETSAT on behalf of the EU’s Copernicus program, with the support of all partner agencies.

JPL, a division of Caltech in Pasadena, contributed three science instruments for each Sentinel-6 satellite: the Advanced Microwave Radiometer, the Global Navigation Satellite System – Radio Occultation, and the Laser Retroreflector Array. NASA also contributed launch services, ground systems supporting operation of the NASA science instruments, the science data processors for two of these instruments, and support for the U.S. members of the international Ocean Surface Topography Science Team.

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