Tag Archives: Madagascar

Monitoring forest soundscapes for conservation and more about whale songs

I don’t understand why anyone would publicize science work featuring soundscapes without including an audio file. However, no one from Princeton University (US) phoned and asked for my advice :).

On the plus side, my whale story does have a sample audio file. However, I’m not sure if I can figure out how to embed it here.

Princeton and monitoring forests

In addition to a professor from Princeton University, there’s the founder of an environmental news organization and someone who’s both a professor at the University of Queensland (Australia) and affiliated with the Nature Conservancy making this of the more unusual collaborations I’ve seen.

Moving on to the news, a January 4, 2019 Princeton University news release (also on EurekAlert but published on Jan. 3, 2019) by B. Rose Kelly announces research into monitoring forests,

Recordings of the sounds in tropical forests could unlock secrets about biodiversity and aid conservation efforts around the world, according to a perspective paper published in Science.

Compared to on-the-ground fieldwork, bioacoustics –recording entire soundscapes, including animal and human activity — is relatively inexpensive and produces powerful conservation insights. The result is troves of ecological data in a short amount of time.

Because these enormous datasets require robust computational power, the researchers argue that a global organization should be created to host an acoustic platform that produces on-the-fly analysis. Not only could the data be used for academic research, but it could also monitor conservation policies and strategies employed by companies around the world.

“Nongovernmental organizations and the conservation community need to be able to truly evaluate the effectiveness of conservation interventions. It’s in the interest of certification bodies to harness the developments in bioacoustics for better enforcement and effective measurements,” said Zuzana Burivalova, a postdoctoral research fellow in Professor David Wilcove’s lab at Princeton University’s Woodrow Wilson School of Public and International Affairs.

“Beyond measuring the effectiveness of conservation projects and monitoring compliance with forest protection commitments, networked bioacoustic monitoring systems could also generate a wealth of data for the scientific community,” said co-author Rhett Butler of the environmental news outlet Mongabay.

Burivalova and Butler co-authored the paper with Edward Game, who is based at the Nature Conservancy and the University of Queensland.

The researchers explain that while satellite imagery can be used to measure deforestation, it often fails to detect other subtle ecological degradations like overhunting, fires, or invasion by exotic species. Another common measure of biodiversity is field surveys, but those are often expensive, time consuming and cover limited ground.

Depending on the vegetation of the area and the animals living there, bioacoustics can record animal sounds and songs from several hundred meters away. Devices can be programmed to record at specific times or continuously if there is solar polar or a cellular network signal. They can also record a range of taxonomic groups including birds, mammals, insects, and amphibians. To date, several multiyear recordings have already been completed.

Bioacoustics can help effectively enforce policy efforts as well. Many companies are engaged in zero-deforestation efforts, which means they are legally obligated to produce goods without clearing large forests. Bioacoustics can quickly and cheaply determine how much forest has been left standing.

“Companies are adopting zero deforestation commitments, but these policies do not always translate to protecting biodiversity due to hunting, habitat degradation, and sub-canopy fires. Bioacoustic monitoring could be used to augment satellites and other systems to monitor compliance with these commitments, support real-time action against prohibited activities like illegal logging and poaching, and potentially document habitat and species recovery,” Butler said.

Further, these recordings can be used to measure climate change effects. While the sounds might not be able to assess slow, gradual changes, they could help determine the influence of abrupt, quick differences to land caused by manufacturing or hunting, for example.

Burivalova and Game have worked together previously as you can see in a July 24, 2017 article by Justine E. Hausheer for a nature.org blog ‘Cool Green Science’ (Note: Links have been removed),

Morning in Musiamunat village. Across the river and up a steep mountainside, birds-of-paradise call raucously through the rainforest canopy, adding their calls to the nearly deafening insect chorus. Less than a kilometer away, small birds flit through a grove of banana trees, taro and pumpkin vines winding across the rough clearing. Here too, the cicadas howl.

To the ear, both garden and forest are awash with noise. But hidden within this dawn chorus are clues to the forest’s health.

New acoustic research from Nature Conservancy scientists indicates that forest fragmentation drives distinct changes in the dawn and dusk choruses of forests in Papua New Guinea. And this innovative method can help evaluate the conservation benefits of land-use planning efforts with local communities, reducing the cost of biodiversity monitoring in the rugged tropics.

“It’s one thing for a community to say that they cut fewer trees, or restricted hunting, or set aside a protected area, but it’s very difficult for small groups to demonstrate the effectiveness of those efforts,” says Eddie Game, The Nature Conservancy’s lead scientist for the Asia-Pacific region.

Aside from the ever-present logging and oil palm, another threat to PNG’s forests is subsistence agriculture, which feeds a majority of the population. In the late 1990s, The Nature Conservancy worked with 11 communities in the Adelbert Mountains to create land-use plans, dividing each community’s lands into different zones for hunting, gardening, extracting forest products, village development, and conservation. The goal was to limit degradation to specific areas of the forest, while keeping the rest intact.

But both communities and conservationists needed a way to evaluate their efforts, before the national government considered expanding the program beyond Madang province. So in July 2015, Game and two other scientists, Zuzana Burivalova and Timothy Boucher, spent two weeks gathering data in the Adelbert Mountains, a rugged lowland mountain range in Papua New Guinea’s Madang province.

Working with conservation rangers from Musiamunat, Yavera, and Iwarame communities, the research team tested an innovative method — acoustic sampling — to measure biodiversity across the community forests. Game and his team used small acoustic recorders placed throughout the forest to record 24-hours of sound from locations in each of the different land zones.

Soundscapes from healthy, biodiverse forests are more complex, so the scientists hoped that these recordings would show if parts of the community forests, like the conservation zones, were more biodiverse than others. “Acoustic recordings won’t pick up every species, but we don’t need that level of detail to know if a forest is healthy,” explains Boucher, a conservation geographer with the Conservancy.

Here’s a link to and a citation for the latest work from Burivalova and Game,

The sound of a tropical forest by Zuzana Burivalova, Edward T. Game, Rhett A. Butler. Science 04 Jan 2019: Vol. 363, Issue 6422, pp. 28-29 DOI: 10.1126/science.aav1902

This paper is behind a paywall. You can find out more about Mongabay and Rhett Butler in its Wikipedia entry.

***ETA July 18, 2019: Cara Cannon Byington, Associate Director, Science Communications for the Nature Conservancy emailed to say that a January 3, 2019 posting on the conservancy’s Cool Green Science Blog features audio files from the research published in ‘The sound of a tropical forest. Scroll down about 75% of the way for the audio.***

Whale songs

Whales share songs when they meet and a January 8, 2019 Wildlife Conservation Society news release (also on EurekAlert) describes how that sharing takes place,

Singing humpback whales from different ocean basins seem to be picking up musical ideas from afar, and incorporating these new phrases and themes into the latest song, according to a newly published study in Royal Society Open Science that’s helping scientists better understand how whales learn and change their musical compositions.

The new research shows that two humpback whale populations in different ocean basins (the South Atlantic and Indian Oceans) in the Southern Hemisphere sing similar song types, but the amount of similarity differs across years. This suggests that males from these two populations come into contact at some point in the year to hear and learn songs from each other.

The study titled “Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins” appears in the latest edition of the Royal Society Open Science journal. The authors are: Melinda L. Rekdahl, Carissa D. King, Tim Collins, and Howard Rosenbaum of WCS (Wildlife Conservation Society); Ellen C. Garland of the University of St. Andrews; Gabriella A. Carvajal of WCS and Stony Brook University; and Yvette Razafindrakoto of COSAP [ (Committee for the Management of the Protected Area of Bezà Mahafaly ] and Madagascar National Parks.

“Song sharing between populations tends to happen more in the Northern Hemisphere where there are fewer physical barriers to movement of individuals between populations on the breeding grounds, where they do the majority of their singing. In some populations in the Southern Hemisphere song sharing appears to be more complex, with little song similarity within years but entire songs can spread to neighboring populations leading to song similarity across years,” said Dr. Melinda Rekdahl, marine conservation scientist for WCS’s Ocean Giants Program and lead author of the study. “Our study shows that this is not always the case in Southern Hemisphere populations, with similarities between both ocean basin songs occurring within years to different degrees over a 5-year period.”

The study authors examined humpback whale song recordings from both sides of the African continent–from animals off the coasts of Gabon and Madagascar respectively–and transcribed more than 1,500 individual sounds that were recorded between 2001-2005. Song similarity was quantified using statistical methods.

Male humpback whales are one of the animal kingdom’s most noteworthy singers, and individual animals sing complex compositions consisting of moans, cries, and other vocalizations called “song units.” Song units are composed into larger phrases, which are repeated to form “themes.” Different themes are produced in a sequence to form a song cycle that are then repeated for hours, or even days. For the most part, all males within the same population sing the same song type, and this population-wide song similarity is maintained despite continual evolution or change to the song leading to seasonal “hit songs.” Some song learning can occur between populations that are in close proximity and may be able to hear the other population’s song.

Over time, the researchers detected shared phrases and themes in both populations, with some years exhibiting more similarities than others. In the beginning of the study, whale populations in both locations shared five “themes.” One of the shared themes, however, had differences. Gabon’s version of Theme 1, the researchers found, consisted of a descending “cry-woop”, whereas the Madagascar singers split Theme 1 into two parts: a descending cry followed by a separate woop or “trumpet.”

Other differences soon emerged over time. By 2003, the song sung by whales in Gabon became more elaborate than their counterparts in Madagascar. In 2004, both population song types shared the same themes, with the whales in Gabon’s waters singing three additional themes. Interestingly, both whale groups had dropped the same two themes from the previous year’s song types. By 2005, songs being sung on both sides of Africa were largely similar, with individuals in both locations singing songs with the same themes and order. However, there were exceptions, including one whale that revived two discontinued themes from the previous year.

The study’s results stands in contrast to other research in which a song in one part of an ocean basin replaces or “revolutionizes” another population’s song preference. In this instance, the gradual changes and degrees of similarity shared by humpbacks on both sides of Africa was more gradual and subtle.

“Studies such as this one are an important means of understanding connectivity between different whale populations and how they move between different seascapes,” said Dr. Howard Rosenbaum, Director of WCS’s Ocean Giants Program and one of the co-authors of the new paper. “Insights on how different populations interact with one another and the factors that drive the movements of these animals can lead to more effective plans for conservation.”

The humpback whale is one of the world’s best-studied marine mammal species, well known for its boisterous surface behavior and migrations stretching thousands of miles. The animal grows up to 50 feet in length and has been globally protected from commercial whaling since the 1960s. WCS has studied humpback whales since that time and–as the New York Zoological Society–played a key role in the discovery that humpback whales sing songs. The organization continues to study humpback whale populations around the world and right here in the waters of New York; research efforts on humpback and other whales in New York Bight are currently coordinated through the New York Aquarium’s New York Seascape program.

I’m not able to embed the audio file here but, for the curious, there is a portion of a humpback whale song from Gabon here at EurekAlert.

Here’s a link to and a citation for the research paper,

Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins by Melinda L. Rekdahl, Ellen C. Garland, Gabriella A. Carvajal, Carissa D. King, Tim Collins, Yvette Razafindrakoto and Howard Rosenbaum. Royal Society Open Science 21 November 2018 Volume 5 Issue 11 https://doi.org/10.1098/rsos.172305 Published:28 November 2018

This is an open access paper.

New gecko species in Madagascar with skin specially adapted to tearing

After all these years of writing about geckos and their adhesive properties (they can hang off a wall or ceiling by a single toe), I’ve developed a mild interest in them. From a Feb. 7, 2017 posting by Dirk Steinke for the One species a day blog,

The new species was found in northern Madagascar and its name was build [sic] from the two Greek stems mégas, meaning ‘very large’ and lepís, meaning ‘scale’, and refers to the large size of the scales of this species in comparison to other geckos.

Caption: The new fish-scale gecko, Geckolepis megalepis, has the largest body scales of all geckos. This nocturnal lizard was discovered in the ‘tsingy’ karst formations in northern Madagascar Credit: F. Glaw

There’s more about the new species and the research in a Feb. 7, 2017 PeerJ news release on EurekAlert,

Many lizards can drop their tails when grabbed, but one group of geckos has gone to particularly extreme lengths to escape predation. Fish-scale geckos in the genus Geckolepis have large scales that tear away with ease, leaving them free to escape whilst the predator is left with a mouth full of scales. Scientists have now described a new species (Geckolepis megalepis) that is the master of this art, possessing the largest scales of any gecko.

The skin of fish-scale geckos is specially adapted to tearing. The large scales are attached only by a relatively narrow region that tears with ease, and beneath them they have a pre-formed splitting zone within the skin itself. Together, these features make them especially good at escaping from predators. Although several other geckos are able to lose their skin like this if they are grasped really firmly, Geckolepis are apparently able to do it actively, and at the slightest touch. And while others might take a long time to regenerate their scales, fish-scale geckos can grow them back, scar-free, in a matter of weeks.

This remarkable (if somewhat gruesome) ability has made these geckos a serious challenge to the scientists who want to study them. Early researchers described how it was necessary to catch them with bundles of cotton wool, to avoid them losing almost all of their skin. Today, little has changed, and researchers try to catch them without touching them if possible, by luring them into plastic bags. But once they are caught, the challenges are not over; identifying and describing them is even harder.

“A study a few years ago showed that our understanding of the diversity of fish-scale geckos was totally inadequate,” says Mark D. Scherz, lead author of the new study and PhD student at the Ludwig Maximilian University of Munich and Zoologische Staatssammlung München, “it showed us that there were actually about thirteen highly distinct genetic lineages in this genus, and not just the three or four species we thought existed. One of the divergent lineages they identified was immediately obvious as a new species, because it had such massive scales. But to name it, we had to find additional reliable characteristics that distinguish it from the other species.” A challenging task indeed: one of the main ways reptile species can be told apart is by their scale patterns, but these geckos lose their scales with such ease that the patterns are often lost by the time they reach adulthood. “You have to think a bit outside the box with Geckolepis. They’re a nightmare to identify. So we turned to micro-CT to get at their skeletons and search there for identifying features.” Micro-CT (micro-computed tomography) is essentially a 3D x-ray of an object. This method is allowing morphologists like Scherz to examine the skeletons of animals without having to dissect them, opening up new approaches to quickly study the internal morphology of animals.

By looking at the skeletons of the geckos, the team was able to identify some features of the skull that distinguish their new species from all others. But they also found some surprises; a species named 150 years ago, Geckolepis maculata, was confirmed to be different from the genetic lineage that it had been thought to be. “This is just typical of Geckolepis. You think you have them sorted out, but then you get a result that turns your hypothesis on its head. We still have no idea what Geckolepis maculata really is–we are just getting more and more certain what it’s not.”

The new species, Geckolepis megalepis, which was described by researchers from the US, Germany, and Columbia [sic] in a paper published today in the open access journal PeerJ, is most remarkable because of its huge scales, which are by far the largest of any gecko. The researchers hypothesize that the larger scales tear more easily than smaller scales, because of their greater surface area relative to the attachment area, and larger friction surface. “What’s really remarkable though is that these scales–which are really dense and may even be bony, and must be quite energetically costly to produce–and the skin beneath them tear away with such ease, and can be regenerated quickly and without a scar,” says Scherz. The mechanism for regeneration, which is not well understood, could potentially have applications in human medicine, where regeneration research is already being informed by studies on salamander limbs and lizard tails.

Here’s a link to and a citation for the paper,

Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales by Mark D. Scherz​, Juan D. Daza, Jörn Köhler, Miguel Vences, Frank Glaw. PeerJ 5:e2955 https://doi.org/10.7717/peerj.2955

This paper is open access.

For anyone unfamiliar with ‘gecko research’, scientists are fascinated by their abilities and have been researching them (in a field known as biomimicry or bioinspired engineering or biomimetics) for years with the hope of mimicking those abilities for new applications. You can check out a March 19, 2015 posting or this July 10, 2014 posting for examples or you can search ‘gecko’ on this blog for more examples.

Artificial intelligence used for wildlife protection

PAWS (Protection Assistant for Wildlife Security), an artificial intelligence (AI) program, has been tested in Uganda and Malaysia. according to an April 22, 2016 US National Science Foundation (NSF) news release (also on EurekAlert but dated April 21, 2016), Note: Links have been removed,

A century ago, more than 60,000 tigers roamed the wild. Today, the worldwide estimate has dwindled to around 3,200. Poaching is one of the main drivers of this precipitous drop. Whether killed for skins, medicine or trophy hunting, humans have pushed tigers to near-extinction. The same applies to other large animal species like elephants and rhinoceros that play unique and crucial roles in the ecosystems where they live.

Human patrols serve as the most direct form of protection of endangered animals, especially in large national parks. However, protection agencies have limited resources for patrols.

With support from the National Science Foundation (NSF) and the Army Research Office, researchers are using artificial intelligence (AI) and game theory to solve poaching, illegal logging and other problems worldwide, in collaboration with researchers and conservationists in the U.S., Singapore, Netherlands and Malaysia.

“In most parks, ranger patrols are poorly planned, reactive rather than pro-active, and habitual,” according to Fei Fang, a Ph.D. candidate in the computer science department at the University of Southern California (USC).

Fang is part of an NSF-funded team at USC led by Milind Tambe, professor of computer science and industrial and systems engineering and director of the Teamcore Research Group on Agents and Multiagent Systems.

Their research builds on the idea of “green security games” — the application of game theory to wildlife protection. Game theory uses mathematical and computer models of conflict and cooperation between rational decision-makers to predict the behavior of adversaries and plan optimal approaches for containment. The Coast Guard and Transportation Security Administration have used similar methods developed by Tambe and others to protect airports and waterways.

“This research is a step in demonstrating that AI can have a really significant positive impact on society and allow us to assist humanity in solving some of the major challenges we face,” Tambe said.

PAWS puts the claws in anti-poaching

The team presented papers describing how they use their methods to improve the success of human patrols around the world at the AAAI Conference on Artificial Intelligence in February [2016].

The researchers first created an AI-driven application called PAWS (Protection Assistant for Wildlife Security) in 2013 and tested the application in Uganda and Malaysia in 2014. Pilot implementations of PAWS revealed some limitations, but also led to significant improvements.

Here’s a video describing the issues and PAWS,

For those who prefer to read about details rather listen, there’s more from the news release,

PAWS uses data on past patrols and evidence of poaching. As it receives more data, the system “learns” and improves its patrol planning. Already, the system has led to more observations of poacher activities per kilometer.

Its key technical advance lies in its ability to incorporate complex terrain information, including the topography of protected areas. That results in practical patrol routes that minimize elevation changes, saving time and energy. Moreover, the system can also take into account the natural transit paths that have the most animal traffic – and thus the most poaching – creating a “street map” for patrols.

“We need to provide actual patrol routes that can be practically followed,” Fang said. “These routes need to go back to a base camp and the patrols can’t be too long. We list all possible patrol routes and then determine which is most effective.”

The application also randomizes patrols to avoid falling into predictable patterns.

“If the poachers observe that patrols go to some areas more often than others, then the poachers place their snares elsewhere,” Fang said.

Since 2015, two non-governmental organizations, Panthera and Rimbat, have used PAWS to protect forests in Malaysia. The research won the Innovative Applications of Artificial Intelligence award for deployed application, as one of the best AI applications with measurable benefits.

The team recently combined PAWS with a new tool called CAPTURE (Comprehensive Anti-Poaching Tool with Temporal and Observation Uncertainty Reasoning) that predicts attacking probability even more accurately.

In addition to helping patrols find poachers, the tools may assist them with intercepting trafficked wildlife products and other high-risk cargo, adding another layer to wildlife protection. The researchers are in conversations with wildlife authorities in Uganda to deploy the system later this year. They will present their findings at the 15th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2016) in May.

“There is an urgent need to protect the natural resources and wildlife on our beautiful planet, and we computer scientists can help in various ways,” Fang said. “Our work on PAWS addresses one facet of the problem, improving the efficiency of patrols to combat poaching.”

There is yet another potential use for PAWS, the prevention of illegal logging,

While Fang and her colleagues work to develop effective anti-poaching patrol planning systems, other members of the USC team are developing complementary methods to prevent illegal logging, a major economic and environmental problem for many developing countries.

The World Wildlife Fund estimates trade in illegally harvested timber to be worth between $30 billion and $100 billion annually. The practice also threatens ancient forests and critical habitats for wildlife.

Researchers at USC, the University of Texas at El Paso and Michigan State University recently partnered with the non-profit organization Alliance Vohoary Gasy to limit the illegal logging of rosewood and ebony trees in Madagascar, which has caused a loss of forest cover on the island nation.

Forest protection agencies also face limited budgets and must cover large areas, making sound investments in security resources critical.

The research team worked to determine the balance of security resources in which Madagascar should invest to maximize protection, and to figure out how to best deploy those resources.

Past work in game theory-based security typically involved specified teams — the security workers assigned to airport checkpoints, for example, or the air marshals deployed on flight tours. Finding optimal security solutions for those scenarios is difficult; a solution involving an open-ended team had not previously been feasible.

To solve this problem, the researchers developed a new method called SORT (Simultaneous Optimization of Resource Teams) that they have been experimentally validating using real data from Madagascar.

The research team created maps of the national parks, modeled the costs of all possible security resources using local salaries and budgets, and computed the best combination of resources given these conditions.

“We compared the value of using an optimal team determined by our algorithm versus a randomly chosen team and the algorithm did significantly better,” said Sara Mc Carthy, a Ph.D. student in computer science at USC.

The algorithm is simple and fast, and can be generalized to other national parks with different characteristics. The team is working to deploy it in Madagascar in association with the Alliance Vohoary Gasy.

“I am very proud of what my PhD students Fei Fang and Sara Mc Carthy have accomplished in this research on AI for wildlife security and forest protection,” said Tambe, the team lead. “Interdisciplinary collaboration with practitioners in the field was key in this research and allowed us to improve our research in artificial intelligence.”

Moreover, the project shows other computer science researchers the potential impact of applying their research to the world’s problems.

“This work is not only important because of the direct beneficial impact that it has on the environment, protecting wildlife and forests, but on the way that it can inspire other to dedicate their efforts into making the world a better place,” Mc Carthy said.

The curious can find out more about Panthera here and about Alliance Vohoary Gasy here (be prepared to use your French language skills). Unfortunately, I could not find more information about Rimbat.