Coping without oxygen, under water.

Blog written by Dr. Noelle Lucey and photos by Mary Collins. Read the full paper here.

When most people think of coastal hypoxia, polluted areas with lots of people living nearby come to mind – not remote tropical coral reefs. Yet, in a large Caribbean bay where tropical jungles are practically kissing the shallow coral reefs in the warm waters below, severe hypoxia has also made its mark.

Our study found seasonally predictable hypoxic waters at the bottom of Almirante Bay, Panama during the warmer half of the year. The bay during this time is highly stratified, with deoxygenated water at depth (20m) separated from a small top layer where oxygen levels are higher. This has resulted in the mortality of reefs deeper than 3 meters in some areas.

Hypoxic waters shoaled to 3 meters on the reef slope off of Cayo Roldon in 2017; coral below this oxycline has been reduced to rubble and sand.

We found that deoxygenation is most extreme close to the mainland, where highly stratified hypoxic waters shoal onto shallow reef sites. It is clear that corals and associated life die after chronic exposures to low oxygen waters, however it isn’t clear to what extent, or how badly these processes are affecting the marine life on the reef sites above this.

One of the most interesting findings of this study was that the intensity of hypoxia documented at depth appears to be reflected in adjacent shallow water as the magnitude of diurnal change in dissolved oxygen. So the shallow reefs that haven’t experienced the impact of persistent, chronic hypoxia at depth (resulting in severe mortality) are still being impacted by a type of hypoxia. The dissolved oxygen here widely fluctuates throughout the day with oxygen levels almost declining to zero at night, and then soaring in the afternoon to super saturated levels.

We wanted to know how such frequent changes in oxygen affect the organisms living on these reefs. To study this we used the widely distributed tropical polychaete fireworm, Hermodice carunculata, which is associated with coral-dominated areas and reef decline. These worms can be as long as your foot and often openly flaunt their brilliant colors on the reef where they can be found sucking down coral polyps. They are called fireworms because of their potent harpoon-like chaetae that line their sides and can cause a nasty sting if touched.

Hermodice carunculata fireworm flaring its white bristle harpoon–like chaetae and attempting to escape from the prying microscope lens

Right next to each bunch of stinging chaetae there are branching gill structures (branchiae) consisting of many filaments that extract oxygen from the environment. More gill filaments should mean an increased capacity for gas exchange, and more oxygen available for the worm to go along with its daily activities.

Fireworm gills

We manipulated oxygen levels in the lab to reflect the shallow hypoxic environment, where oxygen levels change widely throughout the day, and kept fireworms in these conditions for eight weeks. We wanted to determine if the gills of these fireworms would grow in response to low oxygen, and if they could regenerate faster if they were cut off.

We thought that worms would grow and regenerate larger gills to compensate for the low oxygen. Sure enough, after only 4 weeks, gills of worms in hypoxic conditions regenerated faster than worms kept in consistently oxygenated waters. Interestingly, worms in these oxygenated conditions regenerated smaller gills than they started with in the same time frame.

Smaller gills seen in the well-oxygenated group

These results suggest that the reefs further from the mainland actually may be experiencing more hypoxia than we thought or measured, and that the worms from these reefs may already be prepared to deal with periodic hypoxia.

Along with gill morphology changes, we expected worms to have an increased ability to take up oxygen from the water after being in hypoxic conditions. We predicted that the worms would be metabolically depressed under low oxygen conditions (breathing less), and after re-oxygenation they would breath more to make up for the oxygen deficit occurring during hypoxia stress. Oxygen consumption rates were measured to see how much oxygen worms were actually taking from the environment immediately after hypoxic exposure. Yet after 8 weeks, we found no significant differences in the oxygen consumption rates of worms exposed to periodic hypoxia. In other words, these worms had the ability to bounce back quickly, metabolically speaking, with normal respiration rates despite previously being in water with very little oxygen. Surprisingly, this was not the case with the worms that had been kept in oxygenated conditions for 8 weeks. After this control group was put in hypoxic conditions, they had dramatically depressed respiration rates upon re-oxygenation.

This suggests that by switching metabolic efforts on and off promptly in response to oxygen availability worms with prior hypoxic conditioning may be able to take advantage of oxygen when it is present in the environment—a trait of great functional importance in rapidly changing environments.

The findings here indicate that hypoxic conditions in shallow coral reefs may be underestimated, and also that H carunculata has the physiological ability to maintain and withstand hypoxia without much of a cost. This is important because it could mean that fireworms have an advantage in rapidly changing environments. They are already considered to be detrimental to coral, degrading living coral reefs and spreading coral disease. As hypoxia is becoming more common and globally prevalent, it is imperative to understand the organismal responses to determine the implications of these processes for reef invertebrates and ecosystems.

Hermodice carunculata

This work would not have been possible without the support and funding from the Smithsonian Tropical Research Institute. We also wish to thank the Bocas Research Station team, Plinio Gondola, Lucia Rodríguez, and Travis Scott, as well as the valuable contributions from reviewers.

Migrants vs residents: a difference in birdsong output

Blog post by Dustin Brewer and Adam Fudickar. Read the full paper here. Photo above of a song sparrow by Mark Hainen

Studying the behavior of animals is like eating a cake and trying to figure out what made it taste the way that it does. Our changing world has baked a spectacular diversity of behaviors into the lives of animals which we are only beginning to understand. Hibernating Arctic ground squirrels, bugling elk, and migrating fish, for example, provide curious people much to feast on, as do multitudes of other species.

Given that behaviors must occur at the right time of year for a species to survive and reproduce, changing conditions can result in mismatches between an animal’s behavior and environment. For example, if an Arctic ground squirrel is still hibernating when its preferred food source is most available, then that squirrel may later starve. When such a mismatch happens, an individual, population, or even a species could disappear from the Earth. For this reason, studying animal behavior can inform conservation efforts in addition to allowing us to ‘eat a tasty cake’ for the fun of it.   

Animals often rely on environmental cues to initiate behaviors. For example, a bird that has migrated to Florida for the winter might migrate back to where it breeds in the spring based on daylength, which also affects when it sings. For many bird species, singing is the primary way for males to attract mates and defend territories.

We asked a simple question, which was, ‘how often, and when, do individual birds that don’t migrate sing compared to individuals that do migrate?’ For some bird species, like Song Sparrows, the breeding population at a location can consist of both ‘residents’ (they spend the entire year where they breed) and ‘migrants’ (they spend the winter away from where they breed). Considering that photoperiod, the amount of time each day that an animal is exposed to daylight, varies based on latitude, we thought that there might be a difference in singing behavior between residents and migrants.

To answer this question, we caught Song Sparrows from a breeding population in Indiana just after the breeding season and randomly assigned them to separate rooms in the lab. In one room, we used photoperiod to simulate a migration from Bloomington, IN to Tampa, FL, then an entire winter in Tampa, and finally a migration back to Bloomington. We called these 10 birds ‘migrants.’ In the other room, we used photoperiod to simulate a winter spent in Bloomington until the breeding season. We called these 10 birds ‘residents.’

Visualisation of a song sparrow song, on a spectrogram

Throughout the 4.5 months that this study took place, we counted the number of songs that each bird in each room sang. Because each Song Sparrow has a unique repertoire of 4 to 13 song types, we were able to identify each individual by its songs and so could count the number of times that it sang, even though many of the birds were singing at the same time. We sampled on 20 November and 6 December (‘non-breeding’ stage), on 27 January and 7 February (‘pre-breeding’ stage), and on 21 March and 4 April (‘breeding’ stage). We found that little singing occurred during the non-breeding stage in the resident group, and that none of the migrants sang. In the pre-breeding stage, however, the residents sang significantly more than the migrants (about 60 songs per bird vs 26 songs per bird in one hour). During the breeding stage, we didn’t find a difference between how much the residents and migrants sang (both sang about 50 songs per bird per hour).

Our results informed us about how Song Sparrows might behave in the wild. Namely, it seems, Song Sparrows that migrate may begin singing at a high rate later than those that don’t migrate. Residents sang more than migrants during the pre-breeding stage, which could help residents establish territories where they will later breed. Given that singing and breeding often co-occur, it could be a disadvantage for migrants if they sang less than residents when they reached the breeding grounds. Our results, however, suggest that both migrants and residents sing the same amount during the beginning of the breeding stage. The act of migrating, it seems, doesn’t put Song Sparrows at a disadvantage with respect to song output during the beginning of the breeding stage.

Recording a song sparrow song in the field. Photo by Dustin Brewer

Understanding when and how much Song Sparrow migrants and residents sing in the wild, and how much other migratory bird species do the same, could help to determine how strategies such as migration affect the ability of individuals to compete for mates. Also, studies like ours could help to determine how much variability exists in the timing of breeding within a population. For example, if migrants begin singing (and breeding) a couple weeks later than residents, then that breeding population of birds would possess variability which could help it to withstand environmental changes, such as climate change.

Our study primarily helps to understand the interplay between two awe-inspiring behaviors, bird migration and bird song. Additionally, our study could provide a framework for determining how much variability in timing of singing (and breeding) particular species display, which could inform conservationists about which species have a better chance of withstanding environmental changes. If so, then we could ‘have our cake and conserve, too.’

Does community-based wildlife conservation work?

Blog written by Talia Speaker, Seth Thomas and Christian Kiffner. Read the full article here.

Since the turn of the century, community-based natural resource management models have risen to the forefront of conservation efforts around the globe. And for good reason—they gained popularity for their promise of meeting both livelihood and conservation goals through empowering local communities to sustainably manage their own land and resources. Particularly in ecologically rich, yet economically poor regions (including many regions in sub-Saharan Africa), this conservation approach sounds like a win-win solution for both human communities lacking basic commodities and declining wildlife populations. But how effective are these conservation models in practice?

Research on these questions has raised major concerns about the socio-economic consequences of current community-based conservation models; namely the results of poor governance and unequal benefit-sharing. These concerns are valid and require urgent attention, but another equally important question has been lacking in the literature: Are these community-managed areas meeting their conservation goals? A handful of studies across East Africa over the last decade suggest a tentative ‘yes’ to this question, but few of these areas have long-term wildlife monitoring programs in place that can be used to assess their sustainability.

Elephant and wildebeest use the swamps and grasslands of Tarangire National Park during the dry season.

Our research takes an important step in addressing this gap by investigating how wildlife populations in a community-based Wildlife Management Area in Tanzania compared to a neighboring state-managed national park over an eight-year study period. More specifically, we tracked changes in species richness and population densities of ten mammal species in both locations from 2011 to 2018 using seasonal and time-matched walking and vehicle based transect surveys. By comparing the community-based model to a national park, we tested it against the “gold standard” of species conservation models, which prioritizes conservation and removes most human disturbances.

Zebra and wildebeest herds aggregate along the Tarangire river during the dry season.

Our results are largely promising. We found that both species richness and population densities across species were comparable between the park and community-managed area, suggesting that these areas can support wildlife communities that are similar to those of a national park, despite different management schemes. We also noted significant increases in the populations of at least three species (elephant, wildebeest, and impala) in the Wildlife Management Area throughout the study period, which further supports the conservation effectiveness of the model but raises concerns about potential negative effects (e.g. crop raiding) of growing wildlife populations on local livelihoods.

Zebras drinking from the Tarangire river during the dry season.

While these findings are good news for this specific Wildlife Management Area, our work is far from done. On a local level, persistent conservation efforts and adaptive management will be critical to the continued success of the wildlife management area model. In the bigger picture, this research only sets the precedent for a much-needed widespread effort to monitor and evaluate the long-term conservation value of community-based models across Tanzania.

Zebras standing in the grasslands of Burunge Wildlife Management Area.

For too long it has been assumed that effective management will come as a de facto result of the (partial) ownership and direct economic benefits derived from wildlife. In our study area, this assumption appears to be valid. We advocate for similar, rigorous assessments of the ecological effectiveness of community-based conservation schemes to test their effectiveness and inform adaptive management. Ideally, assessments are done neither from a wildlife-only nor a livelihood-only perspective but from a holistic and interdisciplinary perspective that takes the social and ecological components into account. To capitalize on this model that holds real potential for facilitating the coexistence of people and wildlife, we must invest now in monitoring its effectiveness and sustainability.

Why does a predatory bird avoid its prey?

Blog written by Karl Busdieker and  Dr. Samantha Patrick. Read the full paper here. Photo above of a South polar skua, Catharacta maccormicki, by Alice Trevail

If you were to ask the average person where they thought an animal might prefer to feed, they would probably reply along the lines of “wherever the most food is”. On a purely logical level, this seems obvious, as high food density provides easy pickings in many cases. However, ecology is rarely so simple. This study investigates a fairly unusual predator-prey system where the opposite case is true, and predators actively avoid high densities of prey despite the seemingly obvious benefits of such a natural buffet.

Our study concerns the effect of prey density on the habitat selection behaviour of a predatory species in Svarthamaren, Antarctica. Svarthamaren has just one predator – the south polar skua, Catharacta maccormicki – and effectively one prey species, the Antarctic petrel,  Thalassoica antarctica. It is also 200km from the nearest coast, meaning that skuas are unable to feed at sea as they might in other habitats, and emphasising their reliance on this single prey species.

An important point to note here is that in Svarthamaren, prey are so abundant that skuas do not need to maintain feeding territories, and instead just feed at will throughout the whole petrel colony. This is particularly unusual for a species that is normally so protective of individual feeding grounds (Trillmich 1978). It is therefore important to understand how and why they choose where to feed within this colony, when food is essentially everywhere (at varying densities).

Antarctic petrel chicks (Thalassoica antarctica) in their nests. Image Credit: Alice Trevail

This study made use of a comprehensive dataset, which used regularly spaced plots to quantify the density of petrel nests during their breeding season, in addition to detailed tracking data for 47 individual skuas (36 of which were sexed). We wanted to investigate the effects of prey density on habitat selection in skuas, as well as the interactions of prey density with skua sex, and the breeding stage of both predator and prey (whether the birds are incubating an egg at a given time, or are rearing a chick in their nest). To do so, we used resource selection models to compare areas which the skuas chose to use (used points) with points they could have used but did not (available points, represented by pseudo-absences).

Our main finding was that as petrel density increases, the likelihood of a skua feeding in the area decreases – which is seemingly counter-intuitive as such areas are full of potential food! However, Antarctic petrel chicks are not helpless, and to defend themselves against attackers they are able to spit up a foul oil, coating skua feathers and severely inconveniencing avian predators on future flights. It therefore seems that skuas prefer to go for “easy prey” – they would rather prey on relatively lonely petrel chicks rather than battle dense groups of them.

Interestingly, this pattern was only visible after petrel hatching – prior to this, skuas feed indiscriminately on petrel eggs, which are indeed helpless when unguarded. Also, when skuas are incubating eggs of their own, they are more likely to select areas of lower petrel density – perhaps being less willing to take risks while their own offspring are so vulnerable. Later on, once their chicks have hatched, they are slightly less likely to avoid areas of high petrel density. Finally, female skuas show a slightly stronger preference for lower prey densities than males, but post-hoc testing suggests that this difference is minimal.

An Antarctic petrel chick (Thalassoica antarctica) is taken by a south polar skua (Catharacta maccormicki). Image Credit: Sébastien Descamps

Readers may wonder why this matters at all, especially in such a remote area. However, we believe our results have some quite significant implications for these species. The Antarctic petrel colony at Svarthamaren is one of the largest in the world (Mehlum et al. 1988), and due to its remoteness and lack of other predatory species could be a “safe haven” for these petrels should their numbers decline elsewhere. However, our findings could mean that if petrel populations do decline, targeted predation on areas of lowered petrel density could exacerbate this effect and speed up population losses.  

Our findings provide an interesting basis from which future studies could begin to look at the effects of prey density on predator behaviour in other populations, perhaps in more typical skua populations with alternative sources of prey available, or in multi-predator ecosystems where competition between predators could play a role. This study also has important implications for skua behavioural studies, as some of the behaviours witnessed at Svarthamaren, such as a lack of individual feeding territories, and attacking prey solely from above are very different to populations elsewhere in the world.

This research was funded by the NFR-NARE program (, and also by a summer internship for recent graduates, provided by the School of Environmental Sciences at the University of Liverpool. We would like to thank Arnaud Tarroux for his help with the skua capture work and for the useful comments provided at the early stage of this project. We also thank Eva Soininen and Johan Nils Swärd for their help in collecting the data. Thanks to Dr Jonathan Green for valuable comments on the manuscript.


Mehlum, F., Y. Gjessing, S. Haftorn, and C. Bech. 1988. Census of breeding Antarctic Petrels Thalassoica antarctica and physical features of the breeding colony at Svarthamaren, Dronning Maud Land, with notes on breeding Snow Petrels Pagodroma nivea and South Polar Skuas Catharacta maccormicki. Polar Research 6:1–9.

Trillmich, F. 1978. Feeding territories and breeding success of south polar skuas. The Auk 95:23–33.

Widespread, generalist birds are riding the wave of Amazon deforestation

Blog written by Cameron L. Rutt, PhD Candidate at Louisiana State University, USA. Read the full paper here

Experimental clearcutting (north of Manaus, Brazil) leaves behind habitat that is very unlike the surrounding rainforest. Photo by Angélica Hernández Palma. 

Recent forest fires throughout the Brazilian Amazon’s southern tier have reignited the international consciousness, bringing renewed focus to the wake left behind by the blazes—deforestation. But, this is not a new phenomenon in the world’s largest rainforest, especially along the so-called “arc of deforestation,” in the Brazilian Amazon’s southern and southeastern reaches. Over the past 30 years, deforestation practices across this entire region have carved a California-sized hole in this once seamless forest, adding to the now 20% that has been clearcut.

One idea is that species might colonize recently cleared areas by traveling along roads, which offer corridors of habitat for species that cannot use mature forest. This is BR-174, the major highway that slices through the rainforest for 1000 km north of Manaus. Photo by Cameron L. Rutt.

Large clearings for agriculture and cattle ranches stand in stark contrast to the surrounding forested areas, which teem with rich plant and animal communities. We now have decades of research following deforestation that illustrate in sobering detail just how devastating habitat loss is for the unique forest biodiversity. But we also need to learn about the kinds of species that colonize and tolerate these human-modified landscapes. What is the legacy of these newly cultivated habitats?

Yellow-headed Caracara (Milvago chimachima) is part of the vanguard of species that arrived after the creation of three cattle pastures. Photo by Cameron L. Rutt.

The first question this begs is one of duration—does it take decades for animals to find and colonize these new areas of disturbance? A large-scale experiment in the central Amazon that once housed three cattle ranches helps us to answer that question for birds. Now largely abandoned by ranchers, scientists have been cataloging birds at the Biological Dynamics of Forest Fragments Project, for nearly 40 years.

The Variable Chachalaca (Ortalis motmot)—a species that favors dense vegetation following disturbance—has now made inroads into expansive tracts of rainforest. Photo by Anselmo d’Affonseca

We used these uniquely rich bird inventories to ask a series of simple questions. When an area is clearcut, do adjacent forest birds move in? If not, what habitat supplies the new arrivals? How quickly do they find these cracks in the Amazon? And how long do these novel avian communities linger? We found that there are dozens of outside species such as flycatchers and tanagers that almost immediately filled these anthropogenic cracks in the forest, even in the absence of large-scale transformation of the landscape.

The Shiny Cowbird (Molothrus bonariensis) is one of about three-dozen widespread habitat generalists that quickly colonized the cattle ranches after clearing. Photo by Cameron L. Rutt.

In all, more than 100 bird species appeared that are not typically found in the surrounding pristine rainforest, and about three dozen of these established small populations within the disturbances. Moreover, these birds arrived quickly—the vast majority appeared within the first decade after the ranches’ establishment. Finally, a disproportionate number of these birds are widespread generalists, species that are commonly found in close association with humans. This includes birds regularly encountered in the largest Amazonian city of Manaus and species that frequent regional backyards and gardens.

A number of established colonists, such as this striking Chestnut-bellied Seedeater (Sporophila castaneiventris), have declined as the forest recovers. Photo by Anselmo d’Affonseca.

This study also serves as an important benchmark to describe what happens when the landscape begins to heal. We found that as the forest recovers on the abandoned cattle ranches, these widespread birds began to retreat and disappear from the landscape because they were restricted to the disturbances. This is good news for the many specialized forest birds that can now regain lost habitat, but which could not survive in pastures or clearcuts. Therefore, for the health of the Amazon rainforest, we should minimize the intensity of human land-use and, should deforestation occur, allow the forest to reassert itself as soon as possible.

However, birds like this female Black-throated Antshrike (Frederickena viridis) rely exclusively on intact, pristine rainforest and do not occur in regenerating forests, even after >30 years. Photo by Cameron L. Rutt

Deforestation rates in the Amazon are once again on the rise, further degrading the habitat of hundreds of species of birds. It is therefore critical that conservationists understand how these organisms, as well as the novel communities of widespread generalists, are coping with these large-scale landscape changes. Only then will we be able to develop best management practices for these impoverished habitats. Although this summer’s headline-grabbing fires in Brazil have ratcheted up the pressure for policymakers to stem the tide of Amazonian deforestation, we shouldn’t wait for another severe burning season to flame our interest and outrage about the state of the world’s most diverse forest.   

This work would not be possible without support from the Biological Dynamics of Forest Fragments Project and funding by the US National Science Foundation (LTREB 0545491 and 1257340).

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