Using acoustic monitoring to understand human impacts on Amazonian wildlife

Posted by Oliver Metcalf

It was dawn on my first morning in the Amazon. 24 hours earlier, I had been walking through the snow in Manchester to catch a bus to the airport, now I was stood 50m up on a scaffolding tower, soaring above the rain forest canopy, listening to the forest come alive. We had been so keen to get here that we hadn’t slept, briefly dropped our bags at the accommodation and then headed straight out on dirt roads, so that my first sight of Brazil should be deep in the heart of pristine rain forest. Moments earlier, there had only been the occasional mournful whistle of a tinamou and the otherworldly, nightmare-ish growl of howler monkeys, but now the dawn chorus had started and songs and calls came from all directions.

The Tapajos National Forest at dawn – the sun glowing red from the smoke of surrounding small wildfires (Photo: Oliver Metcalf)

Alex Lees, my PhD Director of Studies, rattled off the species names like a football commentator during a particularly frenzied passage of play, recording each species on eBird as he pointed them out – cryptic forest-falcon, black-tailed trogon, rufous-winged antwren, three-striped flycatcher - before long my head was spinning and I couldn’t keep up. Zoning out of trying to identify individual species, I took a minute to feel this new environment, to indulge the surreal feeling of being so far from home, in the world’s greatest rain forest. But something jarred with the image my eyes were providing of pristine wilderness, there in the background of sensory overload was the acrid, lingering smell of smoke. 

Above: Undisturbed forest looks dark because of an intact canopy layer. Below: Burned forest lets in more light as dying trees open up gaps in the canopy. Many species in the Amazon are photophobic and won't cope well with these brighter conditions (Photos: Oliver Metcalf)

The ecological and environmental impact of deforestation in the Amazon are well known and well publicised. Many of us have watched news reports of falling canopy giants accompanied by the soundtrack of screaming chainsaws, or learnt in geography classes about the harm slash-and-burn agriculture can cause. However, the high visibility of this environmental destruction has led to the Brazilian government taking action, and the rate of deforestation has declined since their 2004 peak (albeit with some recent increases). Various sustainable forestry initiatives have been used to slow the rate of deforestation– including extractive reserves which permit selective logging. These allow large areas to be set aside ostensibly for conservation purposes whilst still generating income from extractive industries.

Delights and dangers of Amazonian fieldwork. Above, the lovely Wing-barred Piprites Piprites chloris (Photo: Nárgila Moura); Below, a Fer-de-lance Bothrops atrox sharing the trail with us (Photo: Oliver Metcalf)

Large swathes of Amazonia are now subject to disturbance from selective logging and fire, yet our understanding of the impacts of such disturbance on biodiversity is still limited (Barlow et al., 2016). One of the most harmful consequences of selective logging is an increase in forest susceptibility to wildfire, exacerbating an already volatile situation caused by drought and climate change. In fact, during the El Nino events of 2015-2016, there were so many wildfires in the Santarem region (where my study site is located), the area was responsible for driving a large rise in atmospheric carbon dioxide levels. Fire can have devastating and immediate impacts on tropical forests. During my PhD, I will be working with the Sustainable Amazon Network, a transdisciplinary research consortium that studies the effects of disturbance on all levels of the rain forest environment and its biodiversity, as well as the best means to avoid and mitigate these impacts. I will be working in a protected area that allows selective logging, the Tapajos National Forest (FLONA) in Para state, Brazil, to establish the impact of logging and fire on the biodiversity of the park, large areas inside and outside of the reserve were burnt in 2015-2016. Consequently, my study design will focus on establishing the impacts of disturbance on biodiversity across a degradation gradient – comparing areas that are variously undisturbed, logged, burned or logged and burned.

Layard's Woodcreeper Lepidocolaptes layardi (Photo: Alex Lees)

Technical innovations in measuring biodiversity in the rain forest

Of course, comparing ‘biodiversity’ in such a diverse and challenging region is easier said than done. Trekking from point count to point count, transect to transect can be extremely hard work, time consuming and even dangerous, with a preponderance of poisonous snakes, bullet ants and wasps. Even if everything goes to plan, observing wildlife can be extremely difficult, frogs hide in hollow logs, birds feed in canopies 50m above and mammals run for cover well before a surveyor can clap eyes on them. This means that the best way to survey a wide range of species in the Amazon is to listen for the sounds they make. Even then, some species will only call at dawn and dusk–particularly birds such as forest falcons and tinamous, whilst others will wait for the dead of night or the heat of the day before making noise. This means that any attempt to survey all species using point counts or transects will inevitably miss a range of species, unless repeated a huge number of times across the day.

Some of the wildlife we hope to record; Above: an Amazonian pygmy owl Glaucidium hardyii, Below: a white-cheeked spider monkey Ateles marginatus (Photos: Oliver Metcalf)

Instead, I will be using passive acoustic recording devices from Frontier Labs to record continuously for a week at each of 40 transects spanning the degradation gradient, once in the wet and once in the dry season. These devices allow a huge amount of data to be collected with comparatively little time required in the field, and have previously been used to survey a wide range of species, as well as anthropogenic disturbance events such as chainsaws and gunshots. The difference here is that I will aim to detect the vocalisations of all the species within each transect, including birds, mammals, frogs and insects (although many of the insects will be morphotyped rather than identified to a species level). This will allow a greater understanding of how entire forest communities are affected by disturbance, rather than particular species within it.

The widespread Forest Elaenia Myiopagis gaimardii should feature on the 'tapes' (Photo: Nárgila Moura)

Of course, analysing the huge amounts of data collected (over 20 terabytes) is a challenge in itself, and it would be impossible to manually listen to all of the sound data that will be collected. I will instead be using Tadarida, a program that utilises machine-learning algorithms, to automatically detect vocalisations. This is a painstaking process in which I must iteratively train the program to recognise each of the call types present in the data. To start with, I will focus my attention on the nocturnal and crepuscular communities, as these are the least studied and hardest to survey using traditional techniques – and the simpler soundscapes will give the automated recognition software the best chance of performing well. Even still, I will have my work cut out for many months to come! After the training process, the program will look through the entire dataset for further similar calls allowing the creation of a database of the presence or absence of a wide range of taxa, equivalent to many hundreds of repeat transect surveys.

A spectrogram of a small section of the data so far recorded – most of the marks below 6kHz are bird calls, whilst the dark line in the centre is an insect being very noisy!

This will allow us to understand, at a broader scale than ever before, how communities respond to the disturbance gradient, and gain a through understanding of how the precious, unique biodiversity of the Amazon is being impacted by ongoing human disturbance.
 
Oliver's PhD at MMU is supervised by Dr Alexander Lees, Professor Jos Barlow (University of Lancaster) and Stu. The PhD is a component of Rede Amazônia Sustentável (RAS), a multidisciplinary project on sustainable land use in the Amazon. 

Parrots and parakeets in the Dominican Republic

Posted by Stu

Hispaniola is an extraordinary place physically, culturally and biologically. The western third of the island is Haiti, born out of a slave rebellion at the end of the 18th Century, and seemingly being punished/punishing itself ever since. The eastern two-thirds is Dominican Republic (DR), with the Caribbean’s tallest mountain, oldest colonial city, and largest tourism business. The island is home to around 38 endemic bird species, including a ‘tropical’ crossbill and the Palmchat, which represents an endemic family on the island. It is also home to the poisonous Hispaniolan Solenodon Solenodon paradoxus, Number 7 in ZSL’s EDGE mammal chart due to its phylogenetic distinctiveness and its Endangered Red list status.

Good forest remains in the Parque Nacional Sierra de Bahoruco (Photo: Stu)

I was in Dominican Republic (DR) with my good friend and ex-PhD student Matt Geary (now University of Chester) to scope out a potential study of the Hispaniolan Amazon Amazona ventralis, Hispaniolan Parakeet Psittacara chloropterus, both Vulnerable, the Near-threatened Hispaniolan Trogon Temnotrogon roseigaster and other important birds on the island. Our hosts were Groupo Jaragua, the DR BirdLife partner.

The first two days were spent meeting Yolanda Leon (President) and Andrea Thomen (Project Manager) of Groupo Jaragua to discuss potential projects and our field visits. We were quite shocked by the volume of parrot ownership in the country’s cities and towns. We also had time to visit a couple of sites in the country’s capital Santo Domingo. The excellent botanical gardens had some of the commoner lowland endemics including the excellent Hispaniolan Lizard Cuckoo and good numbers of wintering American passerines including Prairie Warbler, many Cape May Warblers, and the lovely Black-throated Blue Warbler. We visited a large Hotel in a posh area of town and watched perhaps more than 500 Hispaniolan Parakeets and a couple of Hispaniolan Amazons arrive from various green spaces across the city to roost in trees in front of the hotel. 
 

Vulnerable Hispaniolan Parakeets Psittacara chloropterus getting ready to roost (Photo: Yolanda Leon)

Then we moved southwest to Groupo’s Oviedo field station for three days. Here we visited southwestern side of the famous Parque Nacional Sierra de Bahoruco. We recorded reasonable numbers of the parrots here, both in the mixed pine/broadleaf forests and in cloud forest patches at  higher altitude. A parrot nestbox scheme didn’t seem to be doing too well – there is a lot of pressure from parrot catchers up here, with apparently little intervention by the poorly paid park guards. Nice birds included both the endemic Hispaniolan and introduced Olive-throated, Hispaniolan Crossbill and Golden Swallow. There were also a lot of American warblers up here – especially Black-throated Blues but also the odd Blackburnian and Black-throated Green, as well as the resident Pine warblers.

Hispaniolan Amazons Amazona ventralis (VU) in Parque Nacional Jaragua (Photo: Yolanda Leon)

A long and hot hike into the Parc Nacional Jaragua with Julio, an ex-parrot trapper, was extremely interesting. Parrot nests in fat-trunked Cherry Palms and the few remaining large trees in this dry spiny forest but are hammered both by local trappers and, more worryingly, by a team of ‘professional’ trappers who apparently took around 150 chicks last year. Nest trees/palms are identified at the start of the breeding season (April) and these are monitored as chicks grow until they are harvested just before fledging. Worryingly, there seems to be so much competition among trappers that chicks are being taken from nests earlier and earlier (to ensure others don’t take them first). One consolation perhaps is that the terrain is very difficult and I (may be wrong) but can imagine that not all nests in the large area are found – the species usually produces four chicks so a few successful nests coupled with the ‘fact’ that adults are not taken might be the key to sustaining the population. The gorgeous Broad-billed Tody occurred in the area at huge densities, and perhaps some signs of Solenodon in the less rocky areas.

Above: Discussions about parrot harvesting in Parque Nacional Jaragua (Photo: Matt Geary), Below: Old parrot nest cavity in Cherry Palm (Photo: Yolanda Leon)

Our final field trip was to Reserva Ebano Verde, a private reserve owned and run for the DR government by Fundacion Progressio, a DR banking trust. The contrast between this and the state-run parks was immediately obvious – no encroachment and proper control of trapping. Here there were high densities of Hispaniolan Trogons, helped in part to nest boxes put up by Simón Guerrero, a retired ornithology lecturer and passionate conservationist. We saw parrots here also but it also became apparent that the Hispaniolan Parakeet is really not doing well across the country. The cause of its decline is not known and is puzzling, especially considering it seems to be taking over the capital city! 

Illegal farming is a problem in DR's national parks (Photo: Stu)

There is much to find out about the hole-nesters on Hispaniola. I was quite surprised how many parrots are taken as pets in the cities, how rare the parakeet was, the level of corruption in the country, and also how much forest loss there has been away from the very dry forests of the lowlands and the montane areas. Hispaniolan Oriole is perhaps a bird to watch as it may be getting very scarce. Certainly not scarce is the endemic woodpecker - I have never seen so many woodpeckers anywhere in my life – they are literally everywhere and these birds must be important in creating holes for the secondary cavity nesters. Matt, Nigel Collar and I hope to be able to find funding for a PhD for a Dominican soon.  

Parrots International Symposium, and Intervales birds

 Posted by Stu

In November, I visited Brazil for the first time in more than ten years. My principal reason for the visit was to speak at the ninth Parrots International Symposium, in Campo Grande. Parrots International (PI) is a US-based NGO, founded by Marie and Mark Stafford, and devoted to welfare of both companion parrots and parrots in the wild. They are involved in funding and running a whole range of projects on wild parrots. 

A major activity of PI is the organisation of an annual parrot symposium, in 2015 held for the first time outside of USA. Simon Valle spoke at the PI symposium in 2013 about his Grey Parrot project on Principe – this time I was there to talk about our Grey Parrot work in general across several African countries. Also speaking were Neiva Guedes (Instituto Arara Azul), Pepe Tella (Estacion Biologica de Doñana), Tom White (USFWS), Indira Lacerna-Widman (Katala Foundation), and Thomas Arndt (Funds for Endangered Parrots). 

A pair of Blue-and-yellow Macaws Ara ararauna on streetlights in Campo Grande (Photo: Peter Widman)

Urban Blue-and-yellow Macaw (Photo: Steve Brookes www.wildparrotsupclose.com)

  
Campo Grande is an amazing city, stuffed with wildlife. There were Agoutis and Bare-faced Curassows by the side of the road, and Blue-and-yellow Macaws hanging off the lamp posts. After the conference, I went with Pedro Develey from SAVE Brasil, the Brazilian BirdLife partner, to help organise a new project on birds in Minas Gerais. More on this soon.
 

Southern Red-shouldered Macaws Diopsittaca cumanensis also live 'comfortably' in Campo Grande (Photo: Steve Brookes www.wildparrotsupclose.com)

Blue-and-yellow Macaw pair at nest in dead palm (Photo: Steve Brookes www.wildparrotsupclose.com)

(Photo: Steve Brookes www.wildparrotsupclose.com)

My final stop was Intervales State Park, around five hours bus and taxi ride from Sao Paulo. I visited this place with Mauro Galetti from UNESP many years ago. Then we stayed at one of the guard/research posts in the lowlands of the park – I’m not sure where we were but I do remember seeing Jacutinga and some other lowland Atlantic Forest goodies. This time I was at the main complex accessed from Ribeirão Grande. This is a stunning place for birding – three nights at Pousada Esquilo, mountains of food and the superb Faustino to guide cost around £120.

Above: Great forest at Intervales State Park (Photo: Stu); Below: the Near-threatened White-breasted Tapaculo (Photo: Dario Sanches).

We saw lots of birds including some like Spot-winged Wood-quail, Hooded Berryeater, and Atlantic Forest Royal Flycatcher which I’ve not seen for years, plus some great new birds including Such’s and Short-tailed Antthrushes, Variegated Antpitta, White-breasted Tapaculo and Rusty-breasted Nunlet. I also finally saw the bamboo-loving Temminck’s Seedeater, and there is even an area where they put out corn for the lovely Red-and-white Crake.

Above: Red-and-white Crake comes to corn at the marsh by the Administration, along with Blackish Rail (Photo: Francesco Veronesi); Below: Atlantic forest from my room at Pousada Esquilo (Photo: Stu).

Photographs capture-recapture Bolivia’s large Andean Condor population

Posted by Diego Mendez and Huw Lloyd

In a new research funded by the Peregrine Fund, The British Ornithological Union, The Neotropical Bird Club and MMU, MSc student Diego Mendez has shown that it is possible to individually identify Andean Condors Vultur gryphus on the basis of selected natural markings through the examination of photographs of perched and flying birds. More importantly, Diego’s research reveals that Andean Condor populations in Bolivia are still reasonably large. However, the population structure may be skewed toward male and sub-adult birds, with fewer females being present within the Bolivian population.

Adult male Condor sunbathing, Reserva Nacional de Fauna y Flora Tariquía, Bolivia (Photo: Diego Mendez).

Surveying condors using a ‘capture-recapture’ photographic method

Between July and December 2014, Andean Condors were surveyed at 28 different locations (which we called survey feeding stations) throughout the eastern Andean region of Bolivia, encompassing the high-Andean vegetation, semi-humid puna, inter-Andean dry forest, Bolivian-Tucuman forest and Chaco Serrano ecoregions in the Cordillera Oriental and Subandino. Condors were attracted to each feeding station using equine carcasses that had been obtained humanely.

Diego at photographic blind waiting for Condors to show up.

At each feeding station, condors were photographed from 7 am to 6 pm whilst they fed at the carcasses. Photos were taken from newly constructed observation hides positioned 35-100 m from the animal carcass to permit optimal viewing of feeding and flying condors. To photograph condors, Diego and his field assistants used a digital camera mounted on a digiscoping adaptor attached to an 82 mm-objective spotting scope with a 20-60 magnification eyepiece, plus one or two bridge cameras with lenses with focal distances of up to 810-1550 mm.

Juvenile female Condor, Parque Nacional Torotoro, Bolivia (Photo: Diego Mendez).

The team took as many photographs as possible aiming to get high quality photographs that clearly showed both flanks of perched adult condors (head and body for males) and fully extended flying and tail feathers of condors in flight. By the end of the surveys, Diego and his team managed to take over 21,000 photographs of Andean Condors, of which nearly 8,000 (37%) were judged to be usable for condor identification.

A total of 566 condors were recorded from all survey feeding stations. From these data, Diego identified 456 different individuals, including 134 adult males, 40 subadult males, 79 juvenile males, 80 adult females, 30 sub-adult females and 93 juvenile females. Thus, the minimum population count for the Andean Condor population was 456 individuals with a population structure composing of adults, sub-adults and juveniles. Closed population capture-recapture homogeneity modelling produced a population estimate of 1,222 ± 99 (SE) condors. This estimate encompasses the population to the eastern Andes of central and southern Bolivia including the Apolobamba Mountains, an area of approximately 42,000 sq km.

Juvenile male Condor flying, Parque Nacional Torotoro, Bolivia (Photo: Diego Mendez).

The observed population structure of Andean Condors in this study is similar to those observed by Ríos-Uzeda & Wallace (2007) and Méndez et al. (2015) in that the population is slightly skewed towards adult males and immature birds (sub-adults and juveniles). These findings support a previous figure for the adult male-sewed population throughout the species’ range (Lambertucci et al. 2012). Studies of White-rumped Vulture Gyps bengalensis have also revealed male skewed sex ratios (Arshad et al. 2009), and the population structure of the California Condor Gymnogyps californianus population – a human managed population – is also slightly male skewed. These findings suggest that perhaps special attention should be allocated to sub-adult individuals to better conserve Andean Condor populations throughout their range.


References

Arshad, M., Chaudhry, M.J.I. & Wink, M. (2009). High mortality and sex ratio imbalance in a critically declining Oriental White-backed vulture population (Gyps bengalensis) in Pakistan. Journal of Ornithology 150: 495-503.

Lambertucci, S.A. (2010). Size and spatio-temporal variations of the Andean condor Vultur gryphus population in north-west Patagonia, Argentina: communal roosts and conservation. Oryx 44: 441-447.

Méndez, D.R., Soria-Auza, W.R., Vargas, F.H. & Herzog, S.K. (2015). Population status of Andean Condors in central and southern Bolivia. Journal of Field Ornithology 86: 205-212.

Ríos-Uzeda, B. & Wallace, R.B. (2007). Estimating the Size of the Andean Condor Population in the Apolobamba Mountains of Bolivia. Journal of Field Ornithology 78: 170-175.

Acknowledgements

Diego's work is part of Proyecto Cóndor Andino - Asociación Armonía and has been supported by