Characterizing soundscapes across diverse ecosystems using a universal acoustic feature set.

Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labor-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we have developed a generalizable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolutional neural network to embed soundscapes from a variety of ecosystems into a common acoustic space. In both supervised and unsupervised modes, this allowed us to accurately quantify variation in habitat quality across space and in biodiversity through time. On the scale of seconds, we learned a typical soundscape model that allowed automatic identification of anomalous sounds in playback experiments, providing a potential route for real-time automated detection of irregular environmental behavior including illegal logging and hunting. Our highly generalizable approach, and the common set of features, will enable scientists to unlock previously hidden insights from acoustic data and offers promise as a backbone technology for global collaborative autonomous ecosystem monitoring efforts.

Extracting physiological information in experimental biology via Eulerian video magnification.

BACKGROUND: Videographic material of animals can contain inapparent signals, such as color changes or motion that hold information about physiological functions, such as heart and respiration rate, pulse wave velocity, and vocalization. Eulerian video magnification allows the enhancement of such signals to enable their detection. The purpose of this study is to demonstrate how signals relevant to experimental physiology can be extracted from non-contact videographic material of animals. RESULTS: We applied Eulerian video magnification to detect physiological signals in a range of experimental models and in captive and free ranging wildlife. Neotenic Mexican axolotls were studied to demonstrate the extraction of heart rate signal of non-embryonic animals from dedicated videographic material. Heart rate could be acquired both in single and multiple animal setups of leucistic and normally colored animals under different physiological conditions (resting, exercised, or anesthetized) using a wide range of video qualities. Pulse wave velocity could also be measured in the low blood pressure system of the axolotl as well as in the high-pressure system of the human being. Heart rate extraction was also possible from videos of conscious, unconstrained zebrafish and from non-dedicated videographic material of sand lizard and giraffe. This technique also allowed for heart rate detection in embryonic chickens in ovo through the eggshell and in embryonic mice in utero and could be used as a gating signal to acquire two-phase volumetric micro-CT data of the beating embryonic chicken heart. Additionally, Eulerian video magnification was used to demonstrate how vocalization-induced vibrations can be detected in infrasound-producing Asian elephants. CONCLUSIONS: Eulerian video magnification provides a technique to extract inapparent temporal signals from videographic material of animals. This can be applied in experimental and comparative physiology where contact-based recordings (e.g., heart rate) cannot be acquired.

Acoustic structure of forest elephant rumbles: a test of the ambiguity reduction hypothesis.

Quantitative assessments of the structure of vocalizations are a fundamental prerequisite to understand a species' vocal communication system and, more broadly, the selective pressures shaping vocal repertoires. For example, to reduce ambiguity in signal interpretation in the absence of auxiliary visual cues, species in densely vegetated habitats should exhibit more discrete vocal signals than species in open habitats. To test this "ambiguity reduction hypothesis", we conducted the first quantitative assessment of the rumble vocalizations of the forest elephant. Based on 686 forest elephant rumbles recorded with autonomous acoustic recording units at four sites across Central Africa, we used model-based cluster analyses paired with subsequent evaluation of cluster-discreteness and discriminant function analyses to quantify the structure of rumbles based on 23 source- and filter-related acoustic parameters. Model-based cluster analyses suggest that rumbles can be classified into five to eight types. Similar to previous findings in savannah elephants and contrary to the ambiguity reduction hypothesis, average silhouette coefficients below 0.34 indicated that these rumble types were highly intergraded. However, discriminant function analyses predicted rumble types with at least 75% accuracy whereby the location of the minimum fundamental frequency, middle slope and peak frequency contributed most to separation between types. In line with an increasing number of studies highlighting that a distinction between discrete and graded repertoires may have little biological significance, we propose that ambiguity reduction may take place through the evolution of perceptual and cognitive mechanisms, rather than acting on vocal production.

Automated detection of low-frequency rumbles of forest elephants: A critical tool for their conservation.

African forest elephants (Loxodonta cyclotis) occupy large ranges in dense tropical forests and often use far-reaching vocal signals to coordinate social behavior. Elephant populations in Central Africa are in crisis, having declined by more than 60% in the last decade. Methods currently used to monitor these populations are expensive and time-intensive, though acoustic monitoring technology may offer an effective alternative if signals of interest can be efficiently extracted from the sound stream. This paper proposes an automated elephant call detection algorithm that was tested on nearly 4000 h of field recordings collected from five forest clearings in Central Africa, including sites both inside protected areas and in logging concessions. Recordings were obtained in different seasons, years, and under diverse weather conditions. The detector achieved an 83.2% true positive rate when the false positive rate is 5.5% (approximately 20 false positives per hour). These results suggest that this algorithm can enable analysis of long-term recording datasets or facilitate near-real-time monitoring of elephants in a wide range of settings and conditions.

Early detection of human impacts using acoustic monitoring: An example with forest elephants.

The impacts of human activities and climate change on animal populations often take considerable time before they are reflected in typical measures of population health such as population size, demography, and landscape use. Earlier detection of such impacts could enhance the effectiveness of conservation strategies, particularly for species with slow population growth. Passive acoustic monitoring is increasingly used to estimate occupancy and population size, but this tool can also monitor subtle shifts in behavior that might be early indicators of changing impacts. Here we use data from an acoustic grid, monitoring 1250 km2 of forest in northern Republic of Congo, to study how forest elephants (Loxodonta cyclotis) assess risk associated with human impacts across a landscape that includes a national park as well as active and inactive logging concessions. By quantifying emerging patterns of behavior at the population level, arising from individual-based decisions, we gain an understanding of how elephants perceive their landscape along an axis of human disturbance. Forest elephants in relatively undisturbed forests are active nearly equally day and night. However, they become more nocturnal when exposed to a perceived risk such as poaching. We assessed elephant perception of risk by monitoring changes in the likelihood of nocturnal vocal activity relative to differing levels of human activity. We show that logging is perceived to be a risk on moderate time and small spatial scales, but with little effect on elephant density. However, risk avoidance persisted in areas with relatively easy access to poachers and in more open habitats where poaching has historically been concentrated. Increased nocturnal activity is a common response in many animals to human intrusion on the landscape. Provided a species is acoustically active, passive acoustic monitoring can measure changes in human impact at early stages of such change, informing management priorities.

Use of acoustic tools to reveal otherwise cryptic responses of forest elephants to oil exploration.

Most evaluations of the effects of human activities on wild animals have focused on estimating changes in abundance and distribution of threatened species; however, ecosystem disturbances also affect aspects of animal behavior such as short-term movement, activity budgets, and reproduction. It may take a long time for changes in behavior to manifest as changes in abundance or distribution. Therefore, it is important to have methods with which to detect short-term behavioral responses to human activity. We used continuous acoustic and seismic monitoring to evaluate the short-term effects of seismic prospecting for oil on forest elephants (Loxodonta cyclotis) in Gabon, Central Africa. We monitored changes in elephant abundance and activity as a function of the frequency and intensity of acoustic and seismic signals from dynamite detonation and human activity. Elephants did not flee the area being explored; the relative number of elephants increased in a seasonal pattern typical of elsewhere in the ecosystem. In the exploration area, however, they became more nocturnal. Neither the intensity nor the frequency of dynamite blasts affected the frequency of calling or the daily pattern of elephant activity. Nevertheless, the shift of activity to nocturnal hours became more pronounced as human activity neared each monitored area of forest. This change in activity pattern and its likely causes would not have been detected through standard monitoring methods, which are not sensitive to behavioral changes over short time scales (e.g., dung transects, point counts) or cover a limited area (e.g., camera traps). Simultaneous acoustic monitoring of animal communication, human, and environmental sounds allows the documentation of short-term behavioral changes in response to human disturbance.

Demography of a forest elephant population.

African forest elephants face severe threats from illegal killing for ivory and bushmeat and habitat conversion. Due to their cryptic nature and inaccessible range, little information on the biology of this species has been collected despite its iconic status. Compiling individual based monitoring data collected over 20 years from the Dzanga Bai population in Central African Republic, we summarize sex and age specific survivorship and female age specific fecundity for a cohort of 1625 individually identified elephants. Annual mortality (average = 3.5%) and natality (average = 5.3%) were lower and markedly less variable relative to rates reported for savanna elephant populations. New individuals consistently entered the study system, leading to a 2.5% average annual increase in the registered population. Calf sex ratios among known birth did not differ from parity. A weak seasonal signal in births was detected suggesting increased conceptions during the wet season. Inter-calf intervals and age of primiparity were longer relative to savanna elephant populations. Within the population, females between the ages of 25-39 demonstrated the shortest inter-calf intervals and highest fecundity, and previous calf sex had no influence on the interval. Calf survivorship was high (97%) the first two years after birth and did not differ by sex. Male and female survival began to differ by the age of 13 years, and males demonstrated significantly lower survival relative to females by the age of 20. It is suspected these differences are driven by human selection for ivory. Forest elephants were found to have one of the longest generation times recorded for any species at 31 years. These data provide fundamental understanding of forest elephant demography, providing baseline data for projecting population status and trends.

Niche expansion, body size, and survival in Galápagos marine iguanas.

Foraging theory predicts that dietary niche breadth should expand as resource availability decreases. However, Galápagos marine iguanas often die during algae shortages (El Niños) although land plants abound where they rest and reproduce. On Seymour Norte island, a subpopulation of iguanas exhibited unique foraging behavior: they consistently included the succulent beach plant B. maritima in their diet. We investigated the consequences of land-plant feeding for body size and survival. Batis-eaters supplemented their algae diet both before and after intertidal zone foraging, and more Batis was eaten during tides unfavorable for intertidal zone foraging (dawn and dusk). Larger, energy-constrained iguanas fed more on land than did smaller animals. Compared to intertidal zone algae, Batis was 39% lower in caloric content (1.6 vs. 2.6 kcal g-1 dry mass), 56% lower in protein (8.3 vs. 18.9% dry mass) and 57% lower in nitrogen (1.3 vs. 3.0% dry mass). In spite of its lower nutrient value, iguanas that supplemented their diet with this plant were able to attain nearly twice the body size of other iguanas on the island. Age estimates indicate that many Batis-eaters survived repeated El Niño episodes during which animals of their relative size-class experienced high mortality on other islands. The larger animals were, however, completely dependent upon this supplementary source of food to maintain condition, and all perished in the 1997-1998 El Niño when high tides inundated and killed Batis on Seymour Norte Island. We hypothesize that Batis feeding developed as a local foraging tradition, and that dietary conservatism and strong foraging site fidelity explain why the inclusion of land plants in the diet has been observed in only a single population. Ultimately, a unique algae-adapted hindgut morphology and physiology may limit a switch from marine to terrestrial diet.

Long-term monitoring of Dzanga Bai forest elephants: forest clearing use patterns.

Individual identification of the relatively cryptic forest elephant (Loxodonta cyclotis) at forest clearings currently provides the highest quality monitoring data on this ecologically important but increasingly threatened species. Here we present baseline data from the first 20 years of an individually based study of this species, conducted at the Dzanga Clearing, Central African Republic. A total of 3,128 elephants were identified over the 20-year study (1,244 adults; 675 females, 569 males). It took approximately four years for the majority of elephants visiting the clearing to be identified, but new elephants entered the clearing every year of the study. The study population was relatively stable, varying from 1,668 to 1,864 individuals (including juveniles and infants), with increasingly fewer males than females over time. The age-class distribution for females remained qualitatively unchanged between 1995 and 2010, while the proportion of adult males decreased from 20% to 10%, likely reflecting increased mortality. Visitation patterns by individuals were highly variable, with some elephants visiting monthly while others were ephemeral users with visits separated by multiple years. The number of individuals in the clearing at any time varied between 40 and 100 individuals, and there was little evidence of a seasonal pattern in this variation. The number of elephants entering the clearing together (defined here as a social group) averaged 1.49 (range 1-12) for males and 2.67 (range 1-14) for females. This collation of 20 years of intensive forest elephant monitoring provides the first detailed, long term look at the ecology of bai visitation for this species, offering insight to the ecological significance and motivation for bai use, social behavior, and threats to forest elephants. We discuss likely drivers (rainfall, compression, illegal killing, etc.) influencing bai visitation rates. This study provides the baseline for future demographic and behavioral studies of this population.

Ivory-billed woodpecker (Campephilus principalis) persists in continental North America.

The ivory-billed woodpecker (Campephilus principalis), long suspected to be extinct, has been rediscovered in the Big Woods region of eastern Arkansas. Visual encounters during 2004 and 2005, and analysis of a video clip from April 2004, confirm the existence of at least one male. Acoustic signatures consistent with Campephilus display drums also have been heard from the region. Extensive efforts to find birds away from the primary encounter site remain unsuccessful, but potential habitat for a thinly distributed source population is vast (over 220,000 hectares).