Windy events detection in big bioacoustics datasets using a pre-trained Convolutional Neural Network.

Passive Acoustic Monitoring (PAM), which involves using autonomous record units for studying wildlife behaviour and distribution, often requires handling big acoustic datasets collected over extended periods. While these data offer invaluable insights about wildlife, their analysis can present challenges in dealing with geophonic sources. A major issue in the process of detection of target sounds is represented by wind-induced noise. This can lead to false positive detections, i.e., energy peaks due to wind gusts misclassified as biological sounds, or false negative, i.e., the wind noise masks the presence of biological sounds. Acoustic data dominated by wind noise makes the analysis of vocal activity unreliable, thus compromising the detection of target sounds and, subsequently, the interpretation of the results. Our work introduces a straightforward approach for detecting recordings affected by windy events using a pre-trained convolutional neural network. This process facilitates identifying wind-compromised data. We consider this dataset pre-processing crucial for ensuring the reliable use of PAM data. We implemented this preprocessing by leveraging YAMNet, a deep learning model for sound classification tasks. We evaluated YAMNet as-is ability to detect wind-induced noise and tested its performance in a Transfer Learning scenario by using our annotated data from the Stony Point Penguin Colony in South Africa. While the classification of YAMNet as-is achieved a precision of 0.71, and recall of 0.66, those metrics strongly improved after the training on our annotated dataset, reaching a precision of 0.91, and recall of 0.92, corresponding to a relative increment of >28 %. Our study demonstrates the promising application of YAMNet in the bioacoustics and ecoacoustics fields, addressing the need for wind-noise-free acoustic data. We released an open-access code that, combined with the efficiency and peak performance of YAMNet, can be used on standard laptops for a broad user base.

Vaccination of African penguins (Spheniscus demersus) against high-pathogenicity avian influenza.

BACKGROUND: High-pathogenicity avian influenza (HPAI) has become a conservation threat to wild birds. Therefore, suitable vaccine technology and practical application methods require investigation. METHODS: Twenty-four African penguins (Spheniscus demersus) were vaccinated with either a conventional inactivated clade 2.3.4.4b H5N8 HPAI whole virus or a tobacco leaf-produced H5 haemagglutinin-based virus-like particle (VLP). Six birds received a second dose of the inactivated vaccine. Antibody responses were assessed and compared by employing haemagglutination inhibition tests. RESULTS: A second dose of inactivated vaccine was required to induce antibody titres above the level required to suppress virus shedding, while a single dose of VLP vaccine produced these levels by day 14, and one bird still had antibodies on day 430. LIMITATIONS: Bacterial contamination of the VLP vaccine limited the monitoring period and sample size in that treatment group, and it was not possible to perform a challenge study with field virus. CONCLUSION: VLP vaccines offer a more practical option than inactivated whole viruses, especially in logistically challenging situations involving wild birds.

Vocal tract shape variation contributes to individual vocal identity in African penguins.

Variation in formant frequencies has been shown to affect social interactions and sexual competition in a range of avian species. Yet, the anatomical bases of this variation are poorly understood. Here, we investigated the morphological correlates of formants production in the vocal apparatus of African penguins. We modelled the geometry of the supra-syringeal vocal tract of 20 specimens to generate a population of virtual vocal tracts with varying dimensions. We then estimated the acoustic response of these virtual vocal tracts and extracted the centre frequency of the first four predicted formants. We demonstrate that: (i) variation in length and cross-sectional area of vocal tracts strongly affects the formant pattern, (ii) the tracheal region determines most of this variation, and (iii) the skeletal size of penguins does not correlate with the trachea length and consequently has relatively little effect on formants. We conclude that in African penguins, while the variation in vocal tract geometry generates variation in resonant frequencies supporting the discrimination of conspecifics, such variation does not provide information on the emitter's body size. Overall, our findings advance our understanding of the role of formant frequencies in bird vocal communication.

Effect of Environmental Variables on African Penguin Vocal Activity: Implications for Acoustic Censusing.

Global biodiversity is in rapid decline, and many seabird species have disproportionally poorer conservation statuses than terrestrial birds. A good understanding of population dynamics is necessary for successful conservation efforts, making noninvasive, cost-effective monitoring tools essential. Here, we set out to investigate whether passive acoustic monitoring (PAM) could be used to estimate the number of animals within a set area of an African penguin (Spheniscus demersus) colony in South Africa. We were able to automate the detection of ecstatic display songs (EDSs) in our recordings, thus facilitating the handling of large datasets. This allowed us to show that calling rate increased with wind speed and humidity but decreased with temperature, and to highlight apparent abundance variations between nesting habitat types. We then showed that the number of EDSs in our recordings positively correlated with the number of callers counted during visual observations, indicating that the density could be estimated based on calling rate. Our observations suggest that increasing temperatures may adversely impact penguin calling behaviour, with potential negative consequences for population dynamics, suggesting the importance of effective conservation measures. Crucially, this study shows that PAM could be successfully used to monitor this endangered species' populations with minimal disturbance.

The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021-2022.

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021-2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho's outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana's outbreaks in 2021 were unrelated, but viruses of Botswana's unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA's commercial poultry cases in 2021-2022 were point introductions from wild birds. Like H5N8 HPAI in 2017-2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.

Is Penguin Circovirus Circulating Only in the Antarctic Circle? Lack of Viral Detection in Namibia.

The known host range of circoviruses is continuously expanding because of more intensive diagnostic activities and advanced sequencing tools. Recently, a new circovirus (penguin circovirus (PenCV)) was identified in the guano and cloacal samples collected from Adélie penguins (Pygoscelis adeliae) and chinstrap penguins (Pygoscelis antarcticus) in Antarctica. Although the virus was detected in several asymptomatic subjects, a potential association with feather disease was speculated. To investigate the occurrence and implications of PenCV in other penguin species located outside of Antarctica, a broad survey was undertaken in African penguins (Spheniscus demersus) on two islands off the southern Namibian coast. For this purpose, specific molecular biology assays were developed and validated. None of the 151 blood samples tested positive for PenCV. Several reasons could explain the lack of PenCV positive samples. African penguins and Pygoscelis species are separated by approximately 6000 km, so there is almost no opportunity for transmission. Similarly, host susceptibility to PenCV might be penguin genus-specific. Overall, the present study found no evidence of PenCV in African penguin colonies in Namibia. Further dedicated studies are required to assess the relevance of PenCV among different penguin species.

Haemoproteus jenniae (Haemoproteidae, Haemosporida) infects gulls (Larus spp.) in South Africa, with redescription of Haemoproteus skuae.

Haemoproteus spp. are dipteran-borne protozoa that infect erythrocytes and reticulo-endothelial cells of birds. These parasites are not usually transmitted between birds belonging to different orders. The suborder Lari (order Charadriiformes) comprises ~170 avian species, the majority of which are aquatic, including gulls, terns, auklets, murres and skuas, among others. In spite of the diversity of this avian group, there is limited known diversity of haemosporidian parasites, with only 4 recorded Haemoproteus morphospecies thus far. We examined the blood smears of 21 kelp gulls (Larus dominicanus) captured at a breeding colony in South Africa, as well as Haemoproteus-positive archival blood smears of 15 kelp gulls and 1 Hartlaub's gull (Larus hartlaubii) sampled while under care at seabird rehabilitation facilities in South Africa. Haemoproteus sp. infection was detected in 19% of wild-caught kelp gulls. All parasites from the gulls were morphologically identified as Haemoproteus jenniae, a species previously recorded in Lari birds at the Galapagos Islands (Ecuador), Rocas Atoll (Brazil) and Poland. Gene sequencing uncovered a new cytochrome b lineage, LARDOM01, which was closely related to the previously reported H. jenniae lineage CREFUR01. Additionally, we evaluated a hapantotype blood smear of Haemoproteus skuae, which had been described infecting a brown skua (Catharacta antarctica) in South Africa. We provide a redescription of H. skuae and discuss the morphological characters distinguishing it from H. jenniae. Further research is necessary to improve our knowledge about the host and geographic distribution, health effects and phylogeny of H. jenniae and H. skuae.

Factors determining the number of seabirds impacted by oil spills and the success of their rehabilitation: Lessons learned from Namibia and South Africa.

The coastal waters of Namibia and South Africa have an extensive history of oil spills, with 71 recorded up to 2021. Thirty-nine spills reportedly affected 83,224 seabirds, with African penguins (Spheniscus demersus; 91.0 %) and Cape gannets (Morus capensis; 8.5 %) most affected. Spills affecting seabirds were caused by unknown sources (46 %), bulk/cargo carriers (43 %), tankers (38 %) and ship-to-ship transfers (14 %). The number of penguins oiled was predicted by the breeding population size within 25 to 75 km, but not the volume of oiled spilled, the month or the year. Rehabilitation records from penguins oiled in spills since 2001 reveal that the day of admission (relative to the start of the spill) was predictive of packed cell volume, body mass, and plasma total solids, with the latter two being predictive of rehabilitation success. Our results highlight the importance of rapid monitoring at colonies to locate oiled birds in the event of spills.

Intercolony variation in reproductive skipping in the African penguin.

In long-lived species, reproductive skipping is a common strategy whereby sexually mature animals skip a breeding season, potentially reducing population growth. This may be an adaptive decision to protect survival, or a non-adaptive decision driven by individual-specific constraints. Understanding the presence and drivers of reproductive skipping behavior can be important for effective population management, yet in many species such as the endangered African penguin (Spheniscus demersus), these factors remain unknown. This study uses multistate mark-recapture methods to estimate African penguin survival and breeding probabilities at two colonies between 2013 and 2020. Overall, survival (mean ± SE) was higher at Stony Point (0.82 ± 0.01) than at Robben Island (0.77 ± 0.02). Inter-colony differences were linked to food availability; under decreasing sardine (Sardinops sagax) abundance, survival decreased at Robben Island and increased at Stony Point. Additionally, reproductive skipping was evident across both colonies; at Robben Island the probability of a breeder becoming a nonbreeder was ~0.22, versus ~0.1 at Stony Point. Penguins skipping reproduction had a lower probability of future breeding than breeding individuals; this lack of adaptive benefit suggests reproductive skipping is driven by individual-specific constraints. Lower survival and breeding propensity at Robben Island places this colony in greater need of conservation action. However, further research on the drivers of inter-colony differences is needed.

Determinants of external and blood parasite load in African penguins (Spheniscus demersus) admitted for rehabilitation.

We investigate the factors associated with the occurrence and abundance of external and blood parasites in African penguins (Spheniscus demersus), an endangered seabird that breeds exclusively on the coasts of Namibia and South Africa. External parasites were collected using the dust-ruffling method from 171 African Penguins admitted at a rehabilitation facility in the Western Cape, South Africa. Additionally, blood smears were obtained upon admission and weekly during rehabilitation and examined for blood parasites. Fleas Parapsyllus longicornis humboldti, ticks Ornithodoros capensis and lice Austrogoniodes demersus were recovered from 93, 63 and 40%, respectively, of the penguins upon admission to the centre. Rescue location and age group were identified as significant determinants of flea abundance, whereas month of admission was a significant determinant of tick abundance. Blood parasites were also common on admission, with Babesia being the most frequent (46% prevalence) whereas Borrelia was recorded sporadically (1.2%) and Plasmodium was recorded once. The prevalence and abundance of ticks on admission was positively associated with Babesia infection on admission. Our findings demonstrate the variability and contributing factor of parasite infections in an endangered species of penguin, and highlight the need for additional research on the parasite-host dynamics involving these potential disease vectors.

Nasal mites (Mesostigmata: Rhinonyssidae) in African penguins (Spheniscus demersus).

Rhinonyssids are obligate haematophagous mites that parasitize the nasal cavity of vertebrates, and occur in a wide range of birds worldwide. Two species of nasal mites are known to occur in penguins: Rhinonyssus sphenisci, which has been recorded from Humboldt and Magellanic penguins (Spheniscus humboldti and S. magellanicus, respectively), and Rhinonyssus schelli, which has been recorded in Adélie and Gentoo penguins (Pygoscelis adeliae and P. papua, respectively). We examined the nasal cavity of African penguins (Spheniscus demersus) that died while under care at a rehabilitation centre (N = 40) or that were found dead at breeding colonies (N = 67). Nasal mites were found in the nasal cavity and/or paranasal of sinuses of 21 penguins, some of which had signs of mild-to-moderate sinusitis. Prevalence was higher in juveniles (29%) and adults (27%) than in chicks (10%). Mean intensity was 5.9 ± 12.9 mites per infected host (range 1-60). The mites presented morphological characteristics that were at times consistent with either R. sphenisci or R. schelli, and therefore we conservatively classified them as 'R. sphenisci sensu lato'. Our morphometric results raise the question of whether the specific status of R. schelli is justified.

From incubation to release: Hand-rearing as a tool for the conservation of the endangered African penguin.

The African penguin (Spheniscus demersus) population is estimated at 25,000 breeding pairs, approximately 5% of that at the start of the 20th century, and the species is currently classified as Endangered. In the last two decades, the hand-rearing of penguin chicks that were abandoned by their parents due to oil spills or other circumstances has become a valuable conservation tool to limit mortality and to bolster the population at specific colonies. We summarize and evaluate the techniques employed by the Southern African Foundation for the Conservation of Coastal Birds (SANCCOB) to incubate and hand-rear African penguin eggs and chicks. From 2012 to 2016, a total of 694 eggs and 2819 chicks were received by SANCCOB's Chick Rearing Unit. It was estimated that 13% of the eggs were infertile, and 81% of the fertile eggs hatched successfully. The overall release rate for chicks was 77%, with a higher release rate for chicks that were pre-emptively removed (93%) followed by chicks that had been abandoned by their parents (78%), chicks admitted due to avian pox lesions (61%), chicks that hatched from artificially-incubated eggs (57%), and chicks admitted due to injuries or deformities (25%). Rescuing and hand-rearing eggs and chicks has been a successful strategy for African penguins, and might be also applicable for the conservation of other threatened seabird species whose population are critically low or during natural or anthropogenic events that could have disastrous population impacts (e.g. oil spills, disease outbreaks, catastrophic weather events, strong El Niño years, etc.).

Metapopulation Tracking Juvenile Penguins Reveals an Ecosystem-wide Ecological Trap.

Climate change and fisheries are transforming the oceans, but we lack a complete understanding of their ecological impact [1-3]. Environmental degradation can cause maladaptive habitat selection, inducing ecological traps with profound consequences for biodiversity [4-6]. However, whether ecological traps operate in marine systems is unclear [7]. Large marine vertebrates may be vulnerable to ecological traps [6], but their broad-scale movements and complex life histories obscure the population-level consequences of habitat selection [8, 9]. We satellite tracked postnatal dispersal in African penguins (Spheniscus demersus) from eight sites across their breeding range to test whether they have become ecologically trapped in the degraded Benguela ecosystem. Bayesian state-space and habitat models show that penguins traversed thousands of square kilometers to areas of low sea surface temperatures (14.5°C-17.5°C) and high chlorophyll-a (∼11 mg m-3). These were once reliable cues for prey-rich waters, but climate change and industrial fishing have depleted forage fish stocks in this system [10, 11]. Juvenile penguin survival is low in populations selecting degraded areas, and Bayesian projection models suggest that breeding numbers are ∼50% lower than if non-impacted habitats were used, revealing the extent and effect of a marine ecological trap for the first time. These cascading impacts of localized forage fish depletion-unobserved in studies on adults-were only elucidated via broad-scale movement and demographic data on juveniles. Our results support suspending fishing when prey biomass drops below critical thresholds [12, 13] and suggest that mitigation of marine ecological traps will require matching conservation action to the scale of ecological processes [14].

Good days, bad days: wind as a driver of foraging success in a flightless seabird, the southern rockhopper penguin.

Due to their restricted foraging range, flightless seabirds are ideal models to study the short-term variability in foraging success in response to environmentally driven food availability. Wind can be a driver of upwelling and food abundance in marine ecosystems such as the Southern Ocean, where wind regime changes due to global warming may have important ecological consequences. Southern rockhopper penguins (Eudyptes chrysocome) have undergone a dramatic population decline in the past decades, potentially due to changing environmental conditions. We used a weighbridge system to record daily foraging mass gain (the difference in mean mass of adults leaving the colony in the morning and returning to the colony in the evening) of adult penguins during the chick rearing in two breeding seasons. We related the day-to-day variability in foraging mass gain to ocean wind conditions (wind direction and wind speed) and tested for a relationship between wind speed and sea surface temperature anomaly (SSTA). Foraging mass gain was highly variable among days, but did not differ between breeding seasons, chick rearing stages (guard and crèche) and sexes. It was strongly correlated between males and females, indicating synchronous changes among days. There was a significant interaction of wind direction and wind speed on daily foraging mass gain. Foraging mass gain was highest under moderate to strong winds from westerly directions and under weak winds from easterly directions, while decreasing under stronger easterly winds and storm conditions. Ocean wind speed showed a negative correlation with daily SSTA, suggesting that winds particularly from westerly directions might enhance upwelling and consequently the prey availability in the penguins' foraging areas. Our data emphasize the importance of small-scale, wind-induced patterns in prey availability on foraging success, a widely neglected aspect in seabird foraging studies, which might become more important with increasing changes in climatic variability.

Evaluating the impact of handling and logger attachment on foraging parameters and physiology in southern rockhopper penguins.

Logger technology has revolutionised our knowledge of the behaviour and physiology of free-living animals but handling and logger attachments may have negative effects on the behaviour of the animals and their welfare. We studied southern rockhopper penguin (Eudyptes chrysocome) females during the guard stage in three consecutive breeding seasons (2008/09-2010/11) to evaluate the effects of handling and logger attachment on foraging trip duration, dive behaviour and physiological parameters. Smaller dive loggers (TDRs) were used in 2010/11 for comparison to larger GPS data loggers used in all three seasons and we included two categories of control birds: handled controls and PIT control birds that were previously marked with passive integrative transponders (PITs), but which had not been handled during this study. Increased foraging trip duration was only observed in GPS birds during 2010/11, the breeding season in which we also found GPS birds foraging further away from the colony and travelling longer distances. Compared to previous breeding seasons, 2010/11 may have been a period with less favourable environmental conditions, which would enhance the impact of logger attachments. A comparison between GPS and TDR birds showed a significant difference in dive depth frequencies with birds carrying larger GPS data loggers diving shallower. Mean and maximum dive depths were similar between GPS and TDR birds. We measured little impact of logger attachments on physiological parameters (corticosterone, protein, triglyceride levels and leucocyte counts). Overall, handling and short-term logger attachments (1-3 days) showed limited impact on the behaviour and physiology of the birds but care must be taken with the size of data loggers on diving seabirds. Increased drag may alter their diving behaviour substantially, thus constraining them in their ability to catch prey. Results obtained in this study indicate that data recorded may also not represent their normal dive behaviour.

Infection by Haemoproteus parasites in four species of frigatebirds and the description of a new species of Haemoproteus (Haemosporida: Haemoproteidae).

Among seabirds, the fregatids stand out with a high prevalence of blood parasites. Four of 5 species in this family have been found to be infected with Haemoproteus; however, complete species descriptions with molecular phylogeny are lacking. Seventy-five samples from 4 species of frigatebirds, i.e., Fregata andrewsi, Fregata minor, Fregata magnificens, and Fregata aquila, were screened for infections caused by species of Haemoproteus. Four different parasite haplotypes were found infecting frigatebirds based on the sequencing of a fragment of the cytochrome b gene. Two haplotypes belong to the subgenus Parahaemoproteus, and the other 2 correspond to haplotypes within the subgenus Haemoproteus . The more prevalent and cosmopolitan Parahaemoproteus haplotype (FregPHae1) was phylogenetically grouped with other Haemoproteus parasites infecting non-passerine birds, but it could not be detected from the single sample from F. aquila. The other Parahaemoproteus haplotype (FregPHae2) was not phylogenetically clustered with parasites infecting non-passerine birds, and it was sequenced from a single (1 each) F. andrewsi and F. minor. Blood smears from F. andrewsi infected only by FregPHae1 haplotype showed sufficient gametocytes to allow description of a new species, Haemoproteus valkiunasi sp. nov. In contrast to Haemoproteus iwa, the only previously known blood parasite infecting frigatebirds and described from F. minor from Galapagos Islands, parasites from F. andrewsi (1) are shorter with no contact of gametocyte with host cell membrane, (2) have fewer pigment granules, and (3) have wider microgametocytes, with a smaller host nuclear displacement. In contrast, patent single infections corresponding to the cosmopolitan haplotype of the subgenus Haemoproteus (FregHae1) were also found in samples from 1 F. andrewsi, 1 F. minor, and 1 F. aquila. In all these cases, the number of microgametocytes was very low, resembling H. iwa, which lacks microgametocytes in the original description. Macrogametocytes of haplotype FregHae1 in F. andrewsi differ significantly from all the characteristics measured from H. valkiunasi. In addition, it also differs from all characteristics of H. iwa despite being genetically identical in the analyzed fragment.

Hemosporidian blood parasites in seabirds--a comparative genetic study of species from Antarctic to tropical habitats.

Whereas some bird species are heavily affected by blood parasites in the wild, others reportedly are not. Seabirds, in particular, are often free from blood parasites, even in the presence of potential vectors. By means of polymerase chain reaction, we amplified a DNA fragment from the cytochrome b gene to detect parasites of the genera Plasmodium, Leucocytozoon, and Haemoproteus in 14 seabird species, ranging from Antarctica to the tropical Indian Ocean. We did not detect parasites in 11 of these species, including one Antarctic, four subantarctic, two temperate, and four tropical species. On the other hand, two subantarctic species, thin-billed prions Pachyptila belcheri and dolphin gulls Larus scoresbii, were found infected. One of 28 thin-billed prions had a Plasmodium infection whose DNA sequence was identical to lineage P22 of Plasmodium relictum, and one of 20 dolphin gulls was infected with a Haemoproteus lineage which appears phylogenetically clustered with parasites species isolated from passeriform birds such as Haemoproteus lanii, Haemoproteus magnus, Haemoproteus fringillae, Haemoproteus sylvae, Haemoproteus payevskyi, and Haemoproteus belopolskyi. In addition, we found a high parasite prevalence in a single tropical species, the Christmas Island frigatebird Fregata andrewsi, where 56% of sampled adults were infected with Haemoproteus. The latter formed a monophyletic group that includes a Haemoproteus line from Eastern Asian black-tailed gulls Larus crassirostris. Our results are in agreement with those showing that (a) seabirds are poor in hemosporidians and (b) latitude could be a determining factor to predict the presence of hemosporidians in birds. However, further studies should explore the relative importance of extrinsic and intrinsic factors on parasite prevalence, in particular using phylogenetically controlled comparative analyses, systematic sampling and screening of vectors, and within-species comparisons.