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1,204 results on '"Downs, Colleen T"'

1. CNN Based Flank Predictor for Quadruped Animal Species

Author

Suessle, Vanessa, Heurich, Marco, Downs, Colleen T., Weinmann, Andreas, and Hergenroether, Elke

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The bilateral asymmetry of flanks of animals with visual body marks that uniquely identify an individual, complicates tasks like population estimations. Automatically generated additional information on the visible side of the animal would improve the accuracy for individual identification. In this study we used transfer learning on popular CNN image classification architectures to train a flank predictor that predicts the visible flank of quadruped mammalian species in images. We automatically derived the data labels from existing datasets originally labeled for animal pose estimation. We trained the models in two phases with different degrees of retraining. The developed models were evaluated in different scenarios of different unknown quadruped species in known and unknown environments. As a real-world scenario, we used a dataset of manually labeled Eurasian lynx (Lynx lynx) from camera traps in the Bavarian Forest National Park to evaluate the model. The best model, trained on an EfficientNetV2 backbone, achieved an accuracy of 88.70 % for the unknown species lynx in a complex habitat.

Published
2024

2. Automated Bioacoustic Monitoring for South African Bird Species on Unlabeled Data

Author

Doell, Michael, Kuehn, Dominik, Suessle, Vanessa, Burnett, Matthew J., Downs, Colleen T., Weinmann, Andreas, and Hergenroether, Elke

Subjects
Computer Science - Sound, Computer Science - Computer Vision and Pattern Recognition, Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract

Analyses for biodiversity monitoring based on passive acoustic monitoring (PAM) recordings is time-consuming and challenged by the presence of background noise in recordings. Existing models for sound event detection (SED) worked only on certain avian species and the development of further models required labeled data. The developed framework automatically extracted labeled data from available platforms for selected avian species. The labeled data were embedded into recordings, including environmental sounds and noise, and were used to train convolutional recurrent neural network (CRNN) models. The models were evaluated on unprocessed real world data recorded in urban KwaZulu-Natal habitats. The Adapted SED-CRNN model reached a F1 score of 0.73, demonstrating its efficiency under noisy, real-world conditions. The proposed approach to automatically extract labeled data for chosen avian species enables an easy adaption of PAM to other species and habitats for future conservation projects., Comment: preprint

Published
2024

6. A genomic basis of vocal rhythm in birds

Author

Sebastianelli, Matteo, Lukhele, Sifiso M, Secomandi, Simona, de Souza, Stacey G, Haase, Bettina, Moysi, Michaella, Nikiforou, Christos, Hutfluss, Alexander, Mountcastle, Jacquelyn, Balacco, Jennifer, Pelan, Sarah, Chow, William, Fedrigo, Olivier, Downs, Colleen T, Monadjem, Ara, Dingemanse, Niels J, Jarvis, Erich D, Brelsford, Alan, vonHoldt, Bridgett M, and Kirschel, Alexander NG

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Human Genome, Animals, Vocalization, Animal, Male, Genomics, Genome, Female, Songbirds, Birds
Abstract

Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

Published
2024

7. Automatic Individual Identification of Patterned Solitary Species Based on Unlabeled Video Data

Author

Suessle, Vanessa, Arandjelovic, Mimi, Kalan, Ammie K., Agbor, Anthony, Boesch, Christophe, Brazzola, Gregory, Deschner, Tobias, Dieguez, Paula, Granjon, Anne-Céline, Kuehl, Hjalmar, Landsmann, Anja, Lapuente, Juan, Maldonado, Nuria, Meier, Amelia, Rockaiova, Zuzana, Wessling, Erin G., Wittig, Roman M., Downs, Colleen T., Weinmann, Andreas, and Hergenroether, Elke

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The manual processing and analysis of videos from camera traps is time-consuming and includes several steps, ranging from the filtering of falsely triggered footage to identifying and re-identifying individuals. In this study, we developed a pipeline to automatically analyze videos from camera traps to identify individuals without requiring manual interaction. This pipeline applies to animal species with uniquely identifiable fur patterns and solitary behavior, such as leopards (Panthera pardus). We assumed that the same individual was seen throughout one triggered video sequence. With this assumption, multiple images could be assigned to an individual for the initial database filling without pre-labeling. The pipeline was based on well-established components from computer vision and deep learning, particularly convolutional neural networks (CNNs) and scale-invariant feature transform (SIFT) features. We augmented this basis by implementing additional components to substitute otherwise required human interactions. Based on the similarity between frames from the video material, clusters were formed that represented individuals bypassing the open set problem of the unknown total population. The pipeline was tested on a dataset of leopard videos collected by the Pan African Programme: The Cultured Chimpanzee (PanAf) and achieved a success rate of over 83% for correct matches between previously unknown individuals. The proposed pipeline can become a valuable tool for future conservation projects based on camera trap data, reducing the work of manual analysis for individual identification, when labeled data is unavailable.

Published
2023

27. Horizon scanning for South African biodiversity: A need for social engagement as well as science

Author

Seymour, Colleen L, Gillson, Lindsey, Child, Matthew F, Tolley, Krystal A, Curie, Jock C, da Silva, Jessica M, Alexander, Graham J, Anderson, Pippin, Downs, Colleen T, Egoh, Benis N, Ehlers Smith, David A, Ehlers Smith, Yvette C, Esler, Karen J, O’Farrell, Patrick J, Skowno, Andrew L, Suleman, Essa, and Veldtman, Ruan

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, History, Heritage and Archaeology, Biodiversity, Conservation of Natural Resources, Politics, South Africa, Biodiversity futures, Consensus and scientific knowledge, Delphi approach, Future scenarios, Step changes, Threats and opportunities, Ecology
Abstract

A horizon scan was conducted to identify emerging and intensifying issues for biodiversity conservation in South Africa over the next 5-10 years. South African biodiversity experts submitted 63 issues of which ten were identified as priorities using the Delphi method. These priority issues were then plotted along axes of social agreement and scientific certainty, to ascertain whether issues might be "simple" (amenable to solutions from science alone), "complicated" (socially agreed upon but technically complicated), "complex" (scientifically challenging and significant levels of social disagreement) or "chaotic" (high social disagreement and highly scientifically challenging). Only three of the issues were likely to be resolved by improved science alone, while the remainder require engagement with social, economic and political factors. Fortunately, none of the issues were considered chaotic. Nevertheless, strategic communication, education and engagement with the populace and policy makers were considered vital for addressing emerging issues.

Published
2020

37. Potential for a commercial inland fishery or just another water storage facility at Spring Grove Dam, KwaZulu-Natal, South Africa?

Author

Burnett, Matthew J, Hanzen, Céline, Whitehead, Alex, O'Brien, Gordon C, and Downs, Colleen T

Subjects
SMALL-scale fisheries, FISH diversity, MUNICIPAL water supply, WATER storage, SOCIAL surveys
Abstract

South Africa's inland fisheries are generally undervalued, though there is developing interest in the sector. Spring Grove Dam in the KwaZulu-Natal Midlands became operational as a water storage facility in 2013 to provide water to the growing urban population in the province. We assessed whether the impoundment could potentially support commercial fisheries as had been proposed during its design and construction. We conducted seasonal fish community surveys from 2020 to 2021 at sites along the impoundment and in the mainstem of the Mooi River which feeds into the impoundment. We recorded a total of nine fish species, including six non-native fishes with invasive characteristics. Only three of 10 expected native species were found, namely the KwaZulu-Natal yellowfish Labeobarbus natalensis, chubbyhead barb Enteromius anoplus and African longfin eel Anguilla mossambica. Catch per unit effort (CPUE) was low in the sampling surveys using mostly gillnets and fyke nets, and relatively low yields (14.97 tonnes yr-1) were subsequently calculated for the impoundment, making commercial fisheries unviable. However, the existing subsistence and recreational fisheries for non-native salmonids and the native L. natalensis would benefit by controlling the distribution range and abundances of non-native centrachids Micropterus spp. We offer recommendations and suggestions for management plans for Spring Grove Dam in the context of local fish diversity, a changing climate, further construction of water storage facilities on east-flowing rivers in the province, and a nationally neglected inland fishery industry. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Shifting to Active Learning: Assessment of a First-Year Biology Course in South Africa

Author

Downs, Colleen T. and Wilson, Amy-Leigh

Abstract

Large first-year class sizes have resulted in many lecturers adopting coping strategies consisting of direct-transmission mode teaching, reduced practical time, and assessment. Recently several strategies have been implemented in an attempt to improve student participation and active learning; however, these changes have to be facilitated and fostered by faculty and administrators. Consequently, we present the implementation, results, and feedback of a new Biology first-year course run for the period 2005-2008. In this course, the number of lectures was reduced, and the number of more co-operative tutorial and practical-based sessions was increased. The aim of these changes was to promote active participation of students and to encourage them to take responsibility for their own learning. Despite some initial problems, most students and staff were positive about the learning experience, and the skills developed were considered of value to other science courses. Other courses are encouraged to follow this example and move to a reduced lecture and increased interactive tutorial/workshop and practical approach to promote student learning and development.

Published
2015

42. Modification of the third phase in the framework for vertebrate species persistence in urban mosaic environments

Author

Downs, Colleen T., Alexander, Jarryd, Brown, Mark, Chibesa, Moses, Ehlers Smith, Yvette C., Gumede, S. Thobeka, Hart, Lorinda, Josiah, Kyrone K., Kalle, Riddhika, Maphalala, Machawe, Maseko, Mfundo, McPherson, Shane, Ngcobo, Samukelisiwe P., Patterson, Lindsay, Pillay, Kerushka, Price, Cormac, Raji, Islamiat Abidemi, Ramesh, Tharmalingam, Schmidt, Warren, Senoge, Ntaki D., Shivambu, Tinyiko C., Shivambu, Ndivhuwo, Singh, Nikisha, Singh, Preshnee, Streicher, Jarryd, Thabethe, Vuyisile, Thatcher, Harriet, Widdows, Craig, Wilson, Amy-Leigh, Zungu, Manqoba M., and Ehlers Smith, David A.

Published
2021
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