Project description:Passive acoustic monitoring (PAM) is a powerful method to study the occurrence, movement and behavior of echolocating odontocetes (toothed whales) in the wild. However, in areas occupied by more than one species, echolocation clicks need to be classified into species. The present study investigated whether the echolocation clicks produced by small, at-risk, resident sympatric populations of Indian Ocean humpback dolphin (Sousa plumbea) and Indo-Pacific bottlenose dolphin (Tursiops aduncus) in Menai Bay, Zanzibar, East Africa, could be classified to allow species specific monitoring. Underwater sounds of S. plumbea and T. aduncus groups were recorded using a SoundTrap 202HF in January and June-August 2015. Eight acoustic parameters, i.e. -10 dB duration, peak, centroid, lower -3 and lower -10 dB frequencies, and -3 dB, -10 dB and root-mean-squared bandwidth, were used to describe and compare the two species' echolocation clicks. Statistical analyses showed that S. plumbea clicks had significantly higher peak, centroid, lower -3 and lower -10 dB frequencies compared to T. aduncus, whereas duration and bandwidth parameters were similar for the two species. Random Forest (RF) classifiers were applied to determine parameters that could be used to classify the two species from echolocation clicks and achieved 28.6% and 90.2% correct species classification rates for S. plumbea and T. aduncus, respectively. Both species were classified at a higher rate than expected at random, however the identified classifiers would only be useful for T. aduncus monitoring. The frequency and bandwidth parameters provided most power for species classification. Further study is necessary to identify useful classifiers for S. plumbea. This study represents a first step in acoustic description and classification of S. plumbea and T. aduncus in the western Indian Ocean region, with potential application for future acoustic monitoring of species-specific temporal and spatial occurrence in these sympatric species.
Project description:Coastal dolphins are regarded as indicators of changes in coastal marine ecosystem health that could impact humans utilizing the marine environment for food or recreation. Necropsy and histology examinations were performed on 35 Indian Ocean bottlenose dolphins (Tursiops aduncus) and five Indo-Pacific humpback dolphins (Sousa plumbea) incidentally caught in shark nets off the KwaZulu-Natal coast, South Africa, between 2010 and 2012. Parasitic lesions included pneumonia (85%), abdominal and thoracic serositis (75%), gastroenteritis (70%), hepatitis (62%), and endometritis (42%). Parasitic species identified were Halocercus sp. (lung), Crassicauda sp. (skeletal muscle) and Xenobalanus globicipitis (skin). Additional findings included bronchiolar epithelial mineralisation (83%), splenic filamentous tags (45%), non-suppurative meningoencephalitis (39%), and myocardial fibrosis (26%). No immunohistochemically positive reaction was present in lesions suggestive of dolphin morbillivirus, Toxoplasma gondii and Brucella spp. The first confirmed cases of lobomycosis and sarcocystosis in South African dolphins were documented. Most lesions were mild, and all animals were considered to be in good nutritional condition, based on blubber thickness and muscle mass. Apparent temporal changes in parasitic disease prevalence may indicate a change in the host/parasite interface. This study provided valuable baseline information on conditions affecting coastal dolphin populations in South Africa and, to our knowledge, constitutes the first reported systematic health assessment in incidentally caught dolphins in the Southern Hemisphere. Further research on temporal disease trends as well as disease pathophysiology and anthropogenic factors affecting these populations is needed.
Project description:This project contains a reference genome for Sporophila hypoxantha and population level re-sequencing for S. hypoxantha, S. nigrorufa, S. pileata, S. palustris, S. melanogaster, S. ruficollis, S. hypochroma, S. cinnamomea, S. bouvreuil, S. iberaensis, S. minuta, S. castaneiventris, S. plumbea, and S. beltoni. Genome sequencing and assembly
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.