Animal cultures matter for conservation

This is the author accepted manuscript. The final version is available from AAAS via the DOI in this record.No abstrac

An Assessment of the Effectiveness of High Definition Cameras as Remote Monitoring Tools for Dolphin Ecology Studies.

Research involving marine mammals often requires costly field programs. This paper assessed whether the benefits of using cameras outweighs the implications of having personnel performing marine mammal detection in the field. The efficacy of video and still cameras to detect Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the Fremantle Harbour (Western Australia) was evaluated, with consideration on how environmental conditions affect detectability. The cameras were set on a tower in the Fremantle Port channel and videos were perused at 1.75 times the normal speed. Images from the cameras were used to estimate position of dolphins at the water’s surface. Dolphin detections ranged from 5.6 m to 463.3 m for the video camera, and from 10.8 m to 347.8 m for the still camera. Detection range showed to be satisfactory when compared to distances at which dolphins would be detected by field observers. The relative effect of environmental conditions on detectability was considered by fitting a Generalised Estimation Equations (GEEs) model with Beaufort, level of glare and their interactions as predictors and a temporal auto-correlation structure. The best fit model indicated level of glare had an effect, with more intense periods of glare corresponding to lower occurrences of observed dolphins. However this effect was not large (-0.264) and the parameter estimate was associated with a large standard error (0.113).The limited field of view was the main restraint in that cameras can be only applied to detections of animals observed rather than counts of individuals. However, the use of cameras was effective for long term monitoring of occurrence of dolphins, outweighing the costs and reducing the health and safety risks to field personal. This study showed that cameras could be effectively implemented onshore for research such as studying changes in habitat use in response to development and construction activities

Sex bias in biopsy samples collected from free-ranging dolphins

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in European Journal of Wildlife Research 56 (2010): 151-158, doi:10.1007/s10344-009-0299-7.Biological samples of free-ranging dolphins are increasingly used to gain information on population structure and ecology. In small cetaceans, the gender of individuals usually cannot be determined at sea, and population sex ratio has to be inferred indirectly. We used molecular sexing to determine the gender of 340 biopsy samples of bottlenose dolphins, Tursiops truncatus, spotted dolphins, Stenella frontalis, and common dolphins, Delphinus delphis, collected around the Azores and Madeira. Sex ratio was globally skewed in favor of males, and differed between species and archipelagos. Skew was probably influenced by the selectivity of biopsy collectors and seasonal or year-round predominance of males in natural populations. Skew was also influenced by sampling duration and intensity. In the Azores, when several samples were successively collected within the same group, the proportion of female samples decreased as a function of sample order. This trend indicated a tendency for females to increasingly avoid the boat while samples were being collected. It showed that males and females reacted differently to the perturbation caused by the biopsy sampling process (i.e. sample collection and driving style).Portuguese Foundation for Science and Technology (FCT) and the FEDER program for funding the CETAMARH (POCTI/BSE/38991/01) and the GOLFINICHO (POCI/BIA-BDE/61009/2004) projects, S.Q.'s post-doctoral grants (IMAR/FCT- PDOC-006/2001-MoleGen and SFRH/BPD/19680/2004), M.A.S.'s doctoral (SFRH/BD/8609/2002) and post-doctoral (SFRH/BPD/29841/2006) grants, S.M.'s investigation assistant grant (CETAMARHII/POCTI/BSE/38991/2001) and I.C.'s investigation assistant grants (IMAR/FCT/GOLFINICHO/001/2005 and IMAR/FCT/GOLFINICHO/004/2006). FCT for its pluri-annual funding to Research Unit #531 and the EU funded program Interreg IIIb for funding the MACETUS project (MAC/4.2/M10) as well as R.P. and S.M.’s grants (IMAR/INTERREGIIIb/MACETUS/MAC1/2)

Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs

Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE. 2013;8(7): e68365.High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome

First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae : a lack of population structure calls for integrated management of this important fisheries target species

BackgroundClupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world's poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population.ResultsWe performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a north-south axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (F-ST=0.0054; 95% CI: 0.0046-0.0066). PCoA, fineRADstructure and global F-ST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (F-ST=0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data.ConclusionOur results show at most very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over a north-south axis. Based on these results, we advise to manage the stock as one population, integrating one management strategy over the four riparian countries. These results are a first comprehensive study on the population structure of these important fisheries target species, and can guide fisheries management.Peer reviewe