A simple tool for linking photo-identification with multimedia data to track mammal behaviour

Photo Identification ◽

In The Wild ◽

The Individual ◽

Future Work ◽

AbstractIdentifying individual animals is critical to describe demographic and behavioural patterns, and to investigate the ecological and evolutionary underpinnings of these patterns. The traditional non-invasive method of individual identification in mammals—comparison of photographed natural marks—has been improved by coupling other sampling methods, such as recording overhead video, audio and other multimedia data. However, aligning, linking and syncing these multimedia data streams are persistent challenges. Here, we provide computational tools to streamline the integration of multiple techniques to identify individual free-ranging mammals when tracking their behaviour in the wild. We developed an open-source R package for organizing multimedia data and for simplifying their processing a posteriori—“MAMMals: Managing Animal MultiMedia: Align, Link, Sync”. The package contains functions to (i) align and link the individual data from photographs to videos, audio recordings and other text data sources (e.g. GPS locations) from which metadata can be accessed; and (ii) synchronize and extract the useful multimedia (e.g. videos with audios) containing photo-identified individuals. To illustrate how these tools can facilitate linking photo-identification and video behavioural sampling in situ, we simultaneously collected photos and videos of bottlenose dolphins using off-the-shelf cameras and drones, then merged these data to track the foraging behaviour of individuals and groups. We hope our simple tools encourage future work that extend and generalize the links between multiple sampling platforms of free-ranging mammals, thereby improving the raw material needed for generating new insights in mammalian population and behavioural ecology.

Physiological Effects of Low Salinity Exposure on Bottlenose Dolphins (Tursiops truncatus)

Journal of Zoological and Botanical Gardens ◽

10.3390/jzbg1010005 ◽

2020 ◽

Vol 1 (1) ◽

pp. 61-75 ◽

Cited By ~ 1

Author(s):

Abby M. McClain ◽

Risa Daniels ◽

Forrest M. Gomez ◽

Sam H. Ridgway ◽

Ryan Takeshita ◽

...

Keyword(s):

Medical Records ◽

Tursiops Truncatus ◽

Bottlenose Dolphins ◽

Blood Samples ◽

Low Salinity ◽

Worldwide Distribution ◽

Salinity Levels ◽

Seawater Environment ◽

Future Work ◽

Bottlenose dolphins (Tursiops truncatus) have a worldwide distribution in temperate and tropical waters and often inhabit estuarine environments, indicating their ability to maintain homeostasis in low salinity for limited periods of time. Epidermal and biochemical changes associated with low salinity exposure have been documented in stranded bottlenose dolphins; however, these animals are often found severely debilitated or deceased and in poor condition. Dolphins in the U.S. Navy Marine Mammal Program travel globally, navigating varied environments comparable to those in which free-ranging dolphins are observed. A retrospective analysis was performed of medical records from 46 Navy dolphins and blood samples from 43 Navy dolphins exposed to a variety of salinity levels for different durations over 43 years (from 1967–2010). Blood values from samples collected during low salinity environmental exposure (salinity ranging from 0–30 parts per thousand (ppt) were compared to samples collected while those same animals were in a seawater environment (31–35 ppt). Epidermal changes associated with low salinity exposure were also assessed. Significant decreases in serum sodium, chloride, and calculated serum osmolality and significant increases in blood urea nitrogen and aldosterone were observed in blood samples collected during low salinity exposure. Epidermal changes were observed in 35% of the animals that spent time in low salinity waters. The prevalence of epidermal changes was inversely proportional to the level of salinity to which the animals were exposed. Future work is necessary to fully comprehend the impacts of low salinity exposure in bottlenose dolphins, but the physiological changes observed in this study will help improve our understanding of the upper limit of duration and the lower limit of salinity in which a bottlenose dolphin can maintain homeostasis.

GenTag: a package to improve animal color tagging protocol

Revista Brasileira de Ornitologia ◽

10.1007/bf03546071 ◽

2019 ◽

Vol 27 (4) ◽

pp. 253-260

Author(s):

Carlos Biagolini ◽

Regina H. Macedo

Keyword(s):

Sexual Selection ◽

Life History ◽

Random Process ◽

Animal Behavior ◽

Methodological Approach ◽

R Package ◽

Life History Parameters ◽

Selection Processes ◽

The Individual

AbstractThe individual identification of animals by means of tagging is a common methodological approach in ornithology. However, several studies suggest that specific colors may affect animal behavior and disrupt sexual selection processes. Thus, methods to choose color tagging combinations should be carefully evaluated. However, reporting of this information is usually neglected. Here, we introduce the GenTag, an R package developed to support biologists in creating color tag sequence combinations using a random process. First, a single-color tag sequence is created from an algorithm selected by the user, followed by verification of the combination. We provide three methods to produce color tag sequences. GenTag provides accessible and simple methods to generate color tag sequences. The use of a random process to define the color tags to be applied to each animal is the best way to deal with the influence of tag color upon behavior and life history parameters.

Difficulties identifying Australian sea lions (Neophoca cinerea) in the wild using whisker spot patterns

Australian Mammalogy ◽

10.1071/am15051 ◽

2017 ◽

Vol 39 (1) ◽

pp. 56 ◽

Cited By ~ 1

Author(s):

Sylvia K. Osterrieder ◽

Iain M. Parnum ◽

Chandra P. Salgado Kent ◽

Randall W. Robinson

Keyword(s):

Distance Transform ◽

Accurate Identification ◽

Sea Lions ◽

Photo Identification ◽

Non Invasive ◽

Neophoca Cinerea ◽

In The Wild ◽

Chamfer Distance ◽

Wild Individual

Individual identification is a beneficial tool in behavioural and ecological research. In mark–recapture studies, for example, it can improve abundance, residency and site fidelity estimates. Two non-invasive, photo-identification approaches, using whisker spot patterns, were tested to identify wild individual Australian sea lions (Neophoca cinerea). The Chamfer distance transform algorithm has shown promising results when applied to captive individuals. An alternative matching method using row/column locations of whisker spots, previously applied to lions (Panthera leo) was also tested. Resighting wild N. cinerea in this study proved unfeasible with both methods. Excessive variation between photographs of the same individual was found when applying the Chamfer distance transform, and similarity between photograph-pairs appeared to decrease with increasing time between photographs. Insufficient variation among N. cinerea row/column pattern was detected to successfully discriminate among individuals, averaging 39 mystacial spots (range 30–46, n = 20) in seven rows and 9–10 columns. Additionally, different observers marking the same photographs introduced considerable variation. Colour difference (red, green and blue colour levels) between the whisker spots and surrounding fur affected marking spot locations significantly, increasing uncertainty when contrast decreased. While other pattern-matching algorithms may improve performance, accurate identification of spot locations was the current limitation.

Iris photo-identification: A new methodology for the individual recognition of Tarentola geckos

Amphibia-Reptilia ◽

10.1163/15685381-00002918 ◽

2013 ◽

Vol 34 (4) ◽

pp. 590-596 ◽

Cited By ~ 5

Author(s):

Ricardo Rocha ◽

Tiago Carrilho ◽

Rui Rebelo

Keyword(s):

Pattern Matching ◽

Individual Recognition ◽

Field Studies ◽

Identification System ◽

Correct Identification ◽

Photo Identification ◽

Horizontal Angle ◽

The Individual

Gekkonid field studies are hampered by the difficulty to individually recognize individuals. In this study we assess the feasibility of using their variegated iris pattern to photo-identify Tarentola boettgeri bischoffi, a threatened Macaronesian endemic. Using a library of 924 photos taken over a 9-month period we also evaluate the use of the pattern matching software Interactive Individual Identification System (I3S) to match photos of known specimens. Individuals were clearly recognized by their iris pattern with no misidentifications, and using I3S lead to a correct identification of 95% of the recaptures in a shorter time than the same process when conducted visually by an observer. The method’s feasibility was improved by increasing the number of images of each animal in the library and hindered by photos that deviate from a horizontal angle.

Underwater Mirror Exposure to Free-Ranging Naïve Atlantic Spotted Dolphins (Stenella frontalis) in the Bahamas

International Journal of Comparative Psychology ◽

10.46867/ijcp.2013.26.02.02 ◽

2013 ◽

Vol 26 (2) ◽

Author(s):

Fabienne Delfour ◽

Denise Herzing

Keyword(s):

Marine Mammals ◽

Bottlenose Dolphins ◽

Killer Whales ◽

California Sea Lions ◽

The Bahamas ◽

Single Male ◽

Stenella Frontalis ◽

Self Recognition ◽

In The Wild ◽

The “mirror state,” described for human self-recognition, has been found in captive or human-raised species. In marine mammals, bottlenose dolphins and killer whales have shown evidence of body examination, self-directed and contingency checking behaviors whereas false killer whales appeared ambiguous and California sea lions did not recognize themselves in a mirror. Self-recognition processes in wild cetaceans remain unknown. Since 1985, a resident community of Atlantic spotted dolphin (Stenella frontalis) has been studied underwater in the Bahamas. We describe the reaction of free-ranging dolphins during 14 exposures to the presence of a mirror from 1994/1995 and 2004/2005. Responses to the mirror were mixed. Initial reactions of mother/calf groups were to swim around mirror and stay in close physical proximity. Others ignored the mirror entirely, or swam around or underneath. A single male became stationary and postured in an aggressive stance in front of the mirror. The wild spotted dolphins showed a significant preference to exposing and/or orienting their right side to the mirror versus their left side. We suggest that the animals assign different meanings to a mirror in the wild versus the same object in captivity.

Evaluation of the video-identification technique applied to bottlenose dolphins (Tursiops truncatus) in Cagarras Archipelago, Rio de Janeiro, Brazil

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315408002993 ◽

2008 ◽

Vol 89 (5) ◽

pp. 1077-1081 ◽

Cited By ~ 6

Author(s):

Liliane Lodi ◽

Luiz Cláudio Mayerhofer ◽

Cassiano Monteiro Neto

Keyword(s):

Tursiops Truncatus ◽

Rio De Janeiro ◽

Bottlenose Dolphins ◽

Photo Identification ◽

Dorsal Fin ◽

Identification Technique ◽

The Individual ◽

Sequential Images ◽

Reliable Methods ◽

Video Identification

Reliable methods to identify and monitor cetacean individuals are important to assess population behaviour and ecology. We describe and evaluate the application of the digital video-identification technique (DVI) for the acquisition and analysis of dorsal fin images in the study of bottlenose dolphins (Tursiops truncatus) in the Cagarras Archipelago, Rio de Janeiro, Brazil. Between August and November 2004, we identified and catalogued 20 individuals; 80% were re-sighted more than twice. The Individual Residence Index varied between 1.0 (N = 1) and 0.2 (N = 4). Compared with traditional photo-identification methods, DVI offers significant advantages in respect to production of sequential images and speed of editing and processing.

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

10.32942/osf.io/epqa7 ◽

2019 ◽

Author(s):

Shinichi Nakagawa ◽

Malgorzata Lagisz ◽

Rose E O'Dea ◽

Joanna Rutkowska ◽

Yefeng Yang ◽

...

Keyword(s):

Meta Analysis ◽

R Package ◽

Effect Sizes ◽

Forest Plot ◽

Point Estimates ◽

Aggregate Effect ◽

The Individual ◽

Meta Analyses ◽

Heterogeneous Effect ◽

Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

Investigation of duck plague virus in hoar areas of Bangladesh

Bangladesh Journal of Livestock Research ◽

10.3329/bjlr.v26i1-2.49939 ◽

2020 ◽

Vol 26 (1-2) ◽

pp. 73-78

Author(s):

A Hossen ◽

MH Rahman ◽

MZ Ali ◽

MA Yousuf ◽

MZ Hassan ◽

...

Keyword(s):

Cytopathic Effect ◽

Clinical Sample ◽

Chorioallantoic Membrane ◽

Clinical Samples ◽

Isolation And Identification ◽

Duck Plague Virus ◽

Pcr Method ◽

Polymerase Chain ◽

The Individual ◽

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78