Lagged Identification Rate Research Articles

Occurence and residency patterns of humpback whales off Réunion Island during 2004–10

Dedicated humpback whale surveys were conducted around Réunion Island during 2004–10. Boat-based surveys were conducted from June to October, in the main objective of collecting photo-identification data. For 2004–10, a total of 501 survey trips, representing 1,530 hours of onsearching effort, and 724 humpback whale sightings were achieved. Although effort had a significant influence on the number of sightings, sighting rate was shown to increase significantly from 2007 onwards, with a peak in 2008. Seasonal variations were observed, with significantly higher numbers of sightings occurring in July–September. Larger number of whales, together with increased survey effort, led to larger datasets collected in 2008–10, allowing further investigation of residency pattern. Within-year recaptures from fluke photographs showed that a relatively large proportion (30%) of the identified whales was recaptured on more than one day around the island. Maximum recapture interval reached 64 days, with a mean ranging 22–29 days for 2008–10. Mean residency, estimated from expected lagged identification rate, was 25 days. Mothers with a calf were shown to reside around the island for longer period of time than other individuals. A seasonal pattern of residency was demonstrated, with single capture individuals occurring early in the season, mainly as singleton or pairs, while individuals showing higher recapture interval were present around the island from August to October. Between-year recaptures were reported for 2009–10, with five individuals re-sighted on consecutive years. The fluke catalogue for Réunion includes 312 distinct individuals identified during 2004–10 surveys, together with 21 additional whales captured opportunistically since 2001. The increasing trend in the number of whales, the high residency time observed for 2008–10 and the recent occurrence of inter-annual recaptures suggest that Réunion Island has become an important migratory site for humpback whales within the south-western Indian Ocean (Breeding Stock C). The species might expand its spatial range by occupying new breeding sites (or re-occupying old ones) within the south-western Indian ocean, as a result of population growth.

A first look at whale sharks in Hawaiian waters: Using citizen science to study the world's largest fish, Rhincodon typus

Abstract The world's largest fish, the whale shark (Rhincodon typus), is a circum‐tropically distributed and globally endangered species, that is widely studied at predictable aggregation sites. The main Hawaiian Islands are not known to have large aggregations of whale sharks; however, they have been anecdotally reported here with some regularity. To date, little is known about this charismatic species in Hawaiian waters. This study is the first effort to examine whale shark demographics and movements in a previously unstudied region of the world. Here, citizen science was used to investigate the abundance, seasonality (if any) and occurrence of whale sharks in the waters around the main Hawaiian Islands. A total of 309 individual whale sharks were identified from sightings between 1991–2020 by their unique spot patterns, most of which (74%) were reported between 2018 and 2020. Estimated whale shark total length ranged from 2–12 m (mean 6.1 m), with both juvenile and mature males and females represented in the dataset. The best‐fit Lagged Identification Rate (LIR) model for these data suggests that individuals sighted in Hawaiian waters are transient in nature, supporting the empirical data (88% of sharks sighted only once). Although using citizen science data can have inherent biases, these results present a conservative first assessment of the demographics of whale sharks in Hawaiian waters. For an Endangered species assessed as Largely Depleted by the IUCN Green Status of Species, highlighting Hawai’i as an important habitat for the whale shark – mainly as a migratory corridor or navigational waypoint – is a crucial step in understanding their ecology in the Pacific in order to develop effective management plans.

Crowdsourced data reveal multinational connectivity, population demographics, and possible nursery ground of endangered oceanic manta rays in the Red Sea

Abstract Despite the large size and economic value of the species, populations of oceanic manta ray (Mobula birostris) are often poorly studied and almost completely undescribed in the Red Sea. Here, photo‐identification (photo‐ID) was used to provide the first description of M. birostris movement patterns and population demographics for the northern Red Sea. Images collated from social media, researchers, and photo‐ID databases from 2004 to 2021 identified 267 individual M. birostris from 395 sightings in Egypt, Israel, Jordan, Saudi Arabia, and Sudan. Sexual parity was observed in the population with 134 females, 111 males, and 22 individuals of undetermined sex. Nearly half of the individuals in this study were first identified through social media searches, highlighting the value of the sightings data collected by the public. The regular presence of juveniles in Sharm el‐Sheikh, Egypt, indicates that this area is a potential nursery, which is the second identified for this species globally and the first in the Indo‐Pacific. Encounter data from this study recorded the first known movements of juvenile M. birostris and demonstrate that they can travel long distances of at least 525 km. Within the recorded population, 24.7% (n = 67) of individuals were resighted, including 21 oceanic manta rays that were encountered in more than one location. These records reveal long‐distance migrations of up to 700 km and confirm the international connectivity of M. birostris in the Red Sea. The lagged identification rate data are best fitted with an open‐population model, implying that the northern Red Sea is represented by one well‐mixed population. The baseline data presented here should encourage the expansion of directed research and citizen science initiatives for M. birostris. Increased knowledge of movement patterns and site use will be crucial to successfully protecting this endangered species in a region characterized by high levels of shipping traffic, unregulated fisheries, and extensive coastal development.

Improving sightings-derived residency estimation for whale shark aggregations: A novel metric applied to a global data set

The world’s largest extant fish, the whale shark Rhincodon typus, is one of the most-studied species of sharks globally. The discovery of predictable aggregation sites where these animals gather seasonally or are sighted year-round – most of which are coastal and juvenile-dominated – has allowed for a rapid expansion of research on this species. The most common method for studying whale sharks at these sites is photographic identification (photo-ID). This technique allows for long-term individual-based data to be collected which can, in turn, be used to evaluate population structure, build population models, identify long-distance movements, and assess philopatry and other population dynamics. Lagged identification rate (LIR) models have fewer underlying assumptions than more traditional capture mark recapture approaches, making them more broadly applicable to marine taxa, especially far-ranging megafauna species like whale sharks. However, the increased flexibility comes at a cost. Parameter estimations based on LIR can be difficult to interpret and may not be comparable between areas with different sampling regimes. Using a unique data-set from the Philippines with ~8 years of nearly continuous survey effort, we were able to derive a metric for converting LIR residency estimates into more intuitive days-per-year units. We applied this metric to 25 different sites allowing for the first quantitatively-meaningful comparison of sightings-derived residence among the world’s whale shark aggregations. We validated these results against the only three published acoustic residence metrics (falling within the ranges established by these earlier works in all cases). The results were then used to understand residency behaviours exhibited by the sharks at each site. The adjusted residency metric is an improvement to LIR-based population modelling, already one of the most widely used tools for describing whale shark aggregations. The standardised methods presented here can serve as a valuable tool for assessing residency patterns of whale sharks, which is crucial for tailored conservation action, and can cautiously be tested in other taxa.

The impact of injury on apparent survival of whale sharks (Rhincodon typus) in South Ari Atoll Marine Protected Area, Maldives

The whale shark (Rhincodon typus) is an endangered species with a declining global population. The South Ari Atoll Marine Protected Area (SAMPA), Maldives, is one of few locations globally where year-long residency of individuals occurs. This SAMPA aggregation appears to consist almost exclusively of immature males. Due to its year-round residency, this local aggregation is subjected to a high degree of tourism pressure. This ecotourism contributes to the high level of interest and protection offered to whale sharks by the local community. Unfortunately, if regulations are not followed or enforced, tourism can bring with it major stressors, such as accidental injuries. We used POPAN capture-mark-recapture models and lagged identification rate analysis to assess the effect of major injuries on whale shark residency within SAMPA. Injuries may be obtained outside SAMPA. We found individuals with major injuries had a higher apparent survival in the area than those without. Lagged identification rates also demonstrated that sharks with major injuries are more likely to return to the area. We suggest that major injuries result in sharks prolonging their time in the developmental habitat. These findings have implications for individual fitness and the population viability of this endangered species. We propose targeted conservation strategies be considered to protect sharks from further injury. Based on the presented spatio-temporal distributions of sharks, and current local knowledge of sighting patterns, speed limit zones and propeller-exclusion zones should be implemented and enforced. If carried out alongside tourist education, these measures will contribute to the protection of whale sharks within SAMPA and beyond. Furthermore, our results can aid research direction, alongside regulation and enforcement development, at similar sites worldwide.

Satellite Tagging and Photographic Identification Reveal Connectivity Between Two UNESCO World Heritage Areas for Reef Manta Rays

Reef manta rays (Mobula alfredi) are capable of long-distance dispersal when habitat is continuous. In the Ningaloo Reef World Heritage Area located on Australia’s mid-west coast, M. alfredi is sighted year-round and is a focal species for ecotourism in the region. Despite value to local tourism and demographic vulnerability to exploitation, basic information regarding M. alfredi movements and area use in this region is lacking. Here we used satellite tags and a long-term photographic-identification database collected by researchers and citizen scientists to examine the species’ visitation patterns and regional space use. Tagged M. alfredi remained in coastal shelf waters, preferentially occupying shallow depths 10 years). Lagged Identification Rate analysis suggested site visitation was best described by a pattern of emigration and reimmigration. While our observations of movement and residency establishes basic information previously unknown for the species in this region, the overlap of core area use with existing UNESCO World Heritage Areas demonstrates the potential for well-positioned marine parks to provide protection of critical habitat for M. alfredi.

Abundance and site fidelity of bottlenose dolphins off a remote oceanic island (Reunion Island, southwest Indian Ocean)

AbstractThis study represents the first comprehensive assessment of the population dynamics and residency of common bottlenose dolphin around Reunion Island (southwest Indian Ocean). Understanding dynamics and movement patterns of this local population is essential to guide effective conservation efforts, notably in a context of growing dolphin‐watching activities. Dedicated surveys based on photo‐identification methods were conducted over 6 years (2010–2015). The species was present year‐round, in groups of 25 individuals on average (1–150). Jolly‐Seber mark‐recapture models resulted in a population estimate of 254 individuals (95% CI = 191–337) and an apparent annual survival rate of 0.83. The population was almost equally split into three residency patterns: residents (33.1%), long‐term visitors (32.6%), and short‐term visitors (34.3%, including transients, i.e., individuals only seen once [14.9%]), suggesting that the majority of the population showed a moderate‐to‐high level of residency in the study area. Individuals from the three residency patterns associated randomly, mixing together and forming a single community. Models based on the lagged identification rate indicated emigration and reimmigration to the survey area, with some individuals occupying the study area for about 2 years (832 days), and remaining outside for an average of 276 days, probably exhibiting larger home ranges and extensive movement behavior.

Abundance and residency dynamics of the Indo‐Pacific humpback dolphin, Sousa chinensis, in the Dafengjiang River Estuary, China

AbstractRobust population size estimates are essential for informing population conservation status. Residency dynamics show population habitat use through time. Population size of Indo‐Pacific humpback dolphins (Sousa chinensis) has been extensively investigated in Chinese waters, but their residency dynamics are rarely known. Mark‐recapture analysis based on photo‐identification records was applied to humpback dolphins in the Dafengjiang River Estuary habitat, one of the key habitats in the northern Beibu Gulf, China. Movement analyses based on lagged identification rate indicated the humpback dolphins spent, on average, 78.5 days inside and 46.9 days outside the survey area. Within the study area, the humpback dolphin abundance was 83 identifiable dolphins. A total of 353–430 humpback dolphins, estimated by POPAN modeling, were involved in this fluid habitat‐use dynamic. Robust Design analysis showed strong seasonality in humpback dolphin abundance and emigration probability, implying a movement‐ and habitat‐use pattern likely associated with spatiotemporal distribution of oceanographic characteristics and prey occurrences. Population surveys and conservation measures currently conducted in Chinese waters seldom consider seasonality in movements between habitat patches, which can be addressed by genetic analyses across habitats and cross‐matching photo‐identification records among neighboring habitats.

Population structure of a whale shark Rhincodon typus aggregation in the Red Sea

The presence of whale sharks Rhincodon typus were recorded around Shib Habil, a small, coastal reef off the Red Sea coast of Saudi Arabia, from 2010 to 2015. A total of 267 suitable photographs resulting in the identification of 136 individuals, were documented from 305 encounters. Sharks were divided evenly between the sexes with no evidence of temporal or spatial segregation. All individuals were immature based on size estimates and, for males, juvenile clasper morphology. Scars were reported for 57% of R. typus with 15% showing evidence of propeller trauma. Estimates of population size and patterns of residency were calculated by modelling the lagged identification rate. Multiple models were run simultaneously and compared using the Akaike information criterion. An open population model was found to best represent the data and estimates a daily abundance between 15 and 34 R. typus during the aggregation season, with local residence times ranging from 4 to 44 days. Residence times away from Shib Habil range from 15 to 156 days with a permanent emigration-death rate between 0·07 and 0·58 individuals year(-1) . These results are broadly similar to those from other aggregations of R. typus, although the observed sexual parity and integration found at this site is unique for the species and needs further study.

Bottlenose dolphin Tursiops truncatus group dynamics, site fidelity, residency and movement patterns in the Madeira Archipelago (North-East Atlantic)

The bottlenose dolphin Tursiops truncatus is one of the most frequently sighted cetacean species in the Madeira Archipelago (North-East Atlantic); however, little is known about its population ecology in these waters. Photo-identification undertaken during systematic, non-systematic and opportunistic surveys conducted between 2001 and 2012 was used to assess group dynamics, site fidelity, residency and movement patterns of bottlenose dolphins in the archipelago. Three different patterns of residency were assigned, based on individual sighting histories. Group size ranged between 2 and 90 individuals (median 12), with no significant monthly difference in group size. All resident dolphins formed a core, complex network with migrant and transient dolphins. In contrast, satellite clusters were formed exclusively by transient individuals. The lagged identification rate (LIR) model indicated that a dolphin remained in the area for an average of 90 days, whereas the average time an individual spent outside the study area was approximately 313 days. The Madeira Archipelago appears to be only a section of a much larger home range for this population, with the dolphins exhibiting three different patterns of occurrence that associate with each other. The information gained about this poorly studied population contributes to the overall knowledge of bottlenose dolphins in insular oceanic habitats.

Population structure, residency patterns and movements of whale sharks in Southern Leyte, Philippines: results from dedicated photo‐ID and citizen science

Abstract The whale shark, Rhincodon typus, is a charismatic umbrella species whose highly mobile nature is not yet fully understood. Whale sharks roam the Philippine archipelago with two major aggregations known to occur at Donsol and at a provisioning site in Cebu. This is the first description of a previously identified aggregation occurring off Panaon Island, Southern Leyte through the use of photographic identification. In total, 93 individual whale sharks were identified, with significant male bias (58%). The mean estimated total length of individuals was 5.72 ± 1.02 m S.D., indicating a juvenile aggregation. Partial or complete fin amputations, potentially resulting from fishing lines, boat propellers or net entanglement, were observed on 27% of animals, highlighting some of the risks human activities can have on this threatened species. Multiple parallel scars, identified as propeller impact, were observed on 45% of animals. Dedicated research seasons in 2013 and 2014 yielded very different whale shark encounters with 366 in 2013 and 12 in 2014, yet highlighted the recurrence of individuals at the study site. Complemented by data collected through citizen science, maximum likelihood methods were used to model mean residency of whale sharks at Panaon Island of 27.04 days. The modelled lagged identification rate showed that many whale sharks return to the study site over time. Whale sharks from Panaon Island were identified through photo‐ID and citizen science at other sites in the Philippines, as well as a match to Taiwan, representing the first international match through photo‐ID in South‐east Asia with a minimum distance covered of 1600 km. Given the highly mobile nature and recent exploitation of this species, management is recommended as a single unit regionally in South‐east Asia. Additional research is needed to focus on the drivers of variation in encounters at whale shark aggregation sites. Copyright © 2016 John Wiley & Sons, Ltd.

Spinner dolphins Stenella longirostris off south-west Mauritius: abundance and residency

Spinner dolphins Stenella longirostris longirostris off the south-west coast of Mauritius are subject to ongoing anthropogenic disturbance in the form of daily dolphin tourism, which has intensified since 1998. Abundance of this species was estimated using photo-identification data and mark-recapture analysis. Between April 2008 and June 2010, identification photographs were collected from dolphins occurring along a 30 km length of the coast of south-west Mauritius. A total of 250 groups were encountered over 229 survey days. Mark-recapture analyses were performed on a photographic dataset of more than 8 000 good- and excellent-quality images and 83 animals were identified as distinctively marked individuals. The majority (85.5%) were seen more than once and resightings indicated a resident population. The compiled version of SOCPROG 2.4 was used to investigate the lagged identification rate. The fitted model supported a mostly resident population with additional animals moving in and out of the study area. The estimated abundance of the total population in the study area ranged between 138 and 399 individuals. Our results can be used for monitoring the population for fluctuations and for encouraging both the enforcement of laws regarding dolphin watching and the development of further means of management needed to ensure the long-term presence of this population.

Influence of body size and ranging patterns on delphinid sociality: Associations among Commerson's dolphins

We investigated the association patterns of 48 identifiable Commerson's dolphins (Cephalorhynchus commersonii) photographed 2 or more times over a 2-year period in Baho´a Engano, Chubut, Argentina. The associations among them were not different from random for short time periods (7 days) but were significantly different from random for longer periods. Lagged identification rate and lagged association rate models show that dolphins remained in the area on average 15 days and then moved away as the original groups dissolved. Commerson's dolphins appear to have a fission-fusion society, and the observed strength of their associations is in concordance with the predictions regarding their body size and ranging patterns. The dolphins seem to rely on Baho ´a Engano as a core area for most of their activities, but the aggregations are labile and some individuals remain associated in a more stable manner with only a few other individuals.

Selection of Models of Lagged Identification Rates and Lagged Association Rates Using AIC and QAIC

The lagged identification rate is the probability of identifying an individual given its identification some time lag earlier. The lagged association rate is the probability that two individuals are associated given their association some time lag earlier. Models of lagged identification and association rates fit by maximizing the sums of non independent log-likelihoods have approximately unbiased parameter estimates. Simulations suggest that: Akaike-Information-Criterion often selects the true model of lagged identification rate data; quasi-Akaike-Information-Criterion performs better for lagged association rates; and confidence intervals for parameters are best obtained by bootstrap methods for lagged identification rates and quasi-likelihood or jackknife methods for lagged association rates.

Analysis of Animal Movement Using Opportunistic Individual Identifications: Application to Sperm Whales

Data sets in which animals are identified individually in different places and times may contain considerable information on movements. However, if the probability that an animal is reidentified depends on its movement pattern, then standard methods of analyzing movement are not applicable. I show that modifications of maximum likelihood methods, in which the identifications themselves establish the spatial and temporal distribution of effort, can be used to derive movement parameters in three situations: (1) Identifications in one location allow calculation of the “lagged identification rate” (the probability of reidentification after various time lags) as well as estimation of residence times inside, and outside, the study area. (2) When more than one study area is sampled, it is possible to derive lagged identification rates between them and to estimate movement rates between areas and other population parameters. (3) Movements through continuous space can be described by diffusion rates (rates of population spread), and plots of squared displacement against time lag. To simplify computation, and to permit the analysis of large data sets, summed nonindependent log-likelihoods can be maximized in place of the true log-likelihood to obtain approximately unbiased parameter estimates, and binomial, multinomial, or hypergeometric models can be approximated by the Poisson distribution. The first and third of the techniques were verified using simulated data, and all were applied to a 13-yr data set of identifications of sperm whales in the South Pacific Ocean. Residence times in waters close to the Galápagos Islands were of the order of 8 d, but during the study period there was a substantial net movement out of the Galápagos region and into waters of the coastal eastern tropical Pacific. Diffusion rates of sperm whales were ∼700 km2/d over time scales from 1 to 100 d but decreased considerably over time scales of years, indicating displacements of ∼50 km/d within home ranges spanning ∼1000 km. Although giving relatively imprecise estimates of movement parameters compared to more standard methods, the techniques considered here should be particularly useful when examining animal movements over long time scales.