A hidden Markov model for estimating age-specific survival when age and size are uncertain.

Estimates of age-specific survival probabilities are needed for age-structured population models and to inform conservation decisions. However, determining the age of individuals in wildlife populations is often problematic. We present a hidden Markov model for estimating age-specific survival from capture-recapture or capture-recapture-recovery data when age is unknown and indicators of age, such as size and growth layer counts, are imprecise. The model is evaluated through simulations, and its implementation is illustrated with maximum likelihood and Bayesian approaches in commonly used software. The model is then applied to genetic capture-recapture data of Florida manatees to estimate age- and time-variant survival probabilities. The approach is broadly applicable to studies aiming to quantify age-specific effects of environmental change and management actions on population dynamics, including studies that rely on minimally invasive methods such as genetic and photo identification.

Accuracy, precision, and error in age estimation of Florida manatees using growth layer groups in earbones.

Ages of Florida manatees (Trichechus manatus latirostris) can be estimated by counting annual growth layer groups (GLGs) in the periotic dome portion of the tympanoperiotic complex of their earbones. The Florida Fish and Wildlife Conservation Commission manages an archive of more than 8,700 Florida manatee earbones collected from salvaged carcasses from 1989 to 2017. Our goal was to comprehensively evaluate techniques used to estimate age, given this large sample size and changes to processing protocols and earbone readers over time. We developed new standards for estimating ages from earbones, involving two independent readers to obtain measurements of within- and between-reader precision. To quantify accuracy, precision, and error, 111 earbones from manatees with approximately known ages (first known as calves: "KAC") and 69 earbones from manatees with minimum known ages ("MKA," based on photo-identification sighting histories) were processed, and their ages were estimated. There was greater precision within readers (coefficient of variation, CV: 2.4-8.5%) than between readers (CV: 13.1-13.3%). The median of age estimates fell within the true age range for 63.1% of KAC cases and was at least the sighting duration for 75.0% of MKA cases. Age estimates were generally unbiased, as indicated by an average raw error ± SD of -0.05 ± 3.05 years for the KAC group. The absolute error (i.e., absolute value of raw error) of the KAC data set averaged 1.75 ± 2.50 years. Accuracy decreased and error increased with increasing known age, especially for animals over 15 years old, whose ages were mostly underestimated due to increasing levels of resorption (the process of bone turnover that obscures GLGs). Understanding the degree of uncertainty in age estimates will help us assess the utility of age data in manatee population models. We emphasize the importance of standardizing and routinely reviewing age estimation and processing protocols to ensure that age data remain consistent and reliable.

The right whale mandatory ship reporting system: a retrospective.

In 1998, the United States sought and received International Maritime Organization-endorsement of two Mandatory Ship Reporting (MSR) systems designed to improve mariner awareness about averting ship collisions with the endangered North Atlantic right whale (Eubalaena glacialis). Vessel collisions are a serious threat to the right whale and the program was among the first formal attempts to reduce this threat. Under the provisions of the MSR, all ships >300 gross tons are required to report their location, speed, and destination to a shore-based station when entering two key right whale habitats: one in waters off New England and one off coastal Georgia and Florida. In return, reporting ships receive an automatically-generated message, delivered directly to the ship's bridge, that provides information about right whale vulnerability to vessel collisions and actions mariners can take to avoid collisions. The MSR has been in operation continuously from July 1999 to the present. Archived incoming reports provided a 15-plus year history of ship operations in these two locations. We analyzed a total of 26,772 incoming MSR messages logged between July 1999 and December 2013. Most ships that were required to report did so, and compliance rates were generally constant throughout the study period. Self-reported vessel speeds when entering the systems indicated that most ships travelled between 10 and 16 (range = 5-20 +) knots. Ship speeds generally decreased in 2009 to 2013 following implementation of vessel speed restrictions. The number of reports into the southern system remained relatively constant following a steady increase through 2007, but numbers in the northern system decreased annually beginning in 2008. If reporting is indicative of long-term patterns in shipping operations, it reflects noteworthy changes in marine transportation. Observed declines in ship traffic are likely attributable to the 2008-2009 economic recession, the containerized shipping industry making increased use of larger ships that made fewer trips, and diminished oil/gas US imports as previously inaccessible domestic deposits were exploited. Recent declines in shipping activity likely resulted in lowered collision risks for right whales and reduced their exposure to underwater noise from ships.

Estimating upper bounds for occupancy and number of manatees in areas potentially affected by oil from the Deepwater Horizon oil spill.

The explosion of the Deepwater Horizon drilling platform created the largest marine oil spill in U.S. history. As part of the Natural Resource Damage Assessment process, we applied an innovative modeling approach to obtain upper estimates for occupancy and for number of manatees in areas potentially affected by the oil spill. Our data consisted of aerial survey counts in waters of the Florida Panhandle, Alabama and Mississippi. Our method, which uses a Bayesian approach, allows for the propagation of uncertainty associated with estimates from empirical data and from the published literature. We illustrate that it is possible to derive estimates of occupancy rate and upper estimates of the number of manatees present at the time of sampling, even when no manatees were observed in our sampled plots during surveys. We estimated that fewer than 2.4% of potentially affected manatee habitat in our Florida study area may have been occupied by manatees. The upper estimate for the number of manatees present in potentially impacted areas (within our study area) was estimated with our model to be 74 (95%CI 46 to 107). This upper estimate for the number of manatees was conditioned on the upper 95%CI value of the occupancy rate. In other words, based on our estimates, it is highly probable that there were 107 or fewer manatees in our study area during the time of our surveys. Because our analyses apply to habitats considered likely manatee habitats, our inference is restricted to these sites and to the time frame of our surveys. Given that manatees may be hard to see during aerial surveys, it was important to account for imperfect detection. The approach that we described can be useful for determining the best allocation of resources for monitoring and conservation.