Effect of matching uncertainty on population parameter estimation in mark-recapture analysis of photo-identification data

Thanks also to the SeaDoc Society, Molly and John Bailey, the Richardson family, Sarah Haney (Canadian Whale Institute), National Geographic, and Beto Bedolfe at the Marisla Foundation for financial support over the years, and to The Willow Grove Foundation for supporting the Knight Inlet expedition that made 2010 so productive. Erin thanks Air Canada’s Aeroplan Beyond Miles program for travel support. Erin was a beneficiary of a writing retreat for women in science supported by Lyda Hill Philanthropies and the National Geographic Explorers Program.Quantifying and dealing with uncertainty are key aspects of ecological studies. Population parameter estimation from mark-recapture analyses of photo-identification data hinges on correctly matching individuals from photographs and assumes that identifications are detected with certainty, marks are not lost over time, and that individuals are recognised when they are resighted. Matching photographs is an inherently subjective process. Traditionally, two photographs are not considered a “match” unless the photo reviewer is 100% certain. This decision may carry implications with respect to sample size and the bias and precision of the resultant parameter estimates. Here, we present results from a photo-identification experiment on Pacific white-sided dolphins to assign one of three levels of certainty that a pair of photographs represented a match. We then illustrate how estimates of abundance and survival varied as a function of the matching certainty threshold used. As expected, requiring 100% certainty of a match resulted in fewer matches, which in turn led to higher estimates of abundance and lower estimates of survival than if a lower threshold were used to determine a match. The tradition to score two photographs as a match only when the photo reviewer is 100% certain stems from a desire to be conservative, but potential over-estimation of abundance means that there may be applications (e.g., assessing sustainability of bycatch) in which it is not precautionary. We recommend exploring the consequences of matching uncertainty and incorporating that uncertainty into the resulting estimates of abundance and survival.Publisher PDFPeer reviewe

Distribution and habitat use modelling from satellite tracking data of humpback whales in Brazil agree with shipboard survey data modelling

Funding: The Monitoring Whales by Satellite Project (Projeto Monitoramento de Baleias por Satélite, PMBS) research cruises were sponsored by Shell Brasil. The Federal University of Rio Grande (FURG) and the R/V Atlântico Sul crew provided essential support during fieldwork. G.A.B.’s PhD work is funded by the Brazilian National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq; Science Without Borders, scholarship number 208203/2014-1).Statistical modelling of animal distributions has been widely applied to explain how mobile species use their habitats. The distribution of and habitat use by humpback whales Megaptera novaeangliae off the eastern coast of Brazil have previously been investigated by modelling visual survey data. Here, we modelled distribution in their breeding range using individual tracking data to compare ecological inferences with those from previous models from line transect data. A generalised estimating equation framework was used to model the tracking data and pseudo-absences as functions of spatial covariates. Covariates considered were latitude and longitude, sea surface temperature (SST), current and wind speeds near the surface, distances to shelf-break and the coast, sea bottom depth and slope, and a factor variable representing ‘shelter’. Two modelling exercises were developed: a habitat use model (HUM) and a distribution model (DIM). Covariates retained in the selected HUM were SST, distance to coast and shelf-break, current and wind speeds and shelter. Covariates retained in the selected DIM were latitude/longitude, current speed and distances to shelf-break and coast. The modelled relationships between whale occurrence and environmental covariates using tracking data were similar to those using line transect data. Distribution maps were also similar, supporting higher densities around the Abrolhos Archipelago and to its south. We showed that habitat use and distribution of this population in the area could be similarly inferred by modelling either line transect or tracking data. Using these 2 approaches in conjunction can strengthen the understanding of important ecological aspects of animal populations.PostprintPeer reviewe

Sperm competition risk drives plasticity in seminal fluid composition

Background Ejaculates contain a diverse mixture of sperm and seminal fluid proteins, the combination of which is crucial to male reproductive success under competitive conditions. Males should therefore tailor the production of different ejaculate components according to their social environment, with particular sensitivity to cues of sperm competition risk (i.e. how likely it is that females will mate promiscuously). Here we test this hypothesis using an established vertebrate model system, the house mouse (Mus musculus domesticus), combining experimental data with a quantitative proteomics analysis of seminal fluid composition. Our study tests for the first time how both sperm and seminal fluid components of the ejaculate are tailored to the social environment. Results Our quantitative proteomics analysis reveals that the relative production of different proteins found in seminal fluid – i.e. seminal fluid proteome composition – differs significantly according to cues of sperm competition risk. Using a conservative analytical approach to identify differential expression of individual seminal fluid components, at least seven of 31 secreted seminal fluid proteins examined showed consistent differences in relative abundance under high versus low sperm competition conditions. Notably three important proteins with potential roles in sperm competition – SVS 6, SVS 5 and CEACAM 10 – were more abundant in the high competition treatment groups. Total investment in both sperm and seminal fluid production also increased with cues of heightened sperm competition risk in the social environment. By contrast, relative investment in different ejaculate components was unaffected by cues of mating opportunities. Conclusions Our study reveals significant plasticity in different ejaculate components, with the production of both sperm and non-sperm fractions of the ejaculate strongly influenced by the social environment. Sperm competition risk is thus shown to be a key factor in male ejaculate production decisions, including driving plasticity in seminal fluid composition

Fin whale survival and abundance in the Gulf of St. Lawrence, Canada

The fin whale Balaenoptera physalus, the second largest species in the animal kingdom to have lived on Earth, was heavily targeted during the industrial whaling era. North Atlantic whaling for this species ended in 1987 and it is unclear if the populations are recovering. The stock structure in the North Atlantic is still under debate, but several lines of evidence suggest that fin whales in the Gulf of St. Lawrence may form a discrete stock with limited exchange with the rest of the North Atlantic. We applied mark-recapture models to 21 yr of photo-identification data from the Jacques-Cartier Passage to estimate the abundance and, for the first time, a survival rate based on live re-sightings for this stock of fin whales. Using the Cormack-Jolly-Seber model, we estimated a unisex non-calf apparent survival rate of 0.955 (95% CI: 0.936 to 0.969) for the period 1990 to 2010, declining in the last 4 yr of the study. The reduced survivorship was likely caused by a lower site fidelity combined with a higher mortality. The POPAN model yielded a super-population estimate of 328 individuals (95% CI: 306 to 350) for the period 2004 to 2010, and confirmed the negative trend in apparent survival and annual abundance, indicating that the population has not increased since the last large-scale surveys from 1974 and 1997.Publisher PDFPeer reviewe

Whale distribution in a breeding area : spatial models of habitat use and abundance of western South Atlantic humpback whales

GA Bortolotto PhD is funded by the Brazilian National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq; Science Without Borders, scholarship #208203/2014 - 1). Cetacean International Society granted GA Bortolotto with small grants which contributed to the development of this study.The western South Atlantic humpback whale population was severely depleted by commercial whaling in the late 19th and 20th centuries, and today inhabits a human-impacted environment in its wintering grounds off the Brazilian coast. We identified distribution patterns related to environmental features and provide new estimates of population size, which can inform future management actions. We fitted spatial models to line transect data from 2 research cruises conducted in 2008 and 2012 to investigate (1) habitat use and (2) abundance of humpback whales wintering in the Brazilian continental shelf. Potential explanatory variables were year, depth, seabed slope, sea-surface temperature (SST), northing and easting, current speed, wind speed, distance to coastline and to the continental shelf break, and shelter (a combination of wind speed and SST categories). Whale density was higher in slower currents, at shorter distances to both the coastline and shelf break, and at SSTs between 24 and 25°C. The distribution of whales was also strongly related to shelter. For abundance estimation, easting and northing were included in the model instead of SST; estimates were 14264 whales (CV = 0.084) for 2008 and 20389 (CV = 0.071) for 2012. Environmental variables explained well the variation in whale density; higher density was found to the south of the Abrolhos Archipelago, and shelter seems to be important for these animals in their breeding area. Estimated distribution patterns presented here can be used to mitigate potential human-related impacts, such as supporting protection in the population’s core habitat near the Abrolhos Archipelago.PostprintPeer reviewe

Intrinsic and extrinsic drivers of activity budgets in sympatric grey and harbour seals

D. J. F. Russell was funded by the UK Department of Energy and Climate Change (DECC) as part of their Offshore Energy Strategic Environmental Assessment programme and by Scottish Government as part of their Marine Mammal Scientific Support Research Programme (MMSS/001/11). The telemetry tags and their deployment were funded by DECC, the Natural Environment Research Council, Scottish Government, Marine Scotland Science and The European Commission.Investigation of activity budgets in relation to seasonal, intrinsic (age, sex) and extrinsic (time of day, spatial) covariates enables an understanding of how such covariates shape behavioural strategies. However, conducting such investigations in the wild is challenging, because of the required large sample size of individuals across the annual cycle, and difficulties in categorising behavioural states and analysing the resulting individual-referenced and serially correlated data. In this study, from telemetry tags deployed on 63 grey seals (Halichoerus grypus) and 126 harbour seals (Phoca vitulina) we used behavioural data, and movement data within a Bayesian state-space model (SSM), to define population-level activity budgets around Britain. Using generalised estimating equations (GEEs) we then examined how time spent in four states (resting on land (hauled out), resting at sea, foraging and travelling) was influenced by seasonal, intrinsic and extrinsic covariates. We present and discuss the following key findings. (1) We found no evidence that regional variation in foraging effort was linked to regional population trajectories in harbour seals. (2) Grey seals demonstrated sex-specific seasonal differences in their activity budgets, independent from those related to reproductive costs. (3) In these sympatric species there was evidence of temporal separation in time hauled out, but not in time foraging. (4) In both species, time spent resting at sea was separated into inshore (associated with tidal haul out availability) and offshore areas. Time spent resting at sea and on land was interchangeable to some extent, suggesting a degree of overlap in their functionality. This may result in a relaxation of the constraints associated with a central place foraging strategy. More generally, we demonstrate how a large dataset, incorporating differing tag parameters, can be analysed to define activity budgets and subsequently address important ecological questions.PostprintPeer reviewe

The CEA/CD3-Bispecific Antibody MEDI-565 (MT111) Binds a Nonlinear Epitope in the Full-Length but Not a Short Splice Variant of CEA

MEDI-565 (also known as MT111) is a bispecific T-cell engager (BiTE®) antibody in development for the treatment of patients with cancers expressing carcinoembryonic antigen (CEA). MEDI-565 binds CEA on cancer cells and CD3 on T cells to induce T-cell mediated killing of cancer cells. To understand the molecular basis of human CEA recognition by MEDI-565 and how polymorphisms and spliced forms of CEA may affect MEDI-565 activity, we mapped the epitope of MEDI-565 on CEA using mutagenesis and homology modeling approaches. We found that MEDI-565 recognized a conformational epitope in the A2 domain comprised of amino acids 326–349 and 388–410, with critical residues F326, T328, N333, V388, G389, P390, E392, I408, and N410. Two non-synonymous single-nucleotide polymorphisms (SNPs) (rs10407503, rs7249230) were identified in the epitope region, but they are found at low homozygosity rates. Searching the National Center for Biotechnology Information GenBank® database, we further identified a single, previously uncharacterized mRNA splice variant of CEA that lacks a portion of the N-terminal domain, the A1 and B1 domains, and a large portion of the A2 domain. Real-time quantitative polymerase chain reaction analysis of multiple cancers showed widespread expression of full-length CEA in these tumors, with less frequent but concordant expression of the CEA splice variant. Because the epitope was largely absent from the CEA splice variant, MEDI-565 did not bind or mediate T-cell killing of cells solely expressing this form of CEA. In addition, the splice variant did not interfere with MEDI-565 binding or activity when co-expressed with full-length CEA. Thus MEDI-565 may broadly target CEA-positive tumors without regard for expression of the short splice variant of CEA. Together our data suggest that MEDI-565 activity will neither be impacted by SNPs nor by a splice variant of CEA

Patterns of space use in sympatric marine colonial predators reveals scales of spatial partitioning

E.L.J. and D.J.F.R. were funded under Scottish Government grant MMSS001/01. D.J.F.R. was funded by the UK Department of Energy and Climate Change (DECC) as part of their Offshore Energy Strategic Environmental Assessment programme. S.S. was part-funded by the EU MYFISH project.Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals Halichoerus grypus and harbour seals Phoca vitulina have overlapping ranges on land and at sea but contrasting population dynamics around Britain: whilst grey seals have generally increased, harbour seals have shown significant regional declines. We analysed two decades of at-sea movement data and terrestrial count data from these species to produce high resolution, broad-scale maps of distribution and associated uncertainty to inform conservation and management. Our results showed that grey seals use offshore areas connected to their haul-out sites by prominent corridors and harbour seals primarily stay within 50km of the coastline. Both species show fine-scale offshore spatial segregation off the east coast of Britain and broad-scale partitioning off western Scotland. These results illustrate that for broad-scale marine spatial planning, the conservation needs of harbour seals (primarily inshore, the exception being selected offshore usage areas) are different from those of grey seals (up to 100km offshore and corridors connecting these areas to haul-out sites). More generally, our results illustrate the importance of detailed knowledge of marine predator distributions to inform marine spatial planning; for instance, spatial prioritisation is not necessarily the most effective spatial planning strategy even when conserving species with similar taxonomy.Peer reviewe

Ocean mass, sterodynamic effects, and vertical land motion largely explain US coast relative sea level rise

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Harvey, T., Hamlington, B. D., Frederikse, T., Nerem, R. S., Piecuch, C. G., Hammond, W. C., Blewitt, G., Thompson, P. R., Bekaert, D. P. S., Landerer, F. W., Reager, J. T., Kopp, R. E., Chandanpurkar, H., Fenty, I., Trossman, D. S., Walker, J. S., & Boening, C. W. Ocean mass, sterodynamic effects, and vertical land motion largely explain US coast relative sea level rise. Communications Earth & Environment, 2(1), (2021): 233, https://doi.org/10.1038/s43247-021-00300-w.Regional sea-level changes are caused by several physical processes that vary both in space and time. As a result of these processes, large regional departures from the long-term rate of global mean sea-level rise can occur. Identifying and understanding these processes at particular locations is the first step toward generating reliable projections and assisting in improved decision making. Here we quantify to what degree contemporary ocean mass change, sterodynamic effects, and vertical land motion influence sea-level rise observed by tide-gauge locations around the contiguous U.S. from 1993 to 2018. We are able to explain tide gauge-observed relative sea-level trends at 47 of 55 sampled locations. Locations where we cannot explain observed trends are potentially indicative of shortcomings in our coastal sea-level observational network or estimates of uncertainty.The research was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. C.G.P. was supported by NASA grant 80NSSC20K1241. B.D.H., T.C.H., and T.F. were supported by NASA JPL Task 105393.281945.02.25.04.59. R.E.K. and J.S.W. were supported by U.S. National Aeronautics and Space Administration (grants 80NSSC17K0698, 80NSSC20K1724 and JPL task 105393.509496.02.08.13.31) and U.S. National Science Foundation (grant ICER-1663807). P.R.T. acknowledges financial support from the NOAA Global Ocean Monitoring and Observing program in support of the University of Hawaii Sea Level Center (NA11NMF4320128). The ECCO project is funded by the NASA Physical Oceanography; Modeling, Analysis, and Prediction; and Cryosphere Programs