Extending the Latent Multinomial Model with Complex Error Processes and Dynamic Markov Bases

The latent multinomial model (LMM) model of Link et al. (2010) provided a general framework for modelling mark-recapture data with potential errors in identification. Key to this approach was a Markov chain Monte Carlo (MCMC) scheme for sampling possible configurations of the counts true capture histories that could have generated the observed data. This MCMC algorithm used vectors from a basis for the kernel of the linear map between the true and observed counts to move between the possible configurations of the true data. Schofield and Bonner (2015) showed that a strict basis was sufficient for some models of the errors, including the model presented by Link et al. (2010), but a larger set called a Markov basis may be required for more complex models. We address two further challenges with this approach: 1) that models with more complex error mechanisms do not fit easily within the LMM and 2) that the Markov basis can be difficult or impossible to compute for even moderate sized studies. We address these issues by extending the LMM to separately model the capture/demographic process and the error process and by developing a new MCMC sampling scheme using dynamic Markov bases. Our work is motivated by a study of Queen snakes (Regina septemvittata) in Kentucky, USA, and we use simulation to compare the use of PIT tags, with perfect identification, and brands, which are prone to error, when estimating survival rates

Anthropogenic Threats to Wild Cetacean Welfare and a Tool to Inform Policy in This Area

Human activities and anthropogenic environmental changes are having a profound effect on biodiversity and the sustainability and health of many populations and species of wild mammals. There has been less attention devoted to the impact of human activities on the welfare of individual wild mammals, although ethical reasoning suggests that the welfare of an individual is important regardless of species abundance or population health. There is growing interest in developing methodologies and frameworks that could be used to obtain an overview of anthropogenic threats to animal welfare. This paper shows the steps taken to develop a functional welfare assessment tool for wild cetaceans (WATWC) via an iterative process involving input from a wide range of experts and stakeholders. Animal welfare is a multidimensional concept, and the WATWC presented made use of the Five Domains model of animal welfare to ensure that all areas of potential welfare impact were considered. A pilot version of the tool was tested and then refined to improve functionality. We demonstrated that the refined version of the WATWC was useful to assess real-world impacts of human activity on Southern Resident killer whales. There was close within-scenario agreement between assessors as well as between-scenario differentiation of overall welfare impact. The current article discusses the challenges raised by assessing welfare in scenarios where objective data on cetacean behavioral and physiological responses are sparse and proposes that the WATWC approach has value in identifying important information gaps and in contributing to policy decisions relating to human impacts on whales, dolphins, and porpoises

A 6,000-year record of environmental change from the eastern Pacific margin of central Mexico

The transition from the mid- to late-Holocene in MesoAmerica saw increasing complexity in spatial patterns of change. Records from the western part of the region are sparse, with lacustrine sequences affected by long term anthropogenic disturbance or lacking chronological resolution. Here, we present a continuous palaeoecological and geochemical record from Laguna de Juanacatlán, a remote lake in the mountains of the western TMVB. Diatom assemblages, XRF scanning data and bulk organic geochemistry from a well-dated, 7.25-m laminated sequence were combined with summary pollen data from a 9-m partially laminated core to provide a continuous record of catchment and lake ecosystem changes over the last c. 6,000 years. Relatively humid conditions prevailed prior to c. 5.1 cal ka, which supported dense oak-pine forest cover around a deep, stratified lake. A trend towards drier conditions began c. 5.1 cal ka, intensifying after 4.0 cal ka, consistent with weakening of the North American Monsoon. Between 3.0 and 1.2 cal ka, lower lake levels and variable catchment run-off are consistent with increasing ENSO influence observed in the Late Holocene in the neotropics. From 1.2 to 0.9 cal ka, a marked change to catchment stability and more intense stratification reflected drier conditions and / or reduced rainfall variability and possibly warmer temperatures. After 0.9 cal ka, conditions were wetter, with an increase in catchment disturbance associated with the combined effects of climate and human activity. In recent decades, the lake ecosystem has changed markedly, possibly in response to recent climate change as well as local catchment dynamics

Intracellular connections between basal bodies promote the coordinated behavior of motile cilia

Hydrodynamic flow produced by multiciliated cells is critical for fluid circulation and cell motility. Hundreds of cilia beat with metachronal synchrony for fluid flow. Cilia-driven fluid flow produces extracellular hydrodynamic forces that cause neighboring cilia to beat in a synchronized manner. However, hydrodynamic coupling between neighboring cilia is not the sole mechanism that drives cilia synchrony. Cilia are nucleated by basal bodies (BBs) that link to each other and to the cell\u27s cortex via BB-associated appendages. The intracellular BB and cortical network is hypothesized to synchronize ciliary beating by transmitting cilia coordination cues. The extent of intracellular ciliary connections and the nature of these stimuli remain unclear. Moreover, how BB connections influence the dynamics of individual cilia has not been established. We show by focused ion beam scanning electron microscopy imaging that cilia are coupled both longitudinally and laterally in the ciliat

Meta-analyses of whale-watching impact studies : Comparisons of cetacean responses to disturbance

Acknowledgements. The International Whaling Commission funded this study through a grant assigned to D.L. D.L. was also funded by the Scottish Funding Council for funding through grant HR09011 to the Marine Alliance for Science and Technology for Scotland. While writing the manuscript, V.S. was sponsored by a Fulbright scholarship. We thank the many people that replied to the 2 MAR - MAM calls and Dr. Stankowich for his previous comments on the manuscript.Peer reviewedPublisher PD

Key questions in marine mammal bioenergetics

Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as ‘key’ questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations

Exercise at Depth Alters Bradycardia and Incidence of Cardiac Anomalies in Deep-Diving Marine Mammals

Unlike their terrestrial ancestors, marine mammals routinely confront extreme physiological and physical challenges while breath-holding and pursuing prey at depth. To determine how cetaceans and pinnipeds accomplish deep-sea chases, we deployed animal-borne instruments that recorded high-resolution electrocardiograms, behaviour and flipper accelerations of bottlenose dolphins (Tursiops truncatus) and Weddell seals (Leptonychotes weddellii) diving from the surface to 4200 m. Here we report that both exercise and depth alter the bradycardia associated with the dive response, with the greatest impacts at depths inducing lung collapse. Unexpectedly, cardiac arrhythmias occurred in 473% of deep, aerobic dives, which we attribute to the interplay between sympathetic and parasympathetic drivers for exercise and diving, respectively. Such marked cardiac variability alters the common view of a stereotypic ‘dive reflex’ in diving mammals. It also suggests the persistence of ancestral terrestrial traits in cardiac function that may help explain the unique sensitivity of some deep-diving marine mammals to anthropogenic disturbances

Evaluation of Phage Display Discovered Peptides as Ligands for Prostate-Specific Membrane Antigen (PSMA)

The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage display random peptide library. After one round of prescreening and two rounds of screening, high-stringency screening at the third round of panning was performed to identify the highest affinity binders. Phages which had a specific binding activity to PSMA in human prostate cancer cells were isolated and the DNA corresponding to the 15-mers were sequenced to provide three consensus sequences: GDHSPFT, SHFSVGS and EVPRLSLLAVFL as well as other sequences that did not display consensus. Two of the peptide sequences deduced from DNA sequencing of binding phages, SHSFSVGSGDHSPFT and GRFLTGGTGRLLRIS were labeled with 5-carboxyfluorescein and shown to bind and co-internalize with PSMA on human prostate cancer cells by fluorescence microscopy. The high stringency requirements yielded peptides with affinities KD∼1 μM or greater which are suitable starting points for affinity maturation. While these values were less than anticipated, the high stringency did yield peptide sequences that apparently bound to different surfaces on PSMA. These peptide sequences could be the basis for further development of peptides for prostate cancer tumor imaging and therapy. © 2013 Shen et al