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Continuous time movement models resolve many of the problems with scaling, sampling, and interpretation that affect discrete movement models. They can, however, be challenging to estimate, have been presented in inconsistent ways, and are not widely used.
We review the literature on integrated Ornstein-Uhlenbeck velocity models and propose four fundamental correlated velocity movement models (CVM’s): random, advective, rotational, and rotational-advective. The models are defined in terms of biologically meaningful speeds and time scales of autocorrelation. We summarize several approaches to estimating the models, and apply these tools for the higher order task of behavioral partitioning via change point analysis.
An array of simulation illustrate the precision and accuracy of the estimation tools. An analysis of a swimming track of a bowhead whale (Balaena mysticetus) illustrates their robustness to irregular and sparse sampling and identifies switches between slower and faster, and directed vs. random movements. An analysis of a short flight of a lesser kestrel (Falco naumanni) identifies exact moments when switches occur between loopy, thermal soaring and directed flapping or gliding flights.
We provide tools to estimate parameters and perform change point analyses in continuous time movement models as an R package (smoove). These resources, together with the synthesis, should facilitate the wider application and development of correlated velocity models among movement ecologists.
Electronic supplementary material
The online version of this article (doi:10.1186/s40462-017-0103-3) contains supplementary material, which is available to authorized users.
Correlated velocity movement, Velocity autocovariance function, Correlated random walk, Integrated Ornstein-Uhlenbeck process, Balaena mysticetus, Thermal soaring, Falco naumanni
Correlated velocity models as a fundamental unit of animal movement: synthesis and applications
Eliezer Gurarie,corresponding author1 Christen H. Fleming,1,2 William F. Fagan,1 Kristin L. Laidre,3 Jesús Hernandez-Pliego,4 and Otso Ovaskainen5,6
A fragmented habitat becomes increasingly fragmented for species at higher trophic levels, such as parasitoids. To persist, these species are expected to possess life-history traits, such as high dispersal, that facilitate their ability to use resources that become scarce in fragmented landscapes. If a specialized parasitoid disperses widely to take advantage of a sparse host, then the parasitoid population should have lower genetic structure than the host. We investigated the temporal and spatial genetic structure of a hyperparasitoid (fourth trophic level) in a fragmented landscape over 50 × 70 km, using microsatellite markers, and compared it with the known structures of its host parasitoid, and the butterfly host which lives as a classic metapopulation. We found that population genetic structure decreases with increasing trophic level. The hyperparasitoid has fewer genetic clusters (K = 4), than its host parasitoid (K = 15), which in turn is less structured than the host butterfly (K = 27). The genetic structure of the hyperparasitoid also shows temporal variation, with genetic differentiation increasing due to reduction of the population size, which reduces the effective population size. Overall, our study confirms the idea that specialized species must be dispersive to use a fragmented host resource, but that this adaptation has limits.
dispersal, host-parasitoid system, hyperparasitoid, Hyposoter horticola, Melitaea cinxia, oviposition behaviour
Spatial and temporal genetic structure at the fourth trophic level in a fragmented landscape
Abhilash Nair,1 Toby Fountain,1 Suvi Ikonen,1 Sami P. Ojanen,1 and Saskya van Nouhuys1,2
2016 May 25
Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified J9 and J8, two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies showed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against DENV with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested that J9 and J8 followed divergent somatic hypermutation pathways, and that a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a new epitope that can be exploited for vaccine design.
Research organism: Human, Virus
Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics
Natasha D Durham,#1,†‡ Aditi Agrawal,#1,† Eric Waltari,1 Derek Croote,2 Fabio Zanini,2§ Mallorie Fouch,3 Edgar Davidson,3 Olivia Smith,1 Esteban Carabajal,1 John E Pak,1 Benjamin J Doranz,3 Makeda Robinson,4,5 Ana M Sanz,6 Ludwig L Albornoz,7 Fernando Rosso,6,8 Shirit Einav,4,5 Stephen R Quake,1,2 Krista M McCutcheon,1 and Leslie Goo1,9 Sara L Sawyer, Reviewing Editor and Satyajit Rath, Senior Editor Sara L Sawyer, University of Colorado Boulder, United States; Contributor Information.