Motion analysis of non-model organisms using a hierarchical model: Influence of setup enclosure dimensions on gait parameters of Swinhoe’s striped squirrels as a test case

Abstract

In in-vivo motion analyses, data from a limited number of subjects and trials is used as proxy for locomotion properties of entire populations, yet the inherent hierarchy of the individual and population level is usually not accounted for. Despite the increasing availability of hierarchical model frameworks for statistical analyses, they have not been applied extensively to comparative motion analysis. As a case study for the use of hierarchical models, we analyzed locomotor parameters of four Swinhoe's striped squirrels. The small-bodied arboreal mammals exhibit brief bouts of rapid asymmetric gaits. Spatio-temporal parameters on runways with experimentally varied dimensions of the setup enclosure were compared to test for their potentially confounding effects. We applied principal component analysis to evaluate changes to the overall locomotor pattern. A common, non-hierarchical, pooled statistical analysis of the data revealed significant differences in some of the parameters depending on enclosure dimensions. In contrast, we used a hierarchical Bayesian generalized linear model (GLM) that considers subject specific differences and population effects to compare the effect of enclosure dimensions on the measured parameters and the principal components. None of the population effects were confirmed by the hierarchical GLM. The confounding effect of a single subject that deviates in its locomotor behavior is potentially bigger than the influence of the experimental variation in enclosure dimensions. Our findings justify the common practice of researchers to intuitively select an enclosure with dimensions assumed as "non-constraining". Hierarchical models can easily be designed to cope with limited sample size and bias introduced by deviating behavior of individuals. When limited data is available-a typical restriction of in-vivo motion analyses of non-model organisms-density distributions of the Bayesian GLM used here remain reliable and the hierarchical structure of the model optimally exploits all available information. We provide code to be adjusted to other research questions.

A Workflow for High Through-Put, High Precision Livestock Diagnostic Screening of Locomotor Kinematics

“…At variable time points afterwards (ages 1 – 10 hours), piglets were briefly taken from their pen and brought to a separate room for video recording (see below). Animals were recorded in pairs (as in Mielke et al, 2018), which drastically reduced anxiety and increased their motivation to cooperate. A few animals were recorded repeatedly, usually with a changing partner.…”

“…The main reason for this is that probabilistic models work on data distributions, and their outcome are distributions and "effect likelihoods", rather than point estimates. This can be informative on an intrinsically varying process such as locomotion (Mielke et al, 2018). Machine Learning methods for video digitization are validly advancing to be the standard in kinematic analysis, whereas probabilistic models still lack recognition in the field, despite their potential.…”

Mechanics of Arboreal Locomotion in Swinhoe’s Striped Squirrels: A Potential Model for Early Euarchontoglires

“…The central part of this pole with a length of 14.6 cm was mounted separately on the force plate underneath leaving a small gap to the adjoining dowels, thus also minimizing the transfer of oscillations. The trackway was covered by an acrylic glass enclosure high enough to not restrain the maximum jumping height of the animals [we previously studied the influence of the enclosure size on locomotor parameters (Mielke et al, 2018)]. Both supports were then either fixed on a table or inclined to form a slope of 45 • .…”

“…We aimed at only including trials approximating a steady running speed. Swinhoe's striped squirrels are non-cursorial animals characterized by fast acceleration and deceleration within a few stride cycles (Mielke et al, 2018). We only analyzed the two cycles ending and beginning with contacting the force plate, respectively.…”

“…100 g. T. swinhoei also has claws on all digits. Moreover, striped squirrels almost entirely employ asymmetrical gaits, i.e., the species relies on full bounds, half-bounds, and gallops (Mielke et al, 2018). Chadwell and Young (2015) proposed the existence of an evolutionary trade-off between the benefits and drawbacks of asymmetrical gaits which is related to body mass and support diameter.…”