Markham, A. | bioRxiv Science

bioRxiv2024

WildPose: A Long-Range 3D wildlife motion capture system

Understanding and monitoring wildlife behavior is crucial in ecology and biomechanics, yet challenging due to the limitations of current methods. To address this issue, we introduce WildPose, a novel long-range motion capture system specifically tailored for free-ranging wildlife observation. This system combines an electronically controllable zoom-lens camera with a LiDAR to capture both 2D videos and 3D point cloud data, thereby allowing researchers to observe high-fidelity animal morphometrics, behavior and interactions in a completely remote manner. Field trials conducted in Kgalagadi Transfrontier Park have successfully demonstrated WildPoses ability to quantify morphological features of different species, accurately track the 3D movements of a springbok herd over time, and observe the respiratory patterns of a distant lion. By facilitating non-intrusive, long-range 3D data collection, WildPose marks a significant complementary technique in ecological and biomechanical studies, offering new possibilities for conservation efforts and animal welfare, and enriching the prospects for interdisciplinary research.

animal behavior and cognition↗

bioRxiv2022

Genome-wide analysis of Structural Variants in Parkinson's Disease using Short-Read Sequencing data

Parkinsons disease is a complex neurodegenerative disorder, affecting approximately one million individuals in the USA alone. A significant proportion of risk for Parkinsons disease is driven by genetics. Despite this, the majority of the common genetic variation that contributes to disease risk is unknown, in-part because previous genetic studies have focussed solely on the contribution of single nucleotide variants. Structural variants represent a significant source of genetic variation in the human genome. However, because assay of this variability is challenging, structural variants have not been cataloged on a genome-wide scale, and their contribution to the risk of Parkinsons disease remains unknown. In this study, we 1) leveraged the GATK-SV pipeline to detect and genotype structural variants in 7,772 short-read sequencing data and 2) generated a subset of matched whole-genome Oxford Nanopore Technologies long-read sequencing data from the PPMI cohort to allow for comprehensive structural variant confirmation. We detected, genotyped, and tested 3,154 "high-confidence" common structural variant loci, representing over 412 million nucleotides of non-reference genetic variation. Using the long-read sequencing data, we validated three structural variants that may drive the association signals at known Parkinsons disease risk loci, including a 2kb intronic deletion within the gene LRRN4. Further, we confirm that the majority of structural variants in the human genome cannot be detected using short-read sequencing alone, encompassing on average around 4 million nucleotides of inaccessible sequence per genome. Therefore, although these data provide the most comprehensive survey of the contribution of structural variants to the genetic risk of Parkinsons disease to date, this study highlights the need for large-scale long-read datasets to fully elucidate the role of structural variants in Parkinsons disease.

genetics↗