Patterns of Learning in the Navigation of Selectively Foraging Mammals

Memory and learning distinguish the movement of animals from other things, resulting in trajectories that change over time, but still repeatedly return to specific locations. The frequency and predictability with which animals return to favored locations, and the patterns of change in the paths they use to get there, offer insights into the cognitive systems of learning and memory that guide them. For animals that rely on resources that are concentrated in sparsely distributed, high value patches, these systems are particularly important for avoiding the costs of inefficient random-search foraging. In this thesis, I analyze the trajectories of such animals across multiple contexts and spatial scales, particularly the trajectories of primates and kinkajous (animals that look and behaves much like a primate, but are in fact *Carnivoran*). I find that most of these animals are quick to learn efficient paths between foraging locations, and some are able to generalize strategies for efficient navigation to novel contexts. There is some evidence that more selective foragers rely more on routine 'traplines' between multiple known locations, but are faster to deploy strategies that exploit changing resource distributions. Taken together, results of these studies suggest that diverse animal species integrate episodic-like memories into a cognitive map that helps them plan movements over large distances. Evidence that kinkajous flexibly use knowledge of detailed route-networks through complex canopy substrate to quickly find and exploit new resources, is particularly important because it highlights that the advanced development of these cognitive systems is not unique to primates and their socially complex groups, but may evolve readily in response to particular resource distributions and environmental properties

Enriched sleep environments lengthen lemur sleep duration

Characteristics of the sleep-site are thought to influence the quality and duration of primate sleep, yet only a handful of studies have investigated these links experimentally. Using actigraphy and infrared videography, we quantified sleep in four lemur species (Eulemur coronatus, Lemur catta, Propithecus coquereli, and Varecia rubra) under two different experimental conditions at the Duke Lemur Center (DLC) in Durham, NC, USA. Individuals from each species underwent three weeks of simultaneous testing to investigate the hypothesis that comfort level of the sleep-site influences sleep. We obtained baseline data on normal sleep, and then, in a pair-wise study design, we compared the daily sleep times, inter-daily activity stability, and intra-daily activity variability of individuals in simultaneous experiments of sleep-site enrichment and sleep-site impoverishment. Over 164 24-hour periods from 8 individuals (2 of each species), we found evidence that enriched sleep-sites increased daily sleep times of lemurs, with an average increase of thirty-two minutes. The effect of sleep-site impoverishment was small and not statistically significant. Though our experimental manipulations altered inter-daily stability and intra-daily variability in activity patterns relative to baseline, the changes did not differ significantly between enriched and impoverished conditions. We conclude that properties of a sleep-site enhancing softness or insulation, more than the factors of surface area or stability, influence lemur sleep, with implications regarding the importance of nest building in primate evolution and the welfare and management of captive lemurs.publishe

Inference by Exclusion in Lion-Tailed Macaques (Macaca silenus), a Hamadryas Baboon (Papio hamadryas), Capuchins (Sapajus apella), and Squirrel Monkeys (Saimiri sciureus)

Previous research has suggested that several primate species may be capable of reasoning by exclusion based on the finding that they can locate a hidden object when given information about where the object is not. The present research replicated and extended the literature by testing 2 Old World monkey species, lion-tailed macaques (Macaca silenus) and a hamadryas baboon (Papio hamadryas), and 2 New World species, capuchin monkeys (Sapajus apella) and squirrel monkeys (Saimiri sciureus). The New World monkeys were tested on the traditional 2-way object choice task, and all 4 species were also tested on a more complex 3-way object choice task. In addition, the squirrel monkeys were tested on a 2-way object choice task with auditory information. The results showed that, whereas the Old World species were able to infer by exclusion on the 3-object task, some of the capuchin monkeys had difficulty on each of the 2- and 3-cup tasks. All but 1 of the squirrel monkeys failed to infer successfully, and their strategies appeared to differ between the visual and auditory versions of the task. Taken together, this research suggests that the ability to succeed on this inference task may be present throughout Old World monkey species, but is fragile in the New World species tested thus far

A Quantitative Framework for Identifying Patterns of Route-Use in Animal Movement Data

Animal movement along repeatedly used, “habitual” routes could emerge from a variety of cognitive mechanisms, as well as in response to a diverse set of environmental features. Because of the high conservation value of identifying wildlife movement corridors, there has been extensive work focusing on environmental factors that contribute to the emergence of habitual routes between protected habitats. In parallel, significant work has focused on disentangling the cognitive mechanisms underlying animal route use, as such movement patterns are of fundamental interest to the study of decision making and navigation. We reviewed the types of processes that can generate routine patterns of animal movement, suggested a new methodological workflow for classifying one of these patterns—high fidelity path reuse—in animal tracking data, and compared the prevalence of this pattern across four sympatric species of frugivorous mammals in Panama. We found the highest prevalence of route-use in kinkajous, the only nocturnal species in our study, and propose that further development of this method could help to distinguish the processes underlying the presence of specific routes in animal movement data.publishe

Supplemental Materials for “Mapping vocal interactions in space and time differentiates signal broadcast vs signal exchange in meerkat groups”

Supplemental methods and result

Introducing molaR: a New R Package for Quantitative Topographic Analysis of Teeth (and Other Topographic Surfaces)

© 2016, Springer Science+Business Media New York.Researchers studying mammalian dentitions from functional and adaptive perspectives increasingly have moved towards using dental topography measures that can be estimated from 3D surface scans, which do not require identification of specific homologous landmarks. Here we present molaR, a new R package designed to assist researchers in calculating four commonly used topographic measures: Dirichlet Normal Energy (DNE), Relief Index (RFI), Orientation Patch Count (OPC), and Orientation Patch Count Rotated (OPCR) from surface scans of teeth, enabling a unified application of these informative new metrics. In addition to providing topographic measuring tools, molaR has complimentary plotting functions enabling highly customizable visualization of results. This article gives a detailed description of the DNE measure, walks researchers through installing, operating, and troubleshooting molaR and its functions, and gives an example of a simple comparison that measured teeth of the primates Alouatta and Pithecia in molaR and other available software packages. molaR is a free and open source software extension, which can be found at the doi:10.13140/RG.2.1.3563.4961 (molaR v. 2.0) as well as on the Internet repository CRAN, which stores R packages

Analysis of shared common genetic risk between amyotrophic lateral sclerosis and epilepsy

Because hyper-excitability has been shown to be a shared pathophysiological mechanism, we used the latest and largest genome-wide studies in amyotrophic lateral sclerosis (n = 36,052) and epilepsy (n = 38,349) to determine genetic overlap between these conditions. First, we showed no significant genetic correlation, also when binned on minor allele frequency. Second, we confirmed the absence of polygenic overlap using genomic risk score analysis. Finally, we did not identify pleiotropic variants in meta-analyses of the 2 diseases. Our findings indicate that amyotrophic lateral sclerosis and epilepsy do not share common genetic risk, showing that hyper-excitability in both disorders has distinct origins

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

Additional file 1: Supplementary Note S1.Additional file 2: Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S6, Figure S7, Figure S8, Figure S9, Figure S10, Figure S11, Figure S12, Figure S13, Figure S14, Figure S15, Figure S16.Additional file 3: Table S1, Table S2, Table S3, Table S4, Table S5, Table S6, Table S7.Additional file 4: Genomic locations and fragment coverage of significant H3K4me3 peaks.Additional file 5: Genomic locations of annotated genes overlapping with significant H3K4me3 peaks.Additional file 6: Genomic locations of low-confidence gene models overlapping with significant H3K4me3 peaks.BACKGROUND : Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. RESULTS : Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. CONCLUSIONS : In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.SH, EM and AM acknowledge funding from the Department of Science and Technology (DST), South Africa, the National Research Foundation of South Africa (NRF) Incentive Funding for Rated Researchers Grant (UID 81111) and NRF Bioinformatics and Functional Genomics Program (UID 71255, UID 86936), Sappi and Mondi through the Forest Molecular Genetics (FMG) Program at the University of Pretoria (UP), and the Technology and Human Resources for Industry Program (THRIP) (UID 80118). AG acknowledges funding from USDA National Institute of Food and Agriculture and the Office of Science (BER), US Department of Energy.http://www.biomedcentral.com/bmcplantbiolam201