Arbor: Comparative Analysis Workflows for the Tree of Life

Abstract

We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive visual interface. Arbor’s user-defined workflows will be exported and shared so that entire analyses can be quickly replicated with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to illustrate the software’s key functionality.

Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences

“…Chelsea Specht (University of California, Berkeley, CA, USA) highlighted results from an ongoing study using targeted exon capture that successfully resolved relationships in Zingiberales, when whole plastid genomes turned out to be insufficient. She also presented ARBOR, a new platform to facilitate diverse comparative analyses based on the idea of customized and publishable workflows, including innovative data visualization tools currently under development (Harmon et al, 2013). Another example of a new tool was provided by Rutger Vos (Naturalis Biodiversity Center), who described SUPERSMART (Self‐Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), a new pipeline for building and dating phylogenetic trees using GenBank data for any given clade or set of species (Antonelli et al, 2016).…”

Indices of Biodiversity Pattern Based on Presence-Absence Matrices: A GIS Implementation

“…However, as long as the different perspectives (phylogenetic, ecologic, morphologic, functional and others, see MacLaurin & Sterelny (2008)) remain unlinked, the analyses are mostly disconnected from one another. In fact, it is possible to say that the fundamental task of biodiversity informatics should be to enable "integration" of different perspectives of biodiversity (Harmon et al 2013;Miller and Jolley-Rogers 2014;Peterson et al 2010). Integration is not a well-defined term, but one possible meaning may be the capacity to display simultaneously different perspectives of the data (Laffan et al 2010), preferably in a linked way.…”

“…The next step in developing the tool is to allow for linking other perspectives of biodiversity as high-end Web Services, a task already under way (Harmon et al 2013). Nevertheless, the future development of "integrating" views of biodiversity goes well beyond linking displays.…”

TraitBank: Practical semantics for organism attribute data

“…This means that the information in many data sets is not easily discovered, integrated or repurposed. This lack of data standards impedes progress in the ecological, conservation, and phylogenetic research communities, who need effective ways to quickly discover and consume data in the coming era of dataintensive science [e.g., [17]- [19]]. For example, marine environmental modelers need high-quality inputs about large numbers of species in order to understand current and historical distributions of species; how these distributions are impacted by environmental changes such as climate change, overharvesting, or invasive species; how biological communities function to provide ecosystem services; and what could happen to these services under future scenarios that change the composition of these communities.…”