phyloregion, computational infrastructure for biogeographic regionalization and macroecology in the R computing environment
Establishing geographical comparisons based on shared biota is crucial to the study of biogeography and for managing biological diversity in the face of rapid warming of the Earth’s climate. However, the computational tools to analyze and manipulate the massive-scale species biogeography data have not been fully developed. The R software package phyloregion – designed for biogeographic regionalization and macroecology – can overcome these computational challenges. It contains tools for biogeographical regionalization, macroecology, conservation, and visualization, with potential applications in various disciplines including evolution, microbial diversity, systematics, ecology, phylogenetics, and many others.
Figure 1. Workflow to identify biogeographic regions using a Grade of Membership model. (A) Community matrix (optionally paired with phylogeny or functional traits) is (B) analyzed using a Grade of Membership Model, which allows the units of analysis (i.e., species or regions) to have partial membership in multiple clusters. (C) This generates values of omega (cluster contribution per grid cell) and theta (species’ contribution per cluster) as outputs. (D) Biogeographic regions are visualized using pie charts that represent the proportional contribution of species to grid cells.
The project will accomplish the following:
Develop and implement new tools in phyloregion for biome evolution and biogeographical investigations;
Develop new tools in phyloregion to visualize patterns of biogeography, macroecology, and evolution; and
Develop new tools in phyloregion for conservation that reflect the key dimensions of phylogenetic diversity including richness, divergence, and regularity.
We welcome enthusiastic individuals, researchers, and organizations to contribute to the "phyloregion" project. Your participation can help enhance the tools and applications of biogeographic regionalization and macroecology, contributing to a better understanding and conservation of biodiversity in the face of climate change.
Provide Feedback and Suggestions: If you have experience using phyloregion or ideas for improvements, share your feedback with us. Your insights can help refine and optimize the tools for the research community.
Collaborate on Development: If you're proficient in R or have expertise in biogeography and macroecology, consider contributing to the development of phyloregion via Github.
Share Use Cases and Success Stories: Share your experiences using phyloregion in your research or projects. Your success stories can inspire others to use the tools and foster a collaborative learning environment.
Propose New Applications: Share your innovative ideas for new applications of phyloregion in different fields of study. Whether it's related to evolutionary biology, conservation, or ecological modeling, we value your input.
Engage in the Community Forum: Join our community forum to engage in discussions, ask questions, and connect with other researchers and users of phyloregion. The forum provides a platform for exchanging ideas and seeking assistance.
Contribute Educational Resources: If you're passionate about science communication and education, contribute educational resources like tutorials and guides to help users better understand phyloregion and its applications.
Sponsorship and Support: If you represent an organization sharing our vision for advancing biogeography and macroecology, consider sponsoring the phyloregion project. Your support can help maintain and expand the platform.
Spread the Word: Help increase the visibility of "phyloregion" by sharing our website (https://phyloregion.com/) and social media channels with your friends.
Your contributions, no matter how big or small, are essential to the success of the phyloregion project. Together, we can advance biogeographic regionalization and macroecology, positively impacting biodiversity conservation.
Join us on this exciting journey, and let's create a sustainable future for our planet's ecological diversity!
