Spatial phylogenetics

Abstract

The metric called phylogenetic diversity (PD) has been employed over the last 30 years to add an evolutionary dimension to the exploration of biodiversity. However, the application of PD was until recently limited by both technology and methodology. Newly available distributional data from global museum databasing efforts, rapidly increasing coverage of DNA sequence data and improvements to computer hardware and software have enabled a new ‘big data’ approach to the application of PD‐based metrics and randomization‐based hypothesis tests called ‘spatial phylogenetics’. It can be defined most simply as turning a phylogeny into a GIS layer, which can then be used with other GIS layers to understand drivers of phylodiversity patterns and for conservation prioritization. Alpha and beta phylodiversity can be measured using different ways of representing branch lengths on a given topology (called ‘facets’), each yielding a different, interesting perspective that are best viewed in combination. Challenges posed by available data need to be addressed through careful cleaning and gathering further data in a targeted manner. Spatial phylogenetics is only in its infancy, showing much promise but with many elements awaiting expansion to address further questions.

How to cross the desert if you are small and need mountains? Out‐of‐Ethiopia dispersal in Afromontane shrews

“…In traditional assessments of biodiversity patterns, the focus has been on 'species', a challenging task for taxonomy. However, to fully comprehend the evolution of biodiversity, it is essential to also consider the number of distinct evolutionary lineages as an additional dimension (Mishler, 2023). Our study highlights the high evolutionary diversity of shrews inhabiting the Ethiopian highlands, compared to other regions of the EABH, despite a lower number of formally described species (8 in Ethiopia vs. 12 outside Ethiopia) (Figure 2).…”

Reshaping biogeography: Perspectives on the past, present and future

“…We encouraged multidisciplinary research teams and new ideas or approaches as well as individualistic papers that may challenge existing norms. Here, we launch the special section Reshaping Biogeography—Perspectives on the Past, Present and Future with the first four contributions: two research articles (Farquhar et al, 2022; Olivos et al, 2023) and two perspectives (Heads, 2023; Mishler, 2023). We briefly consider how they impinge on debates in biogeography, and look forward to a suite of additional papers in the coming months.…”

“…Mishler (2023) approaches the problem of understanding distributions from another novel angle. As Mishler notes, the overwhelming majority of biogeography is species‐centric.…”

“…This last property is particularly intriguing as it steps us ever closer to cross‐scale analyses that encapsulate the true dynamism of the biogeographical processes that shape life on Earth. Spatial phylogenetics, then, is an exciting, modern, synthetic ‘big data’ approach to biogeography, benefitting from the rapid accumulation of genetic and geographical data in multiple databases over the past 1–2 decades (Mishler, 2023).…”

“…That brings us back to the problem identified by Farquhar et al (2022)—that a persistent challenge in biogeography has been obtaining sufficient data to study patterns in detail—but with a twist: while biogeographical data are now rapidly increasing in availability, sources, and types and facilitating new perspectives (e.g., Han et al, 2023), with big data come potentially big problems such as systematic biases in missing data or data types, data quality, and inference (Mishler, 2023). These are problems that will require analytical and philosophical discussions, about new concepts, methodologies and tools that allow us to see the world in different ways (e.g.…”