Research overview

My research group embraces the urgent need for mammal phylogenetic ecology, which we frame as the application of phylogeny-informed taxonomic knowledge to the study of species ecological interactions. More colloquially: Know your species and their history to ask how and why organisms interact.

Our integrative specimen-based research unites organismal, genomic, computational, and synthetic approaches to study eco-evolutionary processes. Why specimens? Well, preserved natural history specimens (including frozen tissues, skins, skeletons, endo-/ecto-parasites, blood, feces, and fluid-preserved whole organisms) are nothing less than the physical basis for our collective knowledge of Earth's biodiversity. Every data point in public databases like GBIF or GenBank comes from some organism however, only the fraction of observations that are preserved as specimens are available for future workers to gather now-unimagined data. Our lab contributes to growing this 300-year record of the natural world while using it to query the processes under which biodiversity was generated.

Types of questions we ask

1. What are the species in a clade / region / community? (taxonomy and phylogenetics)

Species are at the core of all biodiversity science circumscribing which species are present is the baseline for studying patterns of ancestor-to-descendent relationship among those species, and, in turn, the historical processes that produced those divergences. Species names are just the beginning: the meaning of names varies widely depending on which data are considered by which authors, so careful data synthesis is often needed. In our lab, we do both species delimitation at a local-to-regional level (e.g., analyses of gene flow, phylogeography) and species synthesis globally (e.g., curating data on genetic relationships, geographic ranges, ecological traits, and their taxonomic history).

PROJECTS

[UNDER CONSTRUCTION BELOW, sorry]

2. How fast are lineages evolving? (phylogenetic rates)

3. By what ecological processes? (comparative methods)

The group is currently focusing on 3 main areas of research:

1. Taxonomic and phylogenetic stewardship of global mammals. This work includes leadership of the Mammal Diversity Database in alliance with the American Society of Mammalogists for keeping track of species- and higher-level taxonomic changes for ~6,500 currently recognized species. It also includes improving upon the mammal tree of life, including the development of more sophisticated tools for updating the species name labels for the millions of primary-source observations in global databases (e.g., GBIF, GenBank).

Taxonomy is generally viewed as external to ecology, a fixed framework that is known without error rather than a variable—the taxonomic variable—that needs tuning to understand its impact on inferences. Since taxonomy is a human-imposed framework rather than someting innate, we need to quantify its impact on our knowledge. When the stakes are high–e.g., modeling risks of extinction or viral spillover–we need to leverage


2. Digitally connecting ecological data from disparate publications, toward building a comprehensive knowledge graph for mammal host-pathogen interactions. This work aims to connect the underlying evidence in support of given ecological interactions with the interaction data itself. This evidence extends from the taxonomic (e.g., voucher specimens of the species in question) to the methodological (e.g., antibodies, gene fragments, or live pathogen recovered in the host animal), with large impact on the resulting confidence of modeling efforts using those data. We have published an initial perspective (The Lancet Planetary Health 2021) and have an NIH-funded R21 to develop this work further.


3. Querying how species traits influence both gene flow and pathogen sharing, focusing on clades of Nearctic and Neotropical rodents. Using data collected in the field (deserts of the US Southwest and Argentina), in museum collections (modern and fossil specimens), and in the lab (population genomics), this work seeks to understand the impact species dispersal ability (=vagility) on ecological interactions. We are studying the trait correlates of vagility (e.g., limb morphology, physiology, and home range allometry) to investigate their dual influences upon historical patterns of gene flow and modern networks of pathogen sharing. This work was inspired by initial tests on the mammal tree (bioRxiv 2020) and prior work studying the largest genome of any mammal, the Tympanoctomys vizcacha rats of Argentina (Genome Biology and Evolution 2017).