Research
Spatial population dynamics of a grassland bird as revealed by the North American Breeding Bird Survey. Code available here.
I’m an ecologist who enjoys making sense of complex systems to advance environmental conservation. My work blends old-fashioned fieldwork with new molecular tools and data science. On the data side, I’m fond of causal modeling, Bayesian inference, bioinformatics, machine learning / AI, and open, reproducible research practices. On the molecular side, I’m most interested in advancing our ability to monitor biodiversity using novel tools based on the DNA organisms leave behind in the environment (eDNA). More info on active research topics below…
Biodiversity Monitoring & Rare Species Detection
improving sampling schemes for rare and hard-to-sample wildlife is vital to effective conservation
I am interested in the special monitoring challenges posed hard-to-sample communities and rare and elusive species. Related to this, I am working on:
Mammals vary greatly in size and behavior, requiring varied survey techniques. We found that combining simple surface eDNA tools like paint rollers with sophisticated eDNA metabarcoding successfully characterized arboreal mammal communities in New Jersey woodlands (Allen et al., Scientific Reports 2023). My colleagues and I then took these and other innovative methods to the XPRIZE Rainforest competion in Brazil in 2024. We joined Yale’s Map of Life’s XPRIZE finalist team, extended the approach to include all vertebrates, and together took second place in the competition!
Arthropods are also a varied group and tricky to monitor. We showed that 40 simple field samples of water applied to leaves and bark (coupled with DNA metabarcoding) revealed a remarkably complete view of the arthropod communities of a NJ Pinelands forest (Allen et al. Environmental DNA 2023).
Reptiles are known for their crypsis. We showed that you can dramatically boost detection rates of standard cover board surveys (up to 16x) by also collecting eDNA swabs (Kyle et al., Conservation Biology 2022).
Animal Populations and Global Change
ecosystems across the planet are vulnerable to global changes in climate and land use
Bobolink relative abundance on two fields at Duke Farms, New Jersey, USA. I’ve participated in on-the-ground monitoring of grassland bird populations using these fields since 2013. Studying responses to management over the years - including ‘conservation grazing’ and habitat associations - has informed my thinking about conservation issues and population dynamics more broadly. The fields were formerly owned by philanthropist Dorris Duke and are about ~1 km long, north to south.
I’m especially interested in making useful models that can directly inform conservation and management actions. I recently collaborated to construct machine learning and Bayesian models to better understand Black Rail response to sea level rise (Allen et al., Environmental Conservation 2023), Pacific shorebird response to conservation actions (Donlan et al., Conservation Biology 2023), Arctic geese response to climate and land use change (Curley et al., Ecography 2024), and grassland bird response to agricultural intensification (Allen & Lockwood, Conservation Biology 2021). The goal, in each case, is to shed light on potential policy actions and management solutions to stem population declines. More recently, I’ve become interested in dynamic range models, with valuable fisheries species as a case study, as they can be especially useful for forecasting changes. I’m also interested in solutions to global climate change, notably forest carbon markets and the biodiversity they can support (see Allen et al. Communications Earth & Environment 2024).
Spatial Population Dynamics & Social-Ecological Systems
spatial population dynamics can be driven by complex interactions within human-natural systems
Spatial synchrony in North American grassland bird populations during two time periods (1968-1993 & 1994-2019). Maps colors indicate higher (red) or lower (blue) levels of local spatial synchrony, or correlated fluctuations with neighboring cells. + indicates cells with 95% credible intervals that do not overlap zero. Data: North American Breeding Bird Survey.
Much of conservation revolves around population size, which is both a spatial and dynamic phenomenon. Human activities can drive spatial population dynamics, directly or indirectly, as part of complex ‘coupled human-natural’ systems. We mapped the spatial synchrony of North American grassland bird populations to highlight regions of conservation concern (Allen & Lockwood, Conservation Biology 2021). For one species, we quantified the social-ecological network of population drivers (Allen et al. J. Applied Ecology 2021). Other projects include evaluating annual-cycle spatial conservation planning in Pacific shorebirds (Donlan et al., Conservation Biology 2023), shifting migrations in arctic geese due to global climate change (Curley et al. Ecography 2024), and an ongoing project with the Pinsky Lab predicting range shifts of commercially important marine species using Dynamic Range Models.
Ecology of Biological Invasions
Biological invasions are costly and pose serious risks to human and ecological health.
An Acadian Flycatcher nesting in the fork of a Hemlock branch. An invasive insect, the Hemlock Woolly Adelgid, kills a preferred nesting tree and negatively alters forest structure for this species.
How do we best deploy resources to provide early detection and response to forest pests and other invasive species? How do disturbances caused by these organisms affect forest flora and fauna? I combine innovative eDNA field survey techniques with occupancy and simulation modeling to inform sampling design and survey protocols. For example, I frequently use Bayesian occupancy models to inform how best to sample (and how much to sample) to detect damaging species such as Spotted Lanternfly within vineyards (Allen et al., Environmental DNA 2021) and khapra beetles in rice shipments (Vastano et al., Environmental DNA 2024). The ecological impacts of biological invasions formed the basis of my MS research, and I maintain an active collaboration with Dr. Terry Master (emeritus faculty, ESU) and Megan Napoli (research ecologist, Mohonk Preserve, NY) to further this work. Our studies focus on the ~ 20 year effects of a destructive invasive insect, the Hemlock Woolly Adelgid, on songbirds within Appalachian hemlock forests.