Projects

Despite decades of protection under the Endangered Species Act, the Mojave desert tortoise (Gopherus agassizii) continues to decline, and inconsistent historical monitoring has made it difficult to pin down exactly why. This study combines two large, previously separate datasets — nearly 4,000 mark-recapture tortoises across 35 sites (1977-2022) and almost 2,900 radio-tracked tortoises across 22 sites (1988-2022) — into a single integrated survival model. Integrating the two data sources revealed patterns that neither dataset could show on its own: males survive better than females, juveniles and subadults survive worse than adults, and survival improves with total precipitation over the prior two winters and active seasons. The integrated approach also let us tease apart “true” survival (via telemetry) from “apparent” survival (via mark-recapture alone), estimating permanent emigration rates directly for the first time at this scale. ...

Black bears along the urban-wildland interface in northwestern Nevada increasingly rely on human food sources when natural forage fails — and this study shows that a late spring frost is a particularly strong trigger for that failure, more so than winter snowpack. Using 25 years of capture-recapture data on 509 bears (1998-2022), we found that late final-freeze dates were associated with lower natural survival and a higher probability that a bear would be killed by a vehicle strike or removed by wildlife managers. ...

In November 2023, we discovered serious errors in an influential population model that had helped convince the U.S. Fish and Wildlife Service to deny the gopher tortoise federal protection under the Endangered Species Act. Once corrected, the model’s predictions changed from a mild population decline to a rangewide collapse — yet our attempts to get the decision re-evaluated have been met with resistance. In this PNAS opinion piece, we use the gopher tortoise case to argue for a broader fix: complex demographic models increasingly underpin high-stakes conservation policy, but agencies have no effective mechanism for correcting or re-evaluating decisions once serious flaws in the underlying science come to light. We call for more rigorous, independent technical review of the algorithms behind these models — not just the policy documents that cite them — especially when so much rides on getting the science right. ...

Nest predation is a major concern for the federally threatened Bog Turtle (Glyptemys muhlenbergii), and wire-mesh predator excluders are a common conservation tool — but caging a nest can also alter its temperature and incubation conditions in ways that might backfire. Over 4 years across 9 New York wetland sites, this study monitored 77 Bog Turtle nests, comparing predation rates and hatching outcomes between nests with and without predator excluders. ...

Florida moves more than 10,000 gopher tortoises (Gopherus polyphemus) a year away from development sites to protected recipient sites — a huge, unplanned “common garden” experiment in what happens when genetically and geographically distant tortoises are suddenly mixed together. Using nest data from Nokuse Plantation, a major recipient site in the Florida panhandle, we found two things: hatching success declined as the genetic and geographic distance between a nest’s mother and father increased (a sign of outbreeding depression), and mothers from northeast Florida had consistently lower hatching success than mothers from other regions, regardless of climate. ...

At the boundary between two woodrat species (Neotoma fuscipes and N. macrotis) in the Sierra Nevada foothills, drought has driven differential survival between the species and their hybrids, changing who is available to mate with whom. Using six years of field-measured parentage data, we show that as conspecific mates became scarcer, hybridization rates increased — but not symmetrically. Reproductive success was skewed between the parental lineages, F1 hybrid males had near-zero reproductive success, and nearly all surviving hybrids had one purebred parent, pointing to partial genomic incompatibility between the two species. ...

In 2022, the U.S. Fish and Wildlife Service withdrew the gopher tortoise (Gopherus polyphemus) as a candidate for federal protection across most of its range, citing a rangewide demographic model that predicted many populations would remain large and self-sustaining. In this note, we identify a serious flaw in that model: rather than modeling immigration as movement between real populations, the model paired each population with an abstract “dummy” metapopulation that could spontaneously generate new immigrants out of nowhere. This created a runaway feedback loop that artificially inflated projected population growth and masked the species’ true vulnerability. ...

The Blanding’s Turtle (Emydoidea blandingii) population at Great Meadows National Wildlife Refuge in Massachusetts had dwindled from an estimated 135 adults in the 1970s to just 54 by 2004, with most survivors old and few juveniles in evidence — a classic signature of a population starved of recruitment. In response, the project began protecting nests in 2003 and headstarting hatchlings (raising them in captivity for their vulnerable first year) before releasing them back into the wetland starting in 2007. ...

Bobcats (Lynx rufus) were extirpated from Ohio by the mid-1800s and have only recently recolonized the state, raising the question of whether a legal harvest season could be sustainably introduced. This study builds a spatial population simulation model that combines habitat suitability and road-mortality risk with bobcat vital rates to project the population’s viability over the next 40 years under a range of harvest and road-mortality scenarios. The baseline simulations (no harvest, current road mortality only) showed no meaningful extinction risk. But as harvest intensity increased — especially when adults were targeted rather than all age classes — population trajectories became more uncertain and more projections showed decline, particularly when combined with anticipated increases in road mortality. The results give Ohio wildlife managers a quantitative starting point for weighing harvest options against this still-recovering population’s resilience. ...

Occupancy surveys for inconspicuous species like the American pika (Ochotona princeps) often rely on indirect sign — scat, haypiles, calls — that varies widely in how reliably it indicates true presence. Standard occupancy models typically pool all of these sign types into a single detection process, ignoring the fact that fresh scat, old haypiles, and calls carry very different risks of being missed or misidentified. This study develops a “multi-sign” occupancy model that instead estimates a separate detection process for each sign type, including its own false-positive rate, and applies it to over a decade of pika surveys across five Pacific Northwest parks. ...

Like many turtles, gopher tortoises (Gopherus polyphemus) have temperature-dependent sex determination, but young individuals lack any visible external difference between males and females — making it hard to track how a warming climate might be skewing sex ratios in wild populations. The current gold standard, laparoscopic surgery, requires specialized equipment, a trained surgeon, and months of captive rearing. This study tests three non-surgical alternatives — baseline blood testosterone, testosterone after a hormone challenge, and morphological measurements — across neonates, hatchlings, and juveniles, validating each against laparoscopy. ...

Long-lived species like Agassiz’s desert tortoise (Gopherus agassizii) hedge against bad years by keeping reproductive output modest and fairly stable — but climate change could push that output below sustainable levels across an entire range. This study pooled 12 datasets spanning two decades and over 500 individual-year observations to build a range-wide Bayesian model linking annual egg production to climate variables and individual attributes (body size and whether a female reproduced the previous year). ...

As part of our field research, members of the A.P.E. lab occasionally stumble on a novel observation worthy of a published ’natural history note’. Here, we note the observation of tail bifurcation in the western skink, Plestiodon skiltonianus: This is the first publication for UNR undergraduate Chasey Danser (pictured below doing field research)- congratulations Chasey!! (Photo credit: Danielle C. Miles) Miles, D.C., Danser, C., and K.T. Shoemaker. 2020. Tail bifurcation in Plestiodon skiltonianus. Herpetology Notes. https://www.biotaxa.org/hn/article/viewFile/57502/60850

The A.P.E. lab is leading a large, multi-institution collaboration investigating the climate resilience of populations of gopher tortoise (Gopherus polyphemus) and Mojave desert tortoise (Gopherus agassizii). In this project, funded by the Department of Defense (SERDP program), we are building models of tortoise vital rates (age-structured survival, fecundity) as functions of environmental and climatic covariates and simultaneously assessing for evidence of local behavioral and physiological adaptations. We are then using these models to quantify the range of environmental change that populations can withstand in situ without the need for natural selection or long-distance movement to more suitable habitats. ...

This project, supported by the Nevada Department of Wildlife and Nevada Waterfowl Association, uses light-level geolocators to understand the annual migratory pathways of waterfowl in the Pacific flyway, and to assess the timing and location of individual breeding activities. This work is part of a larger effort to monitor wood duck population dynamics and movements in and around Fallon, NV (Fallon Wood Duck Project, PI Chris Nicolai). Delta Waterfowl: Dr. Chris Nicolai Publications Cook, N.A., Nicolai, C.A., Shoemaker, K.T. In prep. Monitoring waterfowl breeding activities with geolocators: a case study with Wood Ducks (Aix sponsa) in northern Nevada. Journal of Animal Ecology. Cook, N.A., Nicolai, C.A., Shoemaker, K.T. Submitted. Movements and staging locations of Canvasback (Aythya valisineria) in the Pacific Flyway. Journal of Fish and Wildlife Management.

Dr. Shoemaker’s PhD dissertation focused on the conservation of bog turtles (Glyptemys muhlenbergii) in New York and Massachusetts. Building upon an existing capture-recapture dataset, he estimated population vital rates and abundance of these turtles in small wetlands in eastern New York (Dutchess County) and assessed for evidence of dispersal within a complex of multiple neighboring wetlands. His work also used microsatellite genotypes to further assess gene flow within these wetland complexes. ...

In the 19th century, populations of giant tortoises in the Galapagos Islands were decimated by whalers and pirates, who kept and killed tortoises on their ships as a resilient source of fresh meat for long ocean voyages. Particularly hard-hit were “saddlebacked” species that inhabited the islands’ arid lowlands closer to the coasts. Of the five saddlebacked species, two have been declared extinct: Chelonoidis elephantopus from Floreana Island and C. abingdonii from Pinta Island (the latter only recently declared extinct in 2012 with the death of the Lonesome George). However, geneticists have recently discovered that, through the translocating behaviors of the very same sailors, the genotypes of these extinct species still exist within individuals of mixed ancestry on Wolf Volcano on Isabela Island. An expedition in 2015 recovered some of these mixed ancestry tortoises and brought them into captivity with the hope of starting a captive breeding program to restore tortoise populations on Floreana and Pinta Islands that represent the original genotype of the native species. ...

The A.P.E. lab is part of a larger team at UNR investigating the population genetics and demography of the pygmy rabbit (Brachylagus idahoensis) in the Great Basin. To stay up to date on the pygmy rabbit project, led by APE lab PhD student Miranda Crowell, check out her website UNR collaborators: Marjorie Matocq Peter Weisberg and Tom Dilts Jim Sedinger Other collaborators: Sheldon and Hart National Wildlife Refuges, Nevada Department of Wildlife, Great Basin Landscape Conservation Cooperative, Greater Hart-Sheldon Fund Publications: Crowell, M.M., Matocq, M.D., Dilts, T., Shoemaker, K.T. In prep. Turnover in pygmy rabbit (Brachylagus idahoensis) site and burrow activity in the Great Basin. Conservation Biology. ...

Crown-of-Thorns Starfish project Crown-of-Thorns Starfish (C.O.T.S.; Acanthaster planci) is a native predator of coral. On occasion, C.O.T.S. populations “explode”, and these outbreaks represent one of the major recognized threats to the Great Barrier Reef in Australia (accounting for 42% of coral loss over the past 30 years). The A.P.E. lab is collaborating with researchers at Australian Institute of Marine Science in Queensland (Sam Matthews and Camille Mellin), James Cook University (Morgan Pratchett) and University of Adelaide (Damien Fordham) to better understand the drivers of C.O.T.S. population explosions and potentially develop strategies for how to reduce this threat to the Great Barrier Reef. ...

Several published studies have already shown that temperature, precipitation and topography can affect the probability of a die-off event. However, a broader synthesis of datasets from across the BTPD range may enable more accurate prediction of when and where die-offs will occur. The APE lab is leading a large collaborative project to create predictive models of BTPD colony die-offs caused by the plague bacterium. We have acquired colony history data from across the BTPD range and are working on using machine learning techniques to create a model of plague outbreaks that can help managers determine how best to target their anti-plague management activities (such as “dusting” for fleas and vaccine administration). This model will also help us better understand the selection pressures that could lead to genetic resistance to plague. ...