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. ...

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. ...

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. ...

Prairie dogs are keystone species of North America’s central grasslands, and have experienced dramatic population reductions over the past century due to sylvatic plague, a highly virulent disease introduced to North America ca. 1900. The APE lab is involved in building a novel host-resistance modeling framework to investigate the genetic, demographic and environmental conditions that promote or impede resistance to plague and other similar virulent pathogens in complex and dynamic ecosystems. The prairie dog-plague system provides an excellent model to understand the conditions under which evolutionary rescue occurs in complex and dynamic ecological systems, and will help illuminate a novel and potential large-scale conservation approach to address 1) the biggest threat facing the prairie dog ecosystem that spans from Canada to Mexico - plague and 2) species around the world threatened with novel diseases and climate change. ...

Investigating the broad ecological impacts of Pinyon and Juniper removal in Nevada Thousands of acres of pinyon and juniper woodlands (PJ) will be removed over the next four years to support targeted wildlife populations, notably Greater sage-grouse. We are investigating the effects of PJ removal on insect communities and the bats and reptile species that rely upon them using a rigorous experimental design. Insects can serve as useful indicators of natural disturbances, provide critical pollination services, and represent a major wildlife food resource for many species, including an impressive diversity of bats and reptiles. Little is known about habitat use and disturbance tolerance for bats and reptiles in the Great Basin. For example, some bat species may benefit from tree removal (e.g., cleared areas may improve foraging or success), while other species may be negatively impacted by tree removal (e.g, loss of roosting sites). We are establishing a set of fixed transects, each spanning a gradient from sagebrush steppe to PJ woodland and monitored 3 to 4 times annually. Transects will be established in four project areas distributed widely across the Great Basin- including the Sheldon-Hart refuges and the Ely region (near Great Basin National Park). ...