A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.

High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.

Niche partitioning in an assemblage of granivorous rodents, and the challenge of community-level conservation.

Coexistence of competing species in the same foraging guild has long puzzled ecologists. In particular, how do small subordinate species persist with larger dominant competitors? This question becomes particularly important when conservation interventions, such as reintroduction or translocation, become necessary for the smaller species. Exclusion of dominant competitors might be necessary to establish populations of some endangered species. Ultimately, however, the goal should be to conserve whole communities. Determining how subordinate species escape competitive exclusion in intact communities could inform conservation decisions by clarifying the ecological conditions and processes required for coexistence at local or regional scales. We tested for spatial and temporal partitioning among six species of native, granivorous rodents using null models, and characterized the microhabitat of each species using resource-selection models. We found that the species' nightly activity patterns are aggregated temporally but segregated spatially. As expected, we found clear evidence that the larger-bodied kangaroo rats drive spatial partitioning, but we also found species-specific microhabitat associations, which suggests that habitat heterogeneity is part of what enables these species to coexist. Restoration of natural disturbance regimes that create habitat heterogeneity, and selection of translocation sites without specific competitors, are among the management recommendations to consider in this case. More generally, this study highlights the need for a community-level approach to conservation and the usefulness of basic ecological data for guiding management decisions.

Using reproductive technologies to assess the development of secondary sexual characteristics, ovarian senescence and hermaphroditism in the endangered mountain yellow-legged frog Rana muscosa.

Anurans can display a host of intriguing sexual syndromes, including hermaphroditism and sex reversal. Using a multifaceted approach for diagnosing and characterising hermaphroditism in the endangered anuran species Rana mucosa, we tracked changes in female reproductive status using hormone monitoring, ultrasound examinations, individual life history, fertilisation records and post-mortem findings. Seven individuals originally sexed as females developed secondary male sexual characteristics, behaviour and hormone profiles and, in some cases, had testicular tissue despite having previously laid eggs. Our results suggest that reproductive technologies can shed light on life history patterns and reproductive anomalies that may affect endangered anuran survival.

Effects of artificial light at night on the foraging behavior of an endangered nocturnal mammal.

Modification of nighttime light levels by artificial illumination (artificial light at night; ALAN) is a rapidly increasing form of human disturbance that affects natural environments worldwide. Light in natural environments influences a variety of physiological and ecological processes directly and indirectly and, as a result, the effects of light pollution on species, communities and ecosystems are emerging as significant. Small prey species may be particularly susceptible to ALAN as it makes them more conspicuous and thus more vulnerable to predation by visually oriented predators. Understanding the effects of disturbance like ALAN is especially important for threatened or endangered species as impacts have the potential to impede recovery, but due to low population numbers inherent to at-risk species, disturbance is rarely studied. The endangered Stephens' kangaroo rat (SKR), Dipodomys stephensi, is a nocturnal rodent threatened by habitat destruction from urban expansion. The degree to which ALAN impacts their recovery is unknown. In this study, we examined the effects of ALAN on SKR foraging decisions across a gradient of light intensity for two types of ALAN, flood and bug lights (756 vs 300 lumen, respectfully) during full and new moon conditions. We found that ALAN decreased probability of resource patch depletion compared to controls. Moreover, lunar illumination, distance from the light source and light type interacted to alter SKR foraging. Under the new moon, SKR were consistently more likely to deplete patches under control conditions, but there was an increasing probability of patch depletion with distance from the source of artificial light. The full moon dampened SKR foraging activity and the effect of artificial lights. Our study underscores that ALAN reduces habitat suitability, and raises the possibility that ALAN may impede the recovery of at-risk nocturnal rodents.

Increasing generations in captivity is associated with increased vulnerability of Tasmanian devils to vehicle strike following release to the wild.

Captive breeding of threatened species, for release to the wild, is critical for conservation. This strategy, however, risks producing captive-raised animals with traits poorly suited to the wild. We describe the first study to characterise accumulated consequences of long-term captive breeding on behaviour, by following the release of Tasmanian devils to the wild. We test the impact of prolonged captive breeding on the probability that captive-raised animals are fatally struck by vehicles. Multiple generations of captive breeding increased the probability that individuals were fatally struck, a pattern that could not be explained by other confounding factors (e.g. age or release site). Our results imply that long-term captive breeding programs may produce animals that are naïve to the risks of the post-release environment. Our analyses have already induced changes in management policy of this endangered species, and serve as model of productive synergy between ecological monitoring and conservation strategy.

Fitness costs of neighborhood disruption in translocations of a solitary mammal.

Translocation is used to reestablish wild populations of animals, but translocation projects often do not meet their objectives because postrelease mortality of animals is high. One reason for translocation failure is that the behavioral or ecological requirements of released animals are unmet. Maintaining founder-group social relationships during release can affect reestablishment of social species. Solitary territorial species with stable neighbors (restricted dispersal and lifetime occupation of a home range) of the same species may also benefit from the maintenance of these social relationships during translocation. We translocated Stephens' kangaroo rats (Dipodomys stephensi), a solitary species listed as endangered under the U.S. Endangered Species Act, with and without neighboring kangaroo rats. We compared the settlement (establishment of a stable home range) decisions and fitness of kangaroo rats between the 2 treatments. Kangaroo rats translocated with neighbors traveled shorter distances before establishing territories, had higher survival rates, and had significantly higher reproductive success than kangaroo rats translocated without neighbors. Number of offspring was 24-fold higher for kangaroo rats translocated with neighbors than those translocated without neighbors. Differences in behavior following release may partially explain differences in survival between the 2 groups. Immediately following release, animals translocated with neighbors fought less and spent significantly more time foraging and digging burrows than animals translocated without neighbors. Our results indicate that even for solitary species, maintaining relationships among members of a translocated group of animals can influence translocation success. This study is the first empirical demonstration of the fitness consequences of disrupting social relationships among territorial neighbors.

Overview: For crying out loud--dangers and opportunities of communicating in the public domain.

Communication often extends into the public domain, inviting "eavesdropping" and other forms of exploitation by other species. Conflict is frequently the result, although interspecific communication can be mutually beneficial even when interests conflict fundamentally, such as between predator and prey. However, the most complex communication systems are likely to involve species with mutual rather than with conflicting interests. When interests do conflict, exploitation of the communication systems of others may impose high costs on signalers and select for signals that are less exploitable. Other costs of communication in the public domain arise from "mistakes" (e.g., mating with the wrong species) and select for more species-specific signal structure. The articles in this section illustrate the complexity of interspecific communication and yield important insights into the dynamic nature of communication systems.