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Abstract 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. 

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. 

Accurate estimates of survival are crucial for many management decisions in translocation programs. Maximizing detection probabilities and reducing sampling biases for released animals can aid in estimates of survival. One important source of sampling bias is an animal’s behavior. For example, individuals that are consistently more exploratory or active may be more likely to be detected visually. Behavioral traits can be related to survival after reintroduction, and because many pre‐release treatments aim to manipulate animal behavior, it is critical to tease apart relationships between behavior and detection probability. Here, we assessed the repeatability (intra‐individual consistency and inter‐individual variation) of behavioral traits for an endangered amphibian, the mountain yellow‐legged frog (Rana muscosa). Because new technological tools offer one potential solution for reducing sampling biases while increasing detection, we also tested whether a long‐range passive integrated transponder (PIT) tag reader could enhance surveys for these individuals after translocation into the wild. After confirming thatex situbredR. muscosaexhibit repeatable behavioral traits (repeatability = 0.25–0.41) and releasing these frogs (N = 196) into the wild, we conducted post‐release surveys visually and with the long‐range PIT tag reader. Integrating the long‐range reader into surveys improved detection probability four‐fold in comparison to visual surveys alone (~0.09 to ~0.36). Moreover, mark–recapture modeling revealed that tag reader detection probability was not biased toward detecting individuals of specific behavioral types, while visual detection was significantly related to behavioral traits. These results will enable a more accurate understanding of individual differences in post‐release success in translocations. This may be particularly important for amphibian species, which can be difficult to detect and are expected to increasingly be involved in human‐managed breeding and translocation programs due to their vulnerable conservation status.