IntroductionĬhromosome-length reference genomes are fundamental tools for addressing questions in biology, from evolutionary innovation to the underpinnings of disease ( Rhie et al. The high degree of contiguity of this reference genome enabled the detection of signatures of contemporary inbreeding, highlighting the value of high-quality reference genomes for the management of endangered species, and conservation of biodiversity. We generated a chromosome-length reference genome for this species, and found massive stretches of homozygosity across a genome with relatively high baseline heterozygosity, reflecting inbreeding in a formerly large population. The design of optimal conservation strategies for the federally endangered Pacific pocket mouse, a subspecies that has undergone substantial declines and is under intensive management, relies on precise estimates of genome-wide heterozygosity, inbreeding, demographic history, and chromosomal variation. 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. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical N e estimates were large. 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. 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. 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 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. L.A.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. SeaWorld’s beloved pilot whale Bubbles diesĭeadly but little-known: Why scientists are so afraid of the San Jacinto fault They also installed mesh cages with biodegradable materials to serve as nests for the writes for the San Diego Union-Tribune. To prepare the Laguna Coast park for the pocket mice, biologists have fenced off an acre of coastal sage scrub habitat to protect against predators such as coyotes and snakes. “These mice were expected to be difficult to breed, but it went really well.” “It was decided that they needed to attempt to save them and bring them in for a captive-breeding program,” Mehlow said. After much deliberation, the zoo’s conservation and research arm took 30 of the rodents into captivity in 2012 based on calculations the species wouldn’t survive on its own. Many wildlife specialists feared the species had died off until some Pacific pocket mice were found again in the early 1990s. This species is the smallest kind of mouse in North America, with the average adult weighing less than 8 grams, or less than a third of an ounce. Pacific pocket mice help ecosystems by eating and dispersing the seeds of native plants, as well as by digging holes that improve soil irrigation and encourage plant growth.
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