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

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 >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of runs of homozygosity, 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.

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high‐arctic wild reindeer

“…However, the shorter-than-expected distribution of RoH in reintroduced individuals, given the known timing of the reintroduction founder effects, suggests our analysis underestimated RoH lengths, and this is consistent with an excess of short (<50-Kbp) gaps between RoH in our data, breaking up otherwize long RoH (Figure S9). RoH after allowing one <50-Kbp gap within each 1-Mbp segment (similar to Wilder et al, 2022) gave qualitatively similar results but showed more long RoH which aligned more closely with the known timing of the reintroduction founder events (Figure S10).…”

Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead

“…The range of ROH in hammerhead extended up to over 3 Mbp, shorter than those arising from very recent inbreeding in some other wildlife (e.g. Soay sheep 34 and endangered Pacific pocket mice 35 ), aquaculture species like coho salmon, 36 and in animal livestock. 37 Our calculations suggest the longest ROH in hammerhead stem from inbreeding within possibly the last ∼60–200 years, assuming a generation time of 25 years and a recombination rate of 6.5 cM/Mb.…”

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer

“…2018), thus lacking a chromosome-level genome assembly, we only included scaffolds longer than 10 Mbp in RoH analyses; (3) Errors in mapping sequence reads or structural variation between the caribou reference genome assembly and the Svalbard reindeer genome could also break up long RoH. Reanalysing RoH after allowing one <50-Kbp gap within each 1-Mbp segment (similar to Wilder et al . (2022)) gave qualitatively similar results but showed more long RoH which aligned more closely with the known timing of the reintroduction bottleneck (Fig S10).…”