Sourcing adequate genetic diversity is an essential consideration when planning reintroductions, because it influences individual fitness and long-term persistence of populations, yet available populations of threatened species may lack diversity. 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.Ĭonservation translocations can restore populations and prevent extinction of threatened species. These patterns of genetic variation suggest recent inbreeding in a formerly large population.
Yet outside of runs of homozygosity, heterozygosity was relatively high (0.0027), and historical Ne estimates were large.
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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. 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. 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. Outbreeding depression, there may be a cost to restoration of gene flow if populations Our findings highlight that, even in the absence of
Remain to be determined, reduced fitness associated with Dana Point ancestry isĬonsistent with high deleterious genetic load in this population, and thus any facilitated Leading to a rapid decrease of Dana Point alleles. Across generations, we saw a strong negativeĬorrelation between individual reproductive success and ancestry to Dana Point, Higher in admixed individuals than founders from Dana Point, the smallest population with the lowest heterozygosity. However, reproductive success was consistently Not explain the fitness patterns, and outbreeding depression was difficult to rule out as Although we observed an increase in fitness in the F1 andį2 generations relative to the founding populations, inbreeding depression alone did Individual fitness (measured by reproductive success) in a captive setting over six
Program founded by individuals from each population. Mitochondrial and microsatellite data indicated that effective population sizes wereĮxtremely small (N e <50), and continued declines prompted a conservation breeding Longimembris pacificus ) persists in three isolated populations in southern California. The endangered Pacific pocket mouse ( Perognathus The introduction of deleterious genetic load is
Preserve genetic diversity, but a common concern is that genomic incompatibilities Restoring gene flow can reduce inbreeding and Habitat fragmentation from urban development leaves species vulnerable to inbreedingĭepression and genomic erosion.
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